7W5M | pdb_00007w5m

Crystal structure of AtNASP in complex of H3 alpha3 helix peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Structural basis for histone H3 recognition by NASP in Arabidopsis.

Liu, Y., Chen, L., Wang, N., Wu, B., Bao, H., Huang, H.

(2022) J Integr Plant Biol 64: 2309-2313

  • DOI: https://doi.org/10.1111/jipb.13277
  • Primary Citation of Related Structures:  
    7W5M

  • PubMed Abstract: 

    The structural basis for histone recognition by the histone chaperone nuclear autoantigenic sperm protein (NASP) remains largely unclear. Here, we showed that Arabidopsis thaliana AtNASP is a monomer and displays robust nucleosome assembly activity in vitro. Examining the structure of AtNASP complexed with a histone H3 α3 peptide revealed a binding mode that is conserved in human NASP. AtNASP recognizes the H3 N-terminal region distinct from human NASP. Moreover, AtNASP forms a co-chaperone complex with ANTI-SILENCING FUNCTION 1 (ASF1) by binding to the H3 N-terminal region. Therefore, we deciphered the structure of AtNASP and the basis of the AtNASP-H3 interaction.

    • Organizational Affiliation: 
    • Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tetratricopeptide repeat (TPR)-like superfamily protein268Arabidopsis thalianaMutation(s): 0 
Gene Names: AP22.13, AP22_13, At4g37210
UniProt
Find proteins for Q94K88 (Arabidopsis thaliana)
Explore Q94K88 
Go to UniProtKB:  Q94K88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94K88
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H3 alpha3 helix peptide20Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
PHAROS:  P84243
GTEx:  ENSG00000132475 ENSG00000163041 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84243
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.278α = 90
b = 62.803β = 90
c = 92.796γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31800619

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2023-01-11
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description