4L1M | pdb_00004l1m

Structure of the first RCC1-like domain of HERC2

• PDB DOI: https://doi.org/10.2210/pdb4L1M/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-03 Released: 2013-07-03 
• Deposition Author(s): Tempel, W., Khan, M.B., Dong, A., Hu, J., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structure of the first RCC1-like domain of HERC2

Tempel, W., Khan, M.B., Dong, A., Hu, J., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 127.24 kDa 
• Atom Count: 7,981 
• Modeled Residue Count: 1,068 
• Deposited Residue Count: 1,176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase HERC2	A, B, C	392	Homo sapiens	Mutation(s): 0  Gene Names: HERC2 EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A], GA [auth C], HA [auth C], IA [auth C], Q [auth B], R [auth B], S [auth B], T [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNX	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], H [auth A], I [auth A], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], U [auth B], UA [auth C], V [auth B], VA [auth C], W [auth B], X [auth B], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.159	α = 90
b = 94.159	β = 90
c = 281.894	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Tempel, W., Khan, M.B., Dong, A., Hu, J., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description