9XJH | pdb_00009xjh

In situ 80S ribosome from intact HEK293T cells - consensus map of 60S region

PDB DOI: https://doi.org/10.2210/pdb9XJH/pdb
EM Map EMD-66936: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Homo sapiens
Mutation(s): Yes

Deposited: 2025-11-04 Released: 2026-11-11
Deposition Author(s): Wang, Y., Zhang, Y., Gao, N.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.97 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

In situ 80S ribosome from intact HEK293T cells - consensus map of 60S region

Wang, Y., Zhang, Y., Gao, N.

To be published.

Macromolecule Content

Total Structure Weight: 2,533.23 kDa
Atom Count: 137,834
Modeled Residue Count: 10,528
Deposited Residue Count: 12,124
Unique protein chains: 44
Unique nucleic acid chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor BTF3	A	29	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P20290 (Homo sapiens) Explore P20290 Go to UniProtKB: P20290
PHAROS: P20290 GTEx: ENSG00000145741
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20290
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL2	B [auth LA]	251	Homo sapiens	Mutation(s): 0
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Find proteins for P62917 (Homo sapiens) Explore P62917 Go to UniProtKB: P62917
GTEx: ENSG00000161016
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62917
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL3	C [auth LB]	402	Homo sapiens	Mutation(s): 0
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Find proteins for P39023 (Homo sapiens) Explore P39023 Go to UniProtKB: P39023
PHAROS: P39023 GTEx: ENSG00000100316
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39023
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL4	G [auth LC]	366	Homo sapiens	Mutation(s): 0
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Find proteins for P36578 (Homo sapiens) Explore P36578 Go to UniProtKB: P36578
PHAROS: P36578 GTEx: ENSG00000174444
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36578
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL5	H [auth LJ]	170	Homo sapiens	Mutation(s): 0
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Find proteins for P62913 (Homo sapiens) Explore P62913 Go to UniProtKB: P62913
PHAROS: P62913 GTEx: ENSG00000142676
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62913
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL6	I [auth LH]	190	Homo sapiens	Mutation(s): 0
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Find proteins for P32969 (Homo sapiens) Explore P32969 Go to UniProtKB: P32969
PHAROS: P32969 GTEx: ENSG00000163682
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32969
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL6	J [auth LE]	288	Homo sapiens	Mutation(s): 0
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Find proteins for Q02878 (Homo sapiens) Explore Q02878 Go to UniProtKB: Q02878
PHAROS: Q02878 GTEx: ENSG00000089009
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02878
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL8	K [auth LG]	241	Homo sapiens	Mutation(s): 0
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Find proteins for P62424 (Homo sapiens) Explore P62424 Go to UniProtKB: P62424
PHAROS: P62424 GTEx: ENSG00000148303
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62424
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL13	L [auth LO]	202	Homo sapiens	Mutation(s): 0
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Find proteins for P40429 (Homo sapiens) Explore P40429 Go to UniProtKB: P40429
PHAROS: P40429 GTEx: ENSG00000142541
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40429
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL13	M [auth LL]	206	Homo sapiens	Mutation(s): 0
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Find proteins for P26373 (Homo sapiens) Explore P26373 Go to UniProtKB: P26373
PHAROS: P26373 GTEx: ENSG00000167526
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26373
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL14	N [auth LV]	133	Homo sapiens	Mutation(s): 0
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Find proteins for P62829 (Homo sapiens) Explore P62829 Go to UniProtKB: P62829
PHAROS: P62829 GTEx: ENSG00000125691
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62829
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL14	O [auth LM]	136	Homo sapiens	Mutation(s): 0
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Find proteins for P50914 (Homo sapiens) Explore P50914 Go to UniProtKB: P50914
PHAROS: P50914 GTEx: ENSG00000188846
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50914
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL15	P [auth La]	147	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P46776 (Homo sapiens) Explore P46776 Go to UniProtKB: P46776
PHAROS: P46776 GTEx: ENSG00000166441
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46776
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL15	Q [auth LN]	203	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61313 (Homo sapiens) Explore P61313 Go to UniProtKB: P61313
