5HZR | pdb_00005hzr

Crystal structure of MtSnf2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.213 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5HZR

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure of chromatin remodeler Swi2/Snf2 in the resting state

Xia, X.Liu, X.Li, T.Fang, X.Chen, Z.C.

(2016) Nat Struct Mol Biol 23: 722-729

  • DOI: https://doi.org/10.1038/nsmb.3259
  • Primary Citation Related Structures: 
    5HZR

  • PubMed Abstract: 

    SWI2/SNF2 family proteins regulate a myriad of nucleic acid transactions by sliding, removing and reconstructing nucleosomes in eukaryotic cells. They contain two RecA-like core domains, which couple ATP hydrolysis and DNA translocation to chromatin remodeling. Here we report the crystal structure of Snf2 from the yeast Myceliophthora thermophila. The data show the two RecA-like core domains of Snf2 stacking together and twisting their ATP-binding motifs away from each other, thus explaining the inactivity of the protein in the ground state. We identified several DNA-binding elements, which are fully exposed to solvent, thus suggesting that the protein is poised for its incoming substrate. The catalytic core of Snf2 showed a high chromatin-remodeling activity, which was suppressed by the N-terminal HSA domain. Our findings reveal that the catalytic core of Snf2 is a competent remodeling machine, which rests in an inactive conformation and requires a large conformational change upon activation.


  • Organizational Affiliation
    • MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 85.75 kDa 
  • Atom Count: 4,724 
  • Modeled Residue Count: 552 
  • Deposited Residue Count: 732 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SNF2-family ATP dependent chromatin remodeling factor like protein732Thermothelomyces thermophilus ATCC 42464Mutation(s): 0 
Gene Names: MYCTH_115909
UniProt
Find proteins for G2QDW1 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2QDW1 
Go to UniProtKB:  G2QDW1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2QDW1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KH2

Query on KH2



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]
3-(1-methylpiperidinium-1-yl)propane-1-sulfonate
C9 H19 N O3 S
DQNQWAVIDNVATL-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA

Query on NA



Download:Ideal Coordinates CCD File
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.213 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.613α = 90
b = 144.266β = 90
c = 121.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Key Research Plan-Protein SciencesChina2014CB910100

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-17
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations