7BP2 | pdb_00007bp2

Structural mechanism directing nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.186 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7BP2

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 43.46 kDa 
  • Atom Count: 3,188 
  • Modeled Residue Count: 352 
  • Deposited Residue Count: 382 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A.6
A, C
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B.1
B, D
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
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
(Subject of Investigation/LOI)

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
H [auth B]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
N [auth D],
O [auth D],
P [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
(Subject of Investigation/LOI)

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B],
Q [auth D],
R [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.186 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.712α = 90
b = 65.712β = 90
c = 96.687γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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: 2023-11-29
    Changes: Data collection, Database references, Refinement description