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- PDB-7bp4: Structural insights into nucleosome reorganization by NAP1-RELATE... -

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Basic information

Entry
Database: PDB / ID: 7bp4
TitleStructural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)
Components
  • ASP-ASP-ASP-ASP-TYR
  • Histone H2A.6
  • Histone H2B.1
KeywordsNUCLEAR PROTEIN / complex / Histone / PLANT PROTEIN
Function / homology
Function and homology information


DNA-mediated transformation / plastid / chloroplast / response to bacterium / response to wounding / structural constituent of chromatin / nucleosome / protein heterodimerization activity / nucleolus / DNA binding ...DNA-mediated transformation / plastid / chloroplast / response to bacterium / response to wounding / structural constituent of chromatin / nucleosome / protein heterodimerization activity / nucleolus / DNA binding / extracellular region / nucleus
Similarity search - Function
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 ...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
Histone H2A.6 / Histone H2B.1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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
G: Histone H2A.6
H: Histone H2B.1
L: ASP-ASP-ASP-ASP-TYR
A: Histone H2A.6
B: Histone H2B.1
C: ASP-ASP-ASP-ASP-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5107
Polymers43,4186
Non-polymers921
Water2,828157
1
G: Histone H2A.6
H: Histone H2B.1
L: ASP-ASP-ASP-ASP-TYR


Theoretical massNumber of molelcules
Total (without water)21,7093
Polymers21,7093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-50 kcal/mol
Surface area8930 Å2
MethodPISA
2
A: Histone H2A.6
B: Histone H2B.1
C: ASP-ASP-ASP-ASP-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8014
Polymers21,7093
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-45 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.748, 62.248, 130.692
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/peptide ASP-ASP-ASP-ASP-TYR


Mass: 641.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.7 M ammonium dihydrogen phosphate, 0.07 M sodium citrate and 30% (v/v) glycerol (pH 5.6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 29973 / % possible obs: 99.8 % / Redundancy: 9.4 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.042 / Rrim(I) all: 0.133 / Χ2: 0.979 / Net I/σ(I): 17.5
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2903 / CC1/2: 0.695 / CC star: 0.906 / Rpim(I) all: 0.215 / Rrim(I) all: 0.569

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→28.93 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.3 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1407 5.2 %RANDOM
Rwork0.1857 ---
obs0.1879 25549 89.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.4 Å2 / Biso mean: 30.462 Å2 / Biso min: 9.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.42 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 2.1→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 6 157 2899
Biso mean--45.11 39.78 -
Num. residues----352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132779
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172761
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.6463742
X-RAY DIFFRACTIONr_angle_other_deg1.3771.5876380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5985346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32821.704135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26515512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0791520
X-RAY DIFFRACTIONr_chiral_restr0.080.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
LS refinement shellResolution: 2.102→2.156 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 50 -
Rwork0.247 1050 -
all-1100 -
obs--50.55 %

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