8RG0

Structure of human eIF3 core from closed 48S translation initiation complex

PDB DOI: https://doi.org/10.2210/pdb8RG0/pdb
EM Map EMD-19128: EMDB EMDataResource
NAKB: 8RG0

Classification: RIBOSOME
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-13 Released: 2024-08-14
Deposition Author(s): Petrychenko, V., Yi, S.-H., Liedtke, D., Peng, B.Z., Rodnina, M.V., Fischer, N.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for translational control by the human 48S initiation complex from codon scanning toward subunit joining

Petrychenko, V., Yi, S.-H., Liedtke, D., Peng, B.Z., Rodnina, M.V., Fischer, N.

(2024) Nat Struct Mol Biol

DOI: https://doi.org/10.1038/s41594-024-01378-4

Macromolecule Content

Total Structure Weight: 1,428.92 kDa
Atom Count: 31,348
Modelled Residue Count: 4,085
Deposited Residue Count: 8,541
Unique protein chains: 17
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 3 subunit K	A [auth 3]	218	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBQ5 (Homo sapiens) Explore Q9UBQ5 Go to UniProtKB: Q9UBQ5
PHAROS: Q9UBQ5 GTEx: ENSG00000178982
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UBQ5
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 3 subunit F	B [auth 4]	357	Homo sapiens	Mutation(s): 0 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for O00303 (Homo sapiens) Explore O00303 Go to UniProtKB: O00303
PHAROS: O00303 GTEx: ENSG00000175390
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00303
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 3 subunit L	C [auth 5]	564	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y262 (Homo sapiens) Explore Q9Y262 Go to UniProtKB: Q9Y262
GTEx: ENSG00000100129
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y262
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 3 subunit M	D [auth 6]	374	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L2H7 (Homo sapiens) Explore Q7L2H7 Go to UniProtKB: Q7L2H7
PHAROS: Q7L2H7 GTEx: ENSG00000149100
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7L2H7
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 3 subunit H	F [auth 8]	352	Homo sapiens	Mutation(s): 0
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Find proteins for O15372 (Homo sapiens) Explore O15372 Go to UniProtKB: O15372
PHAROS: O15372 GTEx: ENSG00000147677
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15372
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S27	H	84	Homo sapiens	Mutation(s): 0
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Find proteins for P42677 (Homo sapiens) Explore P42677 Go to UniProtKB: P42677
PHAROS: P42677 GTEx: ENSG00000177954
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42677
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S13	I	151	Homo sapiens	Mutation(s): 0
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Find proteins for P62277 (Homo sapiens) Explore P62277 Go to UniProtKB: P62277
PHAROS: P62277 GTEx: ENSG00000110700
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62277
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S17	J [auth M]	135	Homo sapiens	Mutation(s): 0
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Find proteins for P08708 (Homo sapiens) Explore P08708 Go to UniProtKB: P08708
PHAROS: P08708 GTEx: ENSG00000182774
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08708
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein SA	K [auth N]	295	Homo sapiens	Mutation(s): 0
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Find proteins for P08865 (Homo sapiens) Explore P08865 Go to UniProtKB: P08865
PHAROS: P08865 GTEx: ENSG00000168028
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08865
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S3a	L [auth O]	264	Homo sapiens	Mutation(s): 0
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Find proteins for P61247 (Homo sapiens) Explore P61247 Go to UniProtKB: P61247
GTEx: ENSG00000145425
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61247
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S14	M [auth P]	151	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62263 (Homo sapiens) Explore P62263 Go to UniProtKB: P62263
PHAROS: P62263 GTEx: ENSG00000164587
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62263
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S26	N [auth Q]	115	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62854 (Homo sapiens) Explore P62854 Go to UniProtKB: P62854
PHAROS: P62854 GTEx: ENSG00000197728
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62854
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S28	O [auth n]	69	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62857 (Homo sapiens) Explore P62857 Go to UniProtKB: P62857
PHAROS: P62857 GTEx: ENSG00000233927
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62857
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 3 subunit A	P [auth u]	1,382	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q14152 (Homo sapiens) Explore Q14152 Go to UniProtKB: Q14152
PHAROS: Q14152 GTEx: ENSG00000107581
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14152
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 3 subunit E	Q [auth v]	445	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P60228 (Homo sapiens) Explore P60228 Go to UniProtKB: P60228
PHAROS: P60228 GTEx: ENSG00000104408
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60228
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 3 subunit D	R [auth x]	548	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O15371 (Homo sapiens) Explore O15371 Go to UniProtKB: O15371
PHAROS: O15371 GTEx: ENSG00000100353
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15371
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 3 subunit C	S [auth y]	913	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q99613 (Homo sapiens) Explore Q99613 Go to UniProtKB: Q99613
PHAROS: Q99613 GTEx: ENSG00000184110
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99613
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
mRNA	E [auth 7]	255	Homo sapiens
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
18S rRNA	G [auth A]	1,869	Homo sapiens
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain U [auth Q] MOL2 format, chain U [auth Q]	U [auth Q]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain U [auth Q] Interactions & Density Focus chain U [auth Q]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A]	T [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]