3RC3

Human Mitochondrial Helicase Suv3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Human Suv3 protein reveals unique features among SF2 helicases.

Jedrzejczak, R.Wang, J.Dauter, M.Szczesny, R.J.Stepien, P.P.Dauter, Z.

(2011) Acta Crystallogr.,Sect.D 67: 988-996

  • DOI: 10.1107/S0907444911040248
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Suv3 is a helicase that is involved in efficient turnover and surveillance of RNA in eukaryotes. In vitro studies show that human Suv3 (hSuv3) in complex with human polynucleotide phosphorylase has RNA degradosome activity. The enzyme is mainly local ...

    Suv3 is a helicase that is involved in efficient turnover and surveillance of RNA in eukaryotes. In vitro studies show that human Suv3 (hSuv3) in complex with human polynucleotide phosphorylase has RNA degradosome activity. The enzyme is mainly localized in mitochondria, but small fractions are found in cell nuclei. Here, two X-ray crystallographic structures of human Suv3 in complex with AMPPNP, a nonhydrolysable analog of ATP, and with a short five-nucleotide strand of RNA are presented at resolutions of 2.08 and 2.9 Å, respectively. The structure of the enzyme is very similar in the two complexes and consists of four domains. Two RecA-like domains form the tandem typical of all helicases from the SF2 superfamily which together with the C-terminal all-helical domain makes a ring structure through which the nucleotide strand threads. The mostly helical N-terminal domain is positioned externally with respect to the core of the enzyme. Most of the typical helicase motifs are present in hSuv3, but the protein shows certain unique characteristics, suggesting that Suv3 enzymes may constitute a separate subfamily of helicases.


    Organizational Affiliation

    Synchrotron Radiation Research Section, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase SUPV3L1, mitochondrial
A
677Homo sapiensMutation(s): 0 
Gene Names: SUPV3L1 (SUV3)
EC: 3.6.4.13
Find proteins for Q8IYB8 (Homo sapiens)
Go to Gene View: SUPV3L1
Go to UniProtKB:  Q8IYB8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ANP
Query on ANP

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Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
AZI
Query on AZI

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Download CCD File 
A
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.160 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 89.390α = 90.00
b = 89.390β = 90.00
c = 88.070γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
SHELXDphasing
ARP/wARPmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-02
    Type: Database references
  • Version 1.3: 2012-03-28
    Type: Database references
  • Version 1.4: 2017-11-08
    Type: Refinement description