4BKG | pdb_00004bkg

crystal structure of human diSUMO-2

• PDB DOI: https://doi.org/10.2210/pdb4BKG/pdb

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


• Deposited: 2013-04-25 Released: 2013-11-06 
• Deposition Author(s): Keusekotten, K., Bade, V.N., Meyer-Teschendorf, K., Sriramachandran, A., Fischer-Schrader, K., Krause, A., Horst, C., Hofmann, K., Dohmen, R.J., Praefcke, G.J.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.231 (Depositor), 0.519 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.519 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Multivalent Interactions of the Sumo-Interaction Motifs in the Ring-Finger Protein 4 (Rnf4) Determine the Specificity for Chains of the Small Ubiquitin-Related Modifier (Sumo).

Keusekotten, K., Bade, V.N., Meyer-Teschendorf, K., Sriramachandran, A.M., Fischer-Schrader, K., Krause, A., Horst, C., Schwarz, G., Hofmann, K., Dohmen, R.J., Praefcke, G.J.

(2014) Biochem J 457: 207

• PubMed: 24151981 
• DOI: https://doi.org/10.1042/BJ20130753
• Primary Citation Related Structures: 
  4BKG


• PubMed Abstract: 
  

  RNF4 (RING finger protein 4) is a STUbL [SUMO (small ubiquitin-related modifier)-targeted ubiquitin ligase] controlling PML (promyelocytic leukaemia) nuclear bodies, DNA double strand break repair and other nuclear functions. In the present paper, we describe that the sequence and spacing of the SIMs (SUMO-interaction motifs) in RNF4 regulate the avidity-driven recognition of substrate proteins carrying SUMO chains of variable length.

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Organizational Affiliation: 
• †Institute for Genetics, University of Cologne, 50674 Köln, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 19.19 kDa 
• Atom Count: 612 
• Modeled Residue Count: 73 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SMALL UBIQUITIN-RELATED MODIFIER 2	A	168	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61956 (Homo sapiens) Explore P61956  Go to UniProtKB:  P61956
PHAROS:  P61956 GTEx:  ENSG00000188612

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.231 (Depositor), 0.519 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.519 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.988	α = 90
b = 74.988	β = 90
c = 33.267	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-06 
Deposition Author(s): Keusekotten, K., Bade, V.N., Meyer-Teschendorf, K., Sriramachandran, A., Fischer-Schrader, K., Krause, A., Horst, C., Hofmann, K., Dohmen, R.J., Praefcke, G.J.K.

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Database references
• Version 1.2: 2016-09-21
  Changes: Source and taxonomy
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2018-06-06
  Changes: Data collection
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description