4W5V | pdb_00004w5v

Crystal structure of Human SUMO E2-conjugating enzyme (Ubc9) in complex with E1-activating enzyme (Uba2) ubiquitin fold domain (Ufd)

• PDB DOI: https://doi.org/10.2210/pdb4W5V/pdb

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


• Deposited: 2014-08-19 Released: 2015-09-09 
• Deposition Author(s): Boucher, L.E., Reiter, K.H., Matunis, M.J., Bosch, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of human SUMO complex

Reiter, K.H., Boucher, L.E., Bosch, J., Matunis, M.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.98 kDa 
• Atom Count: 2,179 
• Modeled Residue Count: 264 
• Deposited Residue Count: 285 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUMO-conjugating enzyme UBC9	A	163	Homo sapiens	Mutation(s): 0  Gene Names: UBE2I, UBC9, UBCE9 EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P63279 (Homo sapiens) Explore P63279  Go to UniProtKB:  P63279
PHAROS:  P63279 GTEx:  ENSG00000103275

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SUMO-activating enzyme subunit 2	B	122	Homo sapiens	Mutation(s): 0  Gene Names: UBA2, SAE2, UBLE1B, HRIHFB2115 EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBT2 (Homo sapiens) Explore Q9UBT2  Go to UniProtKB:  Q9UBT2
PHAROS:  Q9UBT2 GTEx:  ENSG00000126261

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
K	E [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.273	α = 90
b = 35.272	β = 96.69
c = 58.672	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XDS	data scaling
XSCALE	data scaling
Blu-Ice	data collection
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Boucher, L.E., Reiter, K.H., Matunis, M.J., Bosch, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM060980

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description