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- PDB-4pby: Structure of the human RbAp48-MTA1(656-686) complex -

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Basic information

Entry
Database: PDB / ID: 4pby
TitleStructure of the human RbAp48-MTA1(656-686) complex
Components
  • Histone-binding protein RBBP4
  • Metastasis-associated protein MTA1
KeywordsCELL CYCLE / RbAp48 / MTA1 / NuRD / sub-complex
Function / homology
Function and homology information


CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Polo-like kinase mediated events / positive regulation of protein autoubiquitination / negative regulation of gene expression, epigenetic / response to ionizing radiation / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / positive regulation of stem cell population maintenance / entrainment of circadian clock by photoperiod / Transcriptional Regulation by E2F6 / locomotor rhythm / RNA Polymerase I Transcription Initiation / histone deacetylase complex / SUMOylation of transcription factors / G0 and Early G1 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / 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 / circadian regulation of gene expression / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / transcription corepressor activity / double-strand break repair / nuclear envelope / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / microtubule / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / transcription coactivator activity / chromatin remodeling / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Metastasis-associated protein MTA1, R1 domain / Mesoderm induction early response protein/metastasis-associated protein / MTA R1 domain / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / ELM2 domain / ELM2 domain ...Metastasis-associated protein MTA1, R1 domain / Mesoderm induction early response protein/metastasis-associated protein / MTA R1 domain / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / SANT domain profile. / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Homeobox-like domain superfamily / 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 / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Histone-binding protein RBBP4 / Metastasis-associated protein MTA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMurthy, A. / Lejon, S. / Alqarni, S.S.M. / Silva, A.P.G. / Watson, A.A. / Mackay, J.P. / Laue, E.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Insight into the architecture of the NuRD complex: Structure of the RbAp48-MTA1 sub-complex.
Authors: Alqarni, S.S. / Murthy, A. / Zhang, W. / Przewloka, M.R. / Silva, A.P. / Watson, A.A. / Lejon, S. / Pei, X.Y. / Smits, A.H. / Kloet, S.L. / Wang, H. / Shepherd, N.E. / Stokes, P.H. / Blobel, ...Authors: Alqarni, S.S. / Murthy, A. / Zhang, W. / Przewloka, M.R. / Silva, A.P. / Watson, A.A. / Lejon, S. / Pei, X.Y. / Smits, A.H. / Kloet, S.L. / Wang, H. / Shepherd, N.E. / Stokes, P.H. / Blobel, G.A. / Vermeulen, M. / Glover, D.M. / Mackay, J.P. / Laue, E.D.
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-binding protein RBBP4
B: Histone-binding protein RBBP4
C: Metastasis-associated protein MTA1
D: Metastasis-associated protein MTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9625
Polymers102,9024
Non-polymers601
Water4,522251
1
A: Histone-binding protein RBBP4
C: Metastasis-associated protein MTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5113
Polymers51,4512
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint2 kcal/mol
Surface area17710 Å2
MethodPISA
2
B: Histone-binding protein RBBP4
D: Metastasis-associated protein MTA1


Theoretical massNumber of molelcules
Total (without water)51,4512
Polymers51,4512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-4 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.560, 59.480, 104.630
Angle α, β, γ (deg.)90.000, 90.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone-binding protein RBBP4 / Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / ...Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / CAF-I p48 / Nucleosome-remodeling factor subunit