7BP4 | pdb_00007bp4

Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.226 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

NAP1-Related Protein 1 (NRP1) has multiple interaction modes for chaperoning histones H2A-H2B.

Luo, Q.Wang, B.Wu, Z.Jiang, W.Wang, Y.Du, K.Zhou, N.Zheng, L.Gan, J.Shen, W.H.Ma, J.Dong, A.

(2020) Proc Natl Acad Sci U S A 117: 30391-30399

  • DOI: https://doi.org/10.1073/pnas.2011089117
  • Primary Citation of Related Structures:  
    7BP2, 7BP4, 7BP5, 7BP6, 7C7X

  • PubMed Abstract: 

    Nucleosome Assembly Protein 1 (NAP1) family proteins are evolutionarily conserved histone chaperones that play important roles in diverse biological processes. In this study, we determined the crystal structure of Arabidopsis NAP1-Related Protein 1 (NRP1) complexed with H2A-H2B and uncovered a previously unknown interaction mechanism in histone chaperoning. Both in vitro binding and in vivo plant rescue assays proved that interaction mediated by the N-terminal α-helix (αN) domain is essential for NRP1 function. In addition, the C-terminal acidic domain (CTAD) of NRP1 binds to H2A-H2B through a conserved mode similar to other histone chaperones. We further extended previous knowledge of the NAP1-conserved earmuff domain by mapping the amino acids of NRP1 involved in association with H2A-H2B. Finally, we showed that H2A-H2B interactions mediated by αN, earmuff, and CTAD domains are all required for the effective chaperone activity of NRP1. Collectively, our results reveal multiple interaction modes of a NAP1 family histone chaperone and shed light on how histone chaperones shield H2A-H2B from nonspecific interaction with DNA.


  • Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438 Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.6A [auth G],
D [auth A]
93Arabidopsis thalianaMutation(s): 0 
Gene Names: RAT5H2A-1At5g54640MRB17.14
UniProt
Find proteins for Q9LD28 (Arabidopsis thaliana)
Explore Q9LD28 
Go to UniProtKB:  Q9LD28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LD28
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B.1B [auth H],
E [auth B]
98Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g07790F24B9.10
UniProt
Find proteins for Q9LQQ4 (Arabidopsis thaliana)
Explore Q9LQQ4 
Go to UniProtKB:  Q9LQQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LQQ4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ASP-ASP-ASP-ASP-TYRC [auth L],
F [auth C]
5Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.748α = 90
b = 62.248β = 90
c = 130.692γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GOLClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)ChinaNSFC31930017
National Basic Research Program of China (973 Program)China2012CB910500

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2020-12-02
    Changes: Database references
  • Version 1.3: 2020-12-16
    Changes: Database references
  • Version 1.4: 2024-03-27
    Changes: Data collection, Database references