9J64 | pdb_00009j64

Cryo-EM structure of neddylated Cul2-Rbx1-EloBC-FEM1B homodimer complexed with FNIP1 degron

• PDB DOI: https://doi.org/10.2210/pdb9J64/pdb
• EM Map EMD-61162: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens, Escherichia coli K-12
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-14 Released: 2025-09-03 
• Deposition Author(s): Dai, Z., Liang, L., Yin, Y.X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Neddylation induces an intermediate auto-inhibited CRL2FEM1B E3 ubiquitin ligase

Dai, Z., Liang, L., Yin, Y.X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A2B2C1D1E1F1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 346.08 kDa 
• Atom Count: 16,354 
• Modeled Residue Count: 2,011 
• Deposited Residue Count: 3,015 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-2	A, B [auth D]	751	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBX1	C [auth E], F [auth H]	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	D [auth F]	98	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
Elongin-B	E [auth G]	104	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein fem-1 homolog B	G [auth I]	628	Homo sapiens	Mutation(s): 0  Gene Names: FEM1B, F1AA, KIAA0396
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK73 (Homo sapiens) Explore Q9UK73  Go to UniProtKB:  Q9UK73
PHAROS:  Q9UK73 GTEx:  ENSG00000169018

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Folliculin interacting protein 1	H [auth J]	467	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: malE, b4034, JW3994, FNIP1
UniProt & NIH Common Fund Data Resources
Find proteins for J3KNG8 (Homo sapiens) Explore J3KNG8  Go to UniProtKB:  J3KNG8
GTEx:  ENSG00000217128

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	I [auth E], J [auth E], K [auth E], L [auth H], M [auth H], N [auth H], O [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Dai, Z., Liang, L., Yin, Y.X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81621063, 31800626

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release