PHAROS: P61313 GTEx: ENSG00000174748
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61313
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL18	R [auth LD]	294	Homo sapiens	Mutation(s): 0
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Find proteins for P46777 (Homo sapiens) Explore P46777 Go to UniProtKB: P46777
PHAROS: P46777 GTEx: ENSG00000122406
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46777
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL18	S [auth LQ]	187	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q07020 (Homo sapiens) Explore Q07020 Go to UniProtKB: Q07020
PHAROS: Q07020 GTEx: ENSG00000063177
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07020
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL19	T [auth LR]	187	Homo sapiens	Mutation(s): 0
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Find proteins for P84098 (Homo sapiens) Explore P84098 Go to UniProtKB: P84098
PHAROS: P84098 GTEx: ENSG00000108298
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84098
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL20	U [auth LS]	176	Homo sapiens	Mutation(s): 0
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Find proteins for Q02543 (Homo sapiens) Explore Q02543 Go to UniProtKB: Q02543
GTEx: ENSG00000105640
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02543
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL21	V [auth LT]	159	Homo sapiens	Mutation(s): 0
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Find proteins for P46778 (Homo sapiens) Explore P46778 Go to UniProtKB: P46778
PHAROS: P46778 GTEx: ENSG00000122026
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46778
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL22	W [auth LP]	159	Homo sapiens	Mutation(s): 0
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Find proteins for P18621 (Homo sapiens) Explore P18621 Go to UniProtKB: P18621
PHAROS: P18621 GTEx: ENSG00000265681
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18621
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL22	X [auth LU]	100	Homo sapiens	Mutation(s): 0
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Find proteins for P35268 (Homo sapiens) Explore P35268 Go to UniProtKB: P35268
PHAROS: P35268 GTEx: ENSG00000116251
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35268
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	Y [auth LX]	118	Homo sapiens	Mutation(s): 0
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Find proteins for P62750 (Homo sapiens) Explore P62750 Go to UniProtKB: P62750
PHAROS: P62750 GTEx: ENSG00000198242
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UniProt Group	P62750
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL24	Z [auth LY]	134	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61254 (Homo sapiens) Explore P61254 Go to UniProtKB: P61254
PHAROS: P61254 GTEx: ENSG00000161970
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UniProt Group	P61254
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL24	AA [auth LW]	124	Homo sapiens	Mutation(s): 0
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Find proteins for P83731 (Homo sapiens) Explore P83731 Go to UniProtKB: P83731
PHAROS: P83731 GTEx: ENSG00000114391
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83731
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL27	BA [auth LZ]	135	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61353 (Homo sapiens) Explore P61353 Go to UniProtKB: P61353
PHAROS: P61353 GTEx: ENSG00000131469
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UniProt Group	P61353
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL28	CA [auth Lr]	126	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P46779 (Homo sapiens) Explore P46779 Go to UniProtKB: P46779
PHAROS: P46779 GTEx: ENSG00000108107
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46779
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL29	DA [auth Lh]	122	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P42766 (Homo sapiens) Explore P42766 Go to UniProtKB: P42766
PHAROS: P42766 GTEx: ENSG00000136942
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UniProt Group	P42766
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL29	EA [auth Lb]	121	Homo sapiens	Mutation(s): 0
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Find proteins for P47914 (Homo sapiens) Explore P47914 Go to UniProtKB: P47914
GTEx: ENSG00000162244
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UniProt Group	P47914
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL30	FA [auth LF]	225	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P18124 (Homo sapiens) Explore P18124 Go to UniProtKB: P18124
PHAROS: P18124 GTEx: ENSG00000147604
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18124
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL30	GA [auth Lc]	99	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62888 (Homo sapiens) Explore P62888 Go to UniProtKB: P62888
PHAROS: P62888 GTEx: ENSG00000156482
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62888
