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- PDB-7c7x: Structural insights into nucleosome reorganization by NAP1-RELATE... -

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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 / nucleosome assembly / response to wounding / structural constituent of chromatin / nucleosome ...somatic cell DNA recombination / DNA-mediated transformation / plastid / chloroplast / response to bacterium / double-strand break repair via homologous recombination / nucleosome assembly / response to wounding / structural constituent of chromatin / nucleosome / 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 H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Glycerol


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


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

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Experimental details

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Experiment

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

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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

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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

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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 %

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