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- PDB-7m3x: Crystal Structure of the Apo Form of Human RBBP7 -

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Basic information

Entry
Database: PDB / ID: 7m3x
TitleCrystal Structure of the Apo Form of Human RBBP7
ComponentsHistone-binding protein RBBP7
KeywordsTRANSCRIPTION / RBBP7 / CHROMATIN / HISTONE / WD-40 REPEAT PROTEIN / CHAPERONE / ACETYLATION / CHROMATIN REGULATOR / DNA REPLICATION / NUCLEUS / PHOSPHOPROTEIN / REPRESSOR / TRANSCRIPTION REGULATION / WD REPEAT / CHROMOSOMAL PROTEIN / NUCLEOSOME CORE / HISTONE-CHAPERONE COMPLEX Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cellular heat acclimation / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / ESC/E(Z) complex / regulation of stem cell differentiation / response to steroid hormone / ATPase complex / positive regulation of stem cell population maintenance ...cellular heat acclimation / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / ESC/E(Z) complex / regulation of stem cell differentiation / response to steroid hormone / ATPase complex / positive regulation of stem cell population maintenance / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / negative regulation of cell growth / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Neddylation / HATs acetylate histones / histone binding / Oxidative Stress Induced Senescence / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone-binding protein RBBP7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsRighetto, G.L. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal Structure of the Apo Form of Human RBBP7
Authors: Righetto, G.L. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionMar 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Histone-binding protein RBBP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0463
Polymers45,9661
Non-polymers802
Water7,476415
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16730 Å2
Unit cell
Length a, b, c (Å)44.726, 88.775, 97.165
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-binding protein RBBP7 / Histone acetyltransferase type B subunit 2 / Nucleosome-remodeling factor subunit RBAP46 / ...Histone acetyltransferase type B subunit 2 / Nucleosome-remodeling factor subunit RBAP46 / Retinoblastoma-binding protein 7 / RBBP-7 / Retinoblastoma-binding protein p46


Mass: 45965.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP7, RBAP46 / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16576
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.2 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 28%(w/v)PEG3350 MME, 0.2M NaCl, 0.1M Hepes pH7.8, 5% MPD, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 68121 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.023 / Rrim(I) all: 0.078 / Χ2: 0.784 / Net I/σ(I): 7 / Num. measured all: 727132
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.46-1.498.10.77733540.8050.2860.8290.48299.8
1.49-1.519.50.70433380.8660.2390.7440.49799.9
1.51-1.5410.40.6133540.9060.1970.6410.504100
1.54-1.57110.52933580.9350.1650.5540.522100
1.57-1.6111.30.42633930.9590.1310.4460.54599.9
1.61-1.6411.20.3833490.9630.1180.3990.54699.7
1.64-1.69110.33533450.970.1040.3510.55799.9
1.69-1.7310.80.28133990.9770.0890.2950.573100
1.73-1.78100.22433840.9850.0740.2360.60399.9
1.78-1.8410.60.18433500.990.0590.1930.632100
1.84-1.9111.50.1533900.9940.0460.1570.67999.9
1.91-1.9811.50.11733860.9960.0360.1230.7399.9
1.98-2.0711.30.09434020.9970.0290.0980.778100
2.07-2.1811.10.08134010.9980.0250.0850.839100
2.18-2.3210.90.06934140.9980.0220.0730.88499.9
2.32-2.5100.06334290.9980.0210.0670.95599.9
2.5-2.7510.80.05634280.9980.0180.0581.064100
2.75-3.1511.50.04934620.9980.0150.0511.309100
3.15-3.9610.90.03934980.9990.0130.0411.46399.9
3.96-5010.20.03536870.9990.0110.0371.3199.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CFS

3cfs


Resolution: 1.46→48.63 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.197 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 3307 4.9 %RANDOM
Rwork0.1699 ---
obs0.171 64741 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.97 Å2 / Biso mean: 15.432 Å2 / Biso min: 5.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0 Å2
2---0.42 Å20 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.46→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3002 0 2 423 3427
Biso mean--38.76 26.09 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133185
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172788
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.6274372
X-RAY DIFFRACTIONr_angle_other_deg1.3741.5726520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5065404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5324.161161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38315509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5751510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023617
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02637
LS refinement shellResolution: 1.46→1.496 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.308 265 -
Rwork0.285 4534 -
obs--96.23 %

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