4H75

Crystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.098 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Distinct mode of methylated lysine-4 of histone H3 recognition by tandem tudor-like domains of Spindlin1.

Yang, N.Wang, W.Wang, Y.Wang, M.Zhao, Q.Rao, Z.Zhu, B.Xu, R.M.

(2012) Proc.Natl.Acad.Sci.USA 109: 17954-17959

  • DOI: 10.1073/pnas.1208517109

  • PubMed Abstract: 
  • Recognition of methylated histone tail lysine residues by tudor domains plays important roles in epigenetic control of gene expression and DNA damage response. Previous studies revealed the binding of methyllysine in a cage of aromatic residues, but ...

    Recognition of methylated histone tail lysine residues by tudor domains plays important roles in epigenetic control of gene expression and DNA damage response. Previous studies revealed the binding of methyllysine in a cage of aromatic residues, but the molecular mechanism by which the sequence specificity for surrounding histone tail residues is achieved remains poorly understood. In the crystal structure of a trimethylated histone H3 lysine 4 (H3K4) peptide bound to the tudor-like domains of Spindlin1 presented here, an atypical mode of methyllysine recognition by an aromatic pocket of Spindlin1 is observed. Furthermore, the histone sequence is recognized in a distinct manner involving the amino terminus and a pair of arginine residues of histone H3, and disruption of the binding impaired stimulation of pre-RNA expression by Spindlin1. Our analysis demonstrates considerable diversities of methyllysine recognition and sequence-specific binding of histone tails by tudor domains, and the revelation furthers the understanding of tudor domain proteins in deciphering epigenetic marks on histone tails.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spindlin-1
A
238Homo sapiensMutation(s): 0 
Gene Names: SPIN1 (OCR, SPIN)
Find proteins for Q9Y657 (Homo sapiens)
Go to Gene View: SPIN1
Go to UniProtKB:  Q9Y657
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3
B
8Homo sapiensMutation(s): 0 
Gene Names: HIST2H3PS2
Find proteins for Q5TEC6 (Homo sapiens)
Go to UniProtKB:  Q5TEC6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NHE
Query on NHE

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Download CCD File 
A
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.098 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 122.429α = 90.00
b = 42.685β = 90.00
c = 50.307γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2012-10-31
    Type: Database references
  • Version 1.2: 2012-11-14
    Type: Database references