9FPZ

Human NatA-MAP2 80S ribosome complex

PDB DOI: https://doi.org/10.2210/pdb9FPZ/pdb
NAKB: 9FPZ
EM Map EMD-50641: EMDB EMDataResource

Classification: TRANSLATION
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-06-14 Released: 2024-07-03
Deposition Author(s): Klein, M.A., Wild, K., Sinning, I.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.69 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

Multi-protein assemblies orchestrate enzymatic processing of the nascent chain on the 80S ribosome

Klein, M.A., Wild, K., Sinning, I.

To be published.

Macromolecule Content

Total Structure Weight: 466.14 kDa
Atom Count: 29,394
Modelled Residue Count: 3,024
Deposited Residue Count: 3,393
Unique protein chains: 11
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-alpha-acetyltransferase 10	A [auth 2]	171	Homo sapiens	Mutation(s): 0 Gene Names: NAA10, ARD1, ARD1A, TE2 EC: 2.3.1.255
UniProt & NIH Common Fund Data Resources
Find proteins for P41227 (Homo sapiens) Explore P41227 Go to UniProtKB: P41227
GTEx: ENSG00000102030
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41227
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase 2	C [auth A]	484	Homo sapiens	Mutation(s): 0 Gene Names: METAP2, MNPEP, P67EIF2 EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for P50579 (Homo sapiens) Explore P50579 Go to UniProtKB: P50579
GTEx: ENSG00000111142
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50579
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
N-alpha-acetyltransferase 15, NatA auxiliary subunit	D [auth B]	840	Homo sapiens	Mutation(s): 0 Gene Names: NAA15, GA19, NARG1, NATH, TBDN100
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXJ9 (Homo sapiens) Explore Q9BXJ9 Go to UniProtKB: Q9BXJ9
GTEx: ENSG00000164134
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BXJ9
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L4	F [auth LC]	427	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P36578 (Homo sapiens) Explore P36578 Go to UniProtKB: P36578
GTEx: ENSG00000174444
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36578
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein eL6	G [auth LE]	288	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q02878 (Homo sapiens) Explore Q02878 Go to UniProtKB: Q02878
PHAROS: Q02878 GTEx: ENSG00000089009
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02878
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L38	H [auth Lk]	70	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P63173 (Homo sapiens) Explore P63173 Go to UniProtKB: P63173
PHAROS: P63173 GTEx: ENSG00000172809
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63173
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL24	I [auth LY]	144	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61254
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35	J [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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42766
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23a	K [auth LX]	156	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62750 (Homo sapiens) Explore P62750 Go to UniProtKB: P62750
PHAROS: P62750 GTEx: ENSG00000198242
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62750
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L19	L [auth LR]	196	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P84098 (Homo sapiens) Explore P84098 Go to UniProtKB: P84098
GTEx: ENSG00000108298
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84098
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28	M [auth Lr]	137	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P46779 (Homo sapiens) Explore P46779 Go to UniProtKB: P46779
PHAROS: P46779 GTEx: ENSG00000108107
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46779
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
5.8S rRNA (58-MER)	B [auth 8]	58	Homo sapiens
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
28S rRNA (300-MER, fragments)	E [auth 1]	300	Homo sapiens
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHP Query on IHP Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B]	P [auth B]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A]	N [auth A], O [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]