9EFM | pdb_00009efm

Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1

PDB DOI: https://doi.org/10.2210/pdb9EFM/pdb
EM Map EMD-47976: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli, Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2024-11-20 Released: 2025-12-03
Deposition Author(s): Shi, H., Zheng, N.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.16 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1

Shi, H., Zheng, N.

To be published.

Macromolecule Content

Total Structure Weight: 439.56 kDa
Atom Count: 24,951
Modeled Residue Count: 3,108
Deposited Residue Count: 3,862
Unique protein chains: 11

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COP9 signalosome complex subunit 1	A	491	Homo sapiens	Mutation(s): 0 Gene Names: GPS1, COPS1, CSN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13098 (Homo sapiens) Explore Q13098 Go to UniProtKB: Q13098
PHAROS: Q13098 GTEx: ENSG00000169727
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13098
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COP9 signalosome complex subunit 2	B	443	Homo sapiens	Mutation(s): 0 Gene Names: COPS2, CSN2, TRIP15
UniProt & NIH Common Fund Data Resources
Find proteins for P61201 (Homo sapiens) Explore P61201 Go to UniProtKB: P61201
PHAROS: P61201 GTEx: ENSG00000166200
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61201
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
COP9 signalosome complex subunit 3	C	423	Homo sapiens	Mutation(s): 0 Gene Names: COPS3, CSN3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNS2 (Homo sapiens) Explore Q9UNS2 Go to UniProtKB: Q9UNS2
PHAROS: Q9UNS2 GTEx: ENSG00000141030
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UNS2
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
COP9 signalosome complex subunit 4	D	406	Homo sapiens	Mutation(s): 0 Gene Names: COPS4, CSN4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BT78 (Homo sapiens) Explore Q9BT78 Go to UniProtKB: Q9BT78
PHAROS: Q9BT78 GTEx: ENSG00000138663
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BT78
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
COP9 signalosome complex subunit 5	E	334	Homo sapiens	Mutation(s): 2 Gene Names: COPS5, CSN5, JAB1 EC: 3.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q92905 (Homo sapiens) Explore Q92905 Go to UniProtKB: Q92905
PHAROS: Q92905 GTEx: ENSG00000121022
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92905
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
COP9 signalosome complex subunit 6	F	327	Homo sapiens	Mutation(s): 0 Gene Names: COPS6, CSN6, HVIP
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L5N1 (Homo sapiens) Explore Q7L5N1 Go to UniProtKB: Q7L5N1
PHAROS: Q7L5N1 GTEx: ENSG00000168090
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7L5N1
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
COP9 signalosome complex subunit 7b	G	264	Homo sapiens	Mutation(s): 0 Gene Names: COPS7B, CSN7B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Q2 (Homo sapiens) Explore Q9H9Q2 Go to UniProtKB: Q9H9Q2
PHAROS: Q9H9Q2 GTEx: ENSG00000144524
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H9Q2
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
COP9 signalosome complex subunit 8	H	209	Homo sapiens	Mutation(s): 0 Gene Names: COPS8, CSN8
UniProt & NIH Common Fund Data Resources
Find proteins for Q99627 (Homo sapiens) Explore Q99627 Go to UniProtKB: Q99627
PHAROS: Q99627 GTEx: ENSG00000198612
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99627
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD8	I	81	Homo sapiens	Mutation(s): 0 Gene Names: NEDD8
UniProt & NIH Common Fund Data Resources
Find proteins for Q15843 (Homo sapiens) Explore Q15843 Go to UniProtKB: Q15843
PHAROS: Q15843 GTEx: ENSG00000129559
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15843
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-1	J	776	Homo sapiens	Mutation(s): 0 Gene Names: CUL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13616 (Homo sapiens) Explore Q13616 Go to UniProtKB: Q13616
PHAROS: Q13616 GTEx: ENSG00000055130
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13616
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBX1	K	108	Homo sapiens	Mutation(s): 0 Gene Names: RBX1, RNF75, ROC1 EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62877 (Homo sapiens) Explore P62877 Go to UniProtKB: P62877
PHAROS: P62877 GTEx: ENSG00000100387
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62877
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain L [auth K] SDF format, chain M [auth K] SDF format, chain N [auth K] MOL2 format, chain L [auth K] MOL2 format, chain M [auth K] MOL2 format, chain N [auth K] mmCIF format, chain L [auth K] mmCIF format, chain M [auth K] mmCIF format, chain N [auth K]	L [auth K], M [auth K], N [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth K] Focus chain M [auth K] Focus chain N [auth K] Interactions & Density Focus chain L [auth K] Focus chain M [auth K] Focus chain N [auth K]