7Q40 | pdb_00007q40

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2

• PDB DOI: https://doi.org/10.2210/pdb7Q40/pdb

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


• Deposited: 2021-10-29 Released: 2022-11-16 
• Deposition Author(s): Demenge, A., Howard, E., Cousido-Siah, A., Mitschler, A., Podjarny, A., McEwen, A.G., Trave, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2

Demenge, A., Howard, E., Cousido-Siah, A., Mitschler, A., Podjarny, A., McEwen, A.G., Trave, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 130.04 kDa 
• Atom Count: 8,623 
• Modeled Residue Count: 1,108 
• Deposited Residue Count: 1,215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase HERC2	A, B [auth C], C [auth E]	405	Homo sapiens	Mutation(s): 0  Gene Names: HERC2 EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for O95714 (Homo sapiens) Explore O95714  Go to UniProtKB:  O95714
PHAROS:  O95714 GTEx:  ENSG00000128731

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth A], E [auth A], F [auth C], G [auth C], H [auth C], I [auth E], J [auth E], K [auth E], L [auth E]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.54	α = 90
b = 108.54	β = 90
c = 243.09	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Demenge, A., Howard, E., Cousido-Siah, A., Mitschler, A., Podjarny, A., McEwen, A.G., Trave, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description