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL31	HA [auth Ld]	107	Homo sapiens	Mutation(s): 0
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Find proteins for P62899 (Homo sapiens) Explore P62899 Go to UniProtKB: P62899
PHAROS: P62899 GTEx: ENSG00000071082
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UniProt Group	P62899
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL32	IA [auth Le]	128	Homo sapiens	Mutation(s): 0
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Find proteins for P62910 (Homo sapiens) Explore P62910 Go to UniProtKB: P62910
PHAROS: P62910 GTEx: ENSG00000144713
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UniProt Group	P62910
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL33	JA [auth Lf]	110	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P18077 (Homo sapiens) Explore P18077 Go to UniProtKB: P18077
PHAROS: P18077 GTEx: ENSG00000182899
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UniProt Group	P18077
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL34	KA [auth Lg]	114	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P49207 (Homo sapiens) Explore P49207 Go to UniProtKB: P49207
PHAROS: P49207 GTEx: ENSG00000109475
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UniProt Group	P49207
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL36	LA [auth Li]	102	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3U8 (Homo sapiens) Explore Q9Y3U8 Go to UniProtKB: Q9Y3U8
PHAROS: Q9Y3U8 GTEx: ENSG00000130255
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UniProt Group	Q9Y3U8
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL37	MA [auth Lj]	86	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61927 (Homo sapiens) Explore P61927 Go to UniProtKB: P61927
PHAROS: P61927 GTEx: ENSG00000145592
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UniProt Group	P61927
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL38	NA [auth Lk]	70	Homo sapiens	Mutation(s): 0
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Find proteins for P63173 (Homo sapiens) Explore P63173 Go to UniProtKB: P63173
PHAROS: P63173 GTEx: ENSG00000172809
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UniProt Group	P63173
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL39	OA [auth Ll]	50	Homo sapiens	Mutation(s): 0
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Find proteins for P62891 (Homo sapiens) Explore P62891 Go to UniProtKB: P62891
GTEx: ENSG00000198918
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UniProt Group	P62891
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL40	PA [auth Lm]	52	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens) Explore P62987 Go to UniProtKB: P62987
PHAROS: P62987 GTEx: ENSG00000221983
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UniProt Group	P62987
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein eS32	QA [auth Ln]	25	Homo sapiens	Mutation(s): 0
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Find proteins for P62945 (Homo sapiens) Explore P62945 Go to UniProtKB: P62945
PHAROS: P62945 GTEx: ENSG00000229117
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UniProt Group	P62945
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL42	RA [auth Lo]	105	Homo sapiens	Mutation(s): 0
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Find proteins for P83881 (Homo sapiens) Explore P83881 Go to UniProtKB: P83881
PHAROS: P83881 GTEx: ENSG00000241343
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UniProt Group	P83881
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL43	SA [auth Lp]	91	Homo sapiens	Mutation(s): 0
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Find proteins for P61513 (Homo sapiens) Explore P61513 Go to UniProtKB: P61513
PHAROS: P61513 GTEx: ENSG00000197756
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UniProt Group	P61513
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
SERPINE1 mRNA-binding protein 1	VA [auth CB]	16	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NC51 (Homo sapiens) Explore Q8NC51 Go to UniProtKB: Q8NC51
PHAROS: Q8NC51 GTEx: ENSG00000142864
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UniProt Group	Q8NC51
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL16	WA [auth LI]	213	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P27635 (Homo sapiens) Explore P27635 Go to UniProtKB: P27635
PHAROS: P27635 GTEx: ENSG00000147403
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UniProt Group	P27635
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
5.8S rRNA	D [auth L8]	156	Homo sapiens
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Molecule	Chains	Length	Organism
Entity ID: 5
28S rRNA	E [auth L5]	5,069	Homo sapiens
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Molecule	Chains	Length	Organism
Entity ID: 6
5S rRNA	F [auth L7]	120	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 46
mRNA	TA [auth mR]	3	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 47
