8B3I

CRL4CSA-E2-Ub (state 2)

• PDB DOI: https://doi.org/10.2210/pdb8B3I/pdb
• EM Map EMD-15829: EMDB EMDataResource

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2022-09-16 Released: 2023-09-27 
• Deposition Author(s): Kokic, G., Cramer, P.
• Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

C(N)RL4CSA-E2-Ub (state 2)

Kokic, G., Cramer, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A1B1C1D1E1F1G1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A2B1C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 305.41 kDa 
• Atom Count: 20,197 
• Modelled Residue Count: 2,537 
• Deposited Residue Count: 2,702 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D2	A [auth D]	147	Homo sapiens	Mutation(s): 0  Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
PHAROS:  P62837 GTEx:  ENSG00000131508

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD8	B [auth N]	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBX1	C [auth R]	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	D [auth U]	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair protein ERCC-8	E [auth a]	396	Homo sapiens	Mutation(s): 0  Gene Names: ERCC8, CKN1, CSA
UniProt & NIH Common Fund Data Resources
Find proteins for Q13216 (Homo sapiens) Explore Q13216  Go to UniProtKB:  Q13216
PHAROS:  Q13216 GTEx:  ENSG00000049167

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	F [auth d]	1,140	Homo sapiens	Mutation(s): 0  Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531  Go to UniProtKB:  Q16531
PHAROS:  Q16531 GTEx:  ENSG00000167986

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-4A	G [auth e]	759	Homo sapiens	Mutation(s): 0  Gene Names: CUL4A
UniProt & NIH Common Fund Data Resources
Find proteins for Q13619 (Homo sapiens) Explore Q13619  Go to UniProtKB:  Q13619
PHAROS:  Q13619 GTEx:  ENSG00000139842

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	H [auth R], I [auth R], J [auth R]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Kokic, G., Cramer, P.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	EXC 2067/1-390729940
European Research Council (ERC)	European Union	Advanced Investigator Grant CHROMATRANS (grant agreement No. 882357)

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release