3HTK

Crystal structure of Mms21 and Smc5 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and functional insights into the roles of the Mms21 subunit of the Smc5/6 complex.

Duan, X.Sarangi, P.Liu, X.Rangi, G.K.Zhao, X.Ye, H.

(2009) Mol Cell 35: 657-668

  • DOI: https://doi.org/10.1016/j.molcel.2009.06.032
  • Primary Citation of Related Structures:  
    3HTK

  • PubMed Abstract: 

    The Smc5/6 complex is an evolutionarily conserved chromosomal ATPase required for cell growth and DNA repair. Its Mms21 subunit supports both functions by docking to the arm region of Smc5 and providing SUMO ligase activity. Here, we report the crystal structure of Mms21 in complex with the Smc5 arm. Our structure revealed two distinct structural and functional domains of the Smc5-bound Mms21: its N-terminal half is dedicated to Smc5 binding by forming a helix bundle with a coiled-coil structure of Smc5; its C-terminal half includes the SUMO ligase domain, which adopts a new type of RING E3 structure. Mutagenesis and structural analyses showed that the Mms21-Smc5 interface is required for cell growth and resistance to DNA damage, while the unique Mms21 RING domain confers specificity to the SUMO E2-E3 interaction. Through structure-based dissection of Mms21 functions, our studies establish a framework for understanding its roles in the Smc5/6 complex.


  • Organizational Affiliation

    James Graham Brown Cancer Center, University of Louisville, KY 40202, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 560Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SMC5YOL034W
UniProt
Find proteins for Q08204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08204 
Go to UniProtKB:  Q08204
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08204
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 573Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SMC5YOL034W
UniProt
Find proteins for Q08204 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08204 
Go to UniProtKB:  Q08204
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08204
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
E3 SUMO-protein ligase MMS21267Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MMS21NSE2YEL019C
EC: 6.3.2
UniProt
Find proteins for P38632 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38632 
Go to UniProtKB:  P38632
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38632
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.465α = 90
b = 91.574β = 90
c = 249.215γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations