5CVD

Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis for histone N-terminal methylation by NRMT1

Wu, R.Yue, Y.Zheng, X.Li, H.

(2015) Genes Dev 29: 2337-2342

  • DOI: 10.1101/gad.270926.115
  • Primary Citation of Related Structures:  
    5CVE, 5CVD

  • PubMed Abstract: 
  • NRMT1 is an N-terminal methyltransferase that methylates histone CENP-A as well as nonhistone substrates. Here, we report the crystal structure of human NRMT1 bound to CENP-A peptide at 1.3 Å. NRMT1 adopts a core methyltransferase fold that resembles DOT1L and PRMT but not SET domain family histone methyltransferases ...

    NRMT1 is an N-terminal methyltransferase that methylates histone CENP-A as well as nonhistone substrates. Here, we report the crystal structure of human NRMT1 bound to CENP-A peptide at 1.3 Å. NRMT1 adopts a core methyltransferase fold that resembles DOT1L and PRMT but not SET domain family histone methyltransferases. Key substrate recognition and catalytic residues were identified by mutagenesis studies. Histone peptide profiling revealed that human NRMT1 is highly selective to human CENP-A and fruit fly H2B, which share a common "Xaa-Pro-Lys/Arg" motif. These results, along with a 1.5 Å costructure of human NRMT1 bound to the fruit fly H2B peptide, underscore the importance of the NRMT1 recognition motif.


    Organizational Affiliation

    MOE Key Laboratory of Protein Sciences, Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-terminal Xaa-Pro-Lys N-methyltransferase 1A, B243Homo sapiensMutation(s): 0 
Gene Names: NTMT1NRMT1C9orf32METTL11ANRMTAD-003
EC: 2.1.1.244
Find proteins for Q9BV86 (Homo sapiens)
Explore Q9BV86 
Go to UniProtKB:  Q9BV86
NIH Common Fund Data Resources
PHAROS:  Q9BV86
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N-teminal peptide from Histone H3-like centromeric protein AC [auth D], D [auth E]9Homo sapiensMutation(s): 0 
Gene Names: CENPA
Find proteins for P49450 (Homo sapiens)
Explore P49450 
Go to UniProtKB:  P49450
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PHAROS:  P49450
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
E [auth A], F [auth B]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.839α = 90
b = 66.245β = 106.69
c = 68.998γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2015-07-26 
  • Released Date: 2015-11-25 
  • Deposition Author(s): Wu, R., Li, H.

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references