8WQC

cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1

• PDB DOI: https://doi.org/10.2210/pdb8WQC/pdb
• EM Map EMD-37739: EMDB EMDataResource

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


• Deposited: 2023-10-11 Released: 2024-04-03 
• Deposition Author(s): Chen, X., Zhang, K., Xu, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1

Chen, X., Zhang, K., Xu, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A2B2C2D2E2F2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A3B2C2D2E2F1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - E2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - F2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - B2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 402.86 kDa 
• Atom Count: 26,832 
• Modelled Residue Count: 3,393 
• Deposited Residue Count: 3,526 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	A [auth D], I	118	Homo sapiens	Mutation(s): 0  Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370  Go to UniProtKB:  Q15370
PHAROS:  Q15370 GTEx:  ENSG00000103363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBX1, N-terminally processed	B [auth F], E [auth J]	96	Homo sapiens	Mutation(s): 0  Gene Names: RBX1, RNF75, ROC1
UniProt & NIH Common Fund Data Resources
Find proteins for P62877 (Homo sapiens) Explore P62877  Go to UniProtKB:  P62877
PHAROS:  P62877 GTEx:  ENSG00000100387

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	C [auth B], H	96	Homo sapiens	Mutation(s): 0  Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369  Go to UniProtKB:  Q15369
PHAROS:  Q15369 GTEx:  ENSG00000154582

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-2	D [auth C], F [auth E]	750	Homo sapiens	Mutation(s): 0  Gene Names: CUL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13617 (Homo sapiens) Explore Q13617  Go to UniProtKB:  Q13617
PHAROS:  Q13617 GTEx:  ENSG00000108094

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD8	G [auth N], J [auth K]	76	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 ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein fem-1 homolog B	K [auth A], L [auth G]	627	Homo sapiens	Mutation(s): 0  Gene Names: FEM1B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK73 (Homo sapiens) Explore Q9UK73  Go to UniProtKB:  Q9UK73
PHAROS:  Q9UK73 GTEx:  ENSG00000169018

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	M [auth F], N [auth F], O [auth F], P [auth J], Q [auth J], R [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Chen, X., Zhang, K., Xu, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release