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 2NS2 | pdb_00002ns2

Crystal Structure of Spindlin1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.260 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2NS2

This is version 1.3 of the entry. See complete history. 

Literature

Structure of human spindlin1. Tandem tudor-like domains for cell cycle regulation

Zhao, Q., Qin, L., Jiang, F., Wu, B., Yue, W., Xu, F., Rong, Z., Yuan, H., Xie, X., Gao, Y., Bai, C., Bartlam, M., Pei, X., Rao, Z.

(2007) J Biol Chem 282: 647-656

  • DOI: https://doi.org/10.1074/jbc.M604029200
  • Primary Citation Related Structures: 
    2NS2

  • PubMed Abstract: 

    Spindlin1, a meiotic spindle-binding protein that is highly expressed in ovarian cancer cells, was first identified as a gene involved in gametogenesis. It appeared to be a target for cell cycle-dependent phosphorylation and was demonstrated to disturb the cell cycle. Here we report the crystal structure of human spindlin1 to 2.2A of resolution, representing the first three-dimensional structure from the spin/ssty (Y-linked spermiogenesis-specific transcript) gene family. The refined structure, containing three repeats of five/four anti-parallel beta-strands, exhibits a novel arrangement of tandem Tudor-like domains. Two phosphate ions, chelated by Thr-95 and other residues, appear to stabilize the long loop between domains I and II, which might mediate the cell cycle regulation activity of spindlin1. Flow cytometry experiments indicate that cells expressing spindlin1 display a different cell cycle distribution in mitosis, whereas those expressing a T95A mutant, which had a great decrease in phosphorous content, have little effect on the cell cycle. We further identified associations of spindlin1 with nucleic acid to provide a biochemical basis for its cell cycle regulation and other functions.


  • Organizational Affiliation: 
    • Tsinghua-Institute of Biophysics Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China.

Macromolecule Content 

  • Total Structure Weight: 55.24 kDa 
  • Atom Count: 3,274 
  • Modeled Residue Count: 373 
  • Deposited Residue Count: 484 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spindlin-1
A, B
242Homo sapiensMutation(s): 0 
Gene Names: SPIN, OCR, SPIN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y657 (Homo sapiens)
Explore Q9Y657 
Go to UniProtKB:  Q9Y657
PHAROS:  Q9Y657
GTEx:  ENSG00000106723 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y657
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.793α = 90
b = 84.876β = 90
c = 136.567γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations