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- PDB-7bp6: Structural insights into nucleosome reorganization by NAP1-RELATE... -

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Basic information

Entry
Database: PDB / ID: 7bp6
TitleStructural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)
Components
  • Histone H2A.6
  • Histone H2B.1
  • NRP1-CTAD
KeywordsNUCLEAR PROTEIN/CHAPERONE / complex / Histone / PLANT PROTEIN / NUCLEAR PROTEIN-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 / nucleosome assembly / structural constituent of chromatin / nucleosome ...somatic cell DNA recombination / DNA-mediated transformation / plastid / chloroplast / response to bacterium / double-strand break repair via homologous recombination / response to wounding / nucleosome assembly / 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 / SAD / Resolution: 1.58 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
DepositionMar 21, 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 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: NRP1-CTAD


Theoretical massNumber of molelcules
Total (without water)21,9073
Polymers21,9073
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-53 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.114, 62.282, 66.838
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.: 1
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.: 1
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/peptide NRP1-CTAD / 7-mer from NAP1-related protein 1


Mass: 839.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q9CA59
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 1.91 Å3/Da / Density % sol: 35.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium nitrate, 0.1 M Bis-Tris propane and 20% (w/v) PEG 3350 (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.58→30 Å / Num. obs: 23604 / % possible obs: 99.7 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.023 / Rrim(I) all: 0.078 / Χ2: 0.992 / Net I/σ(I): 28.5
Reflection shellResolution: 1.58→1.64 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2302 / CC1/2: 0.897 / CC star: 0.972 / Rpim(I) all: 0.135 / Rrim(I) all: 0.382

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→29.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.5 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.086
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 1251 5.3 %RANDOM
Rwork0.162 ---
obs0.1641 22146 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.59 Å2 / Biso mean: 14.706 Å2 / Biso min: 5.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.08 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.58→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 0 161 1569
Biso mean---26.96 -
Num. residues----186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131426
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171411
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.6441921
X-RAY DIFFRACTIONr_angle_other_deg1.5281.5843262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07822.29561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46515258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.081158
X-RAY DIFFRACTIONr_chiral_restr0.0830.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02278
LS refinement shellResolution: 1.58→1.621 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 76 -
Rwork0.215 1524 -
all-1600 -
obs--93.13 %

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