[English] 日本語
Yorodumi
- PDB-7c7x: Structural insights into nucleosome reorganization by NAP1-RELATE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c7x
TitleStructural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)
Components
  • Histone H2A.6
  • Histone H2B.1
  • NAP1-related protein 1
KeywordsTRANSCRIPTION/CHAPERONE / complex / Histone / PLANT PROTEIN / CHAPERONE / TRANSCRIPTION-CHAPERONE complex
Function / homology
Function and homology information


somatic cell DNA recombination / DNA-mediated transformation / plastid / chloroplast / response to bacterium / double-strand break repair via homologous recombination / response to wounding / structural constituent of chromatin / nucleosome / nucleosome assembly ...somatic cell DNA recombination / DNA-mediated transformation / plastid / chloroplast / response to bacterium / double-strand break repair via homologous recombination / response to wounding / structural constituent of chromatin / nucleosome / nucleosome assembly / histone binding / protein heterodimerization activity / chromatin binding / nucleolus / DNA binding / extracellular region / nucleus / cytoplasm
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain ...Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
NAP1-related protein 1 / Histone H2A.6 / Histone H2B.1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLuo, Q. / Baihui, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC31930017 China
National Basic Research Program of China (973 Program)2012CB910500 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: NAP1-Related Protein 1 (NRP1) has multiple interaction modes for chaperoning histones H2A-H2B.
Authors: 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.
History
DepositionMay 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Histone H2A.6
D: Histone H2B.1
E: NAP1-related protein 1
F: NAP1-related protein 1
A: Histone H2A.6
B: Histone H2B.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,47310
Polymers97,1046
Non-polymers3684
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-101 kcal/mol
Surface area40620 Å2
Unit cell
Length a, b, c (Å)66.710, 128.396, 140.275
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Histone H2A.6 / HTA1 / Protein RESISTANT TO AGROBACTERIUM TRANSFORMATION 5


Mass: 10033.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RAT5, H2A-1, At5g54640, MRB17.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LD28
#2: Protein Histone H2B.1 / HTB1


Mass: 11033.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g07790, F24B9.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LQQ4
#3: Protein NAP1-related protein 1 / Histone chaperone NRP1 / Nucleosome/chromatin assembly factor group A6 / Protein SET homolog 1


Mass: 27484.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NRP1, NFA6, At1g74560, F1M20.24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9CA59
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1 M NaCl, 0.1 M sodium cacodylate, 30% (v/v) PEG 600, 10% (v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 24251 / % possible obs: 96.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.033 / Rrim(I) all: 0.099 / Χ2: 0.971 / Net I/σ(I): 7.4 / Num. measured all: 184525
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.113.60.39320900.1670.2150.4520.72285
3.11-3.234.10.3822170.2880.1940.430.75390.1
3.23-3.385.20.34123900.6460.1550.3770.84797.1
3.38-3.566.40.31424310.7810.1290.3410.92498.9
3.56-3.787.40.24824620.9170.0940.2661.03399.4
3.78-4.078.30.18524610.9660.0650.1971.10299.6
4.07-4.4890.12424930.9890.0420.1321.15899.6
4.48-5.129.30.09225130.9940.030.0971.13599.6
5.12-6.4410.30.08925320.9950.0280.0930.97899.8
6.44-30110.03826620.9990.0110.040.74799.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DAY

5day


Resolution: 3→29.62 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.85 / SU B: 18.801 / SU ML: 0.338 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 1042 4.9 %RANDOM
Rwork0.2229 ---
obs0.2248 20062 84.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 215.82 Å2 / Biso mean: 74.159 Å2 / Biso min: 6.01 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å2-0 Å20 Å2
2--2.82 Å2-0 Å2
3----1.41 Å2
Refinement stepCycle: final / Resolution: 3→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 0 24 24 5502
Biso mean--37.7 38.95 -
Num. residues----683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135573
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175354
X-RAY DIFFRACTIONr_angle_refined_deg1.541.6427515
X-RAY DIFFRACTIONr_angle_other_deg1.2581.58112436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9635671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.47523.613274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.388151019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4141524
X-RAY DIFFRACTIONr_chiral_restr0.070.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026040
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021112
LS refinement shellResolution: 3→3.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 25 -
Rwork0.306 496 -
all-521 -
obs--29.37 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more