P-site tRNA	UA [auth Pt]	77	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain SB [auth L5] MOL2 format, chain SB [auth L5] mmCIF format, chain SB [auth L5]	SB [auth L5]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain SB [auth L5] Interactions & Density Focus chain SB [auth L5]
SPM Query on SPM Download:Ideal Coordinates CCD File SDF format, chain OB [auth L5] SDF format, chain PB [auth L5] SDF format, chain RB [auth L5] SDF format, chain QB [auth L5] SDF format, chain NB [auth L5] SDF format, chain MB [auth L5] SDF format, chain LB [auth L5] SDF format, chain IB [auth L5] MOL2 format, chain OB [auth L5] MOL2 format, chain PB [auth L5] MOL2 format, chain RB [auth L5] MOL2 format, chain QB [auth L5] MOL2 format, chain NB [auth L5] MOL2 format, chain MB [auth L5] MOL2 format, chain LB [auth L5] MOL2 format, chain IB [auth L5] mmCIF format, chain OB [auth L5] mmCIF format, chain PB [auth L5] mmCIF format, chain RB [auth L5] mmCIF format, chain QB [auth L5] mmCIF format, chain NB [auth L5] mmCIF format, chain MB [auth L5] mmCIF format, chain LB [auth L5] mmCIF format, chain IB [auth L5]	IB [auth L5] LB [auth L5] MB [auth L5] NB [auth L5] OB [auth L5] IB [auth L5], LB [auth L5], MB [auth L5], NB [auth L5], OB [auth L5], PB [auth L5], QB [auth L5], RB [auth L5]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain IB [auth L5] Focus chain LB [auth L5] Focus chain MB [auth L5] Focus chain NB [auth L5] Focus chain OB [auth L5] Focus chain PB [auth L5] Focus chain QB [auth L5] Focus chain RB [auth L5] Interactions & Density Focus chain IB [auth L5] Focus chain LB [auth L5] Focus chain MB [auth L5] Focus chain NB [auth L5] Focus chain OB [auth L5] Focus chain PB [auth L5] Focus chain QB [auth L5] Focus chain RB [auth L5]
SPD Query on SPD Download:Ideal Coordinates CCD File SDF format, chain AB [auth L5] SDF format, chain FB [auth L5] SDF format, chain GB [auth L5] SDF format, chain JB [auth L5] SDF format, chain KB [auth L5] SDF format, chain ZA [auth L5] SDF format, chain YA [auth L5] SDF format, chain XA [auth L8] SDF format, chain TB [auth LN] SDF format, chain EB [auth L5] SDF format, chain DB [auth L5] SDF format, chain CB [auth L5] SDF format, chain BB [auth L5] MOL2 format, chain AB [auth L5] MOL2 format, chain FB [auth L5] MOL2 format, chain GB [auth L5] MOL2 format, chain JB [auth L5] MOL2 format, chain KB [auth L5] MOL2 format, chain ZA [auth L5] MOL2 format, chain YA [auth L5] MOL2 format, chain XA [auth L8] MOL2 format, chain TB [auth LN] MOL2 format, chain EB [auth L5] MOL2 format, chain DB [auth L5] MOL2 format, chain CB [auth L5] MOL2 format, chain BB [auth L5] mmCIF format, chain AB [auth L5] mmCIF format, chain FB [auth L5] mmCIF format, chain GB [auth L5] mmCIF format, chain JB [auth L5] mmCIF format, chain KB [auth L5] mmCIF format, chain ZA [auth L5] mmCIF format, chain YA [auth L5] mmCIF format, chain XA [auth L8] mmCIF format, chain TB [auth LN] mmCIF format, chain EB [auth L5] mmCIF format, chain DB [auth L5] mmCIF format, chain CB [auth L5] mmCIF format, chain BB [auth L5]	AB [auth L5] BB [auth L5] CB [auth L5] DB [auth L5] EB [auth L5] AB [auth L5], BB [auth L5], CB [auth L5], DB [auth L5], EB [auth L5], FB [auth L5], GB [auth L5], JB [auth L5], KB [auth L5], TB [auth LN], XA [auth L8], YA [auth L5], ZA [auth L5]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain AB [auth L5] Focus chain BB [auth L5] Focus chain CB [auth L5] Focus chain DB [auth L5] Focus chain EB [auth L5] Focus chain FB [auth L5] Focus chain GB [auth L5] Focus chain JB [auth L5] Focus chain KB [auth L5] Focus chain TB [auth LN] Focus chain XA [auth L8] Focus chain YA [auth L5] Focus chain ZA [auth L5] Interactions & Density Focus chain AB [auth L5] Focus chain BB [auth L5] Focus chain CB [auth L5] Focus chain DB [auth L5] Focus chain EB [auth L5] Focus chain FB [auth L5] Focus chain GB [auth L5] Focus chain JB [auth L5] Focus chain KB [auth L5] Focus chain TB [auth LN] Focus chain XA [auth L8] Focus chain YA [auth L5] Focus chain ZA [auth L5]
PUT Query on PUT Download:Ideal Coordinates CCD File SDF format, chain HB [auth L5] MOL2 format, chain HB [auth L5] mmCIF format, chain HB [auth L5]	HB [auth L5]	1,4-DIAMINOBUTANE C₄ H₁₂ N₂ KIDHWZJUCRJVML-UHFFFAOYSA-N		Interactions Focus chain HB [auth L5] Interactions & Density Focus chain HB [auth L5]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain WB [auth Lm] SDF format, chain YB [auth Lp] SDF format, chain XB [auth Lo] SDF format, chain VB [auth Lj] SDF format, chain UB [auth Lg] MOL2 format, chain WB [auth Lm] MOL2 format, chain YB [auth Lp] MOL2 format, chain XB [auth Lo] MOL2 format, chain VB [auth Lj] MOL2 format, chain UB [auth Lg] mmCIF format, chain WB [auth Lm] mmCIF format, chain YB [auth Lp] mmCIF format, chain XB [auth Lo] mmCIF format, chain VB [auth Lj] mmCIF format, chain UB [auth Lg]	UB [auth Lg], VB [auth Lj], WB [auth Lm], XB [auth Lo], YB [auth Lp]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain UB [auth Lg] Focus chain VB [auth Lj] Focus chain WB [auth Lm] Focus chain XB [auth Lo] Focus chain YB [auth Lp] Interactions & Density Focus chain UB [auth Lg] Focus chain VB [auth Lj] Focus chain WB [auth Lm] Focus chain XB [auth Lo] Focus chain YB [auth Lp]

Modified Residues 4 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
V5N Query on V5N	B [auth LA], P [auth La]	HIS	Hydroxylation	C₆ H₉ N₃ O₃
HIC Query on HIC	C [auth LB]	HIS	Methylation	C₇ H₁₁ N₃ O₂
MLZ Query on MLZ	EA [auth Lb], RA [auth Lo]	LYS	Methylation	C₇ H₁₆ N₂ O₂
M3L Query on M3L	PA [auth Lm]	LYS	Methylation	C₉ H₂₁ N₂ O₂

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 1.97 Å
Aggregation State: CELL
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158
RECONSTRUCTION	RELION	3.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Wang, Y.

Zhang, Y.

Gao, N.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2024YFA1306200; 2024YFA1306202
National Natural Science Foundation of China (NSFC)	China	32230051

Revision History (Full details and data files)

Version 1.0: 2026-11-11
Type: Initial release

9XJH | pdb_00009xjh

In situ 80S ribosome from intact HEK293T cells - consensus map of 60S region

Literature

In situ 80S ribosome from intact HEK293T cells - consensus map of 60S region

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt & NIH Common Fund Data Resources

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Entity ID: 3

UniProt & NIH Common Fund Data Resources

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Entity ID: 7

UniProt & NIH Common Fund Data Resources

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Entity ID: 8

UniProt & NIH Common Fund Data Resources

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Entity ID: 9

UniProt & NIH Common Fund Data Resources

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Entity ID: 10

UniProt & NIH Common Fund Data Resources

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Entity ID: 11

UniProt & NIH Common Fund Data Resources

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Entity ID: 12

UniProt & NIH Common Fund Data Resources

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Entity ID: 13

UniProt & NIH Common Fund Data Resources

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Entity ID: 14

UniProt & NIH Common Fund Data Resources

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Entity ID: 15

UniProt & NIH Common Fund Data Resources

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Entity ID: 16

UniProt & NIH Common Fund Data Resources

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Entity ID: 17

UniProt & NIH Common Fund Data Resources

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Entity ID: 18

UniProt & NIH Common Fund Data Resources

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Entity ID: 19

UniProt & NIH Common Fund Data Resources

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Sequence Annotations

Entity ID: 20

UniProt & NIH Common Fund Data Resources

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Sequence Annotations

Entity ID: 21

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 22

UniProt & NIH Common Fund Data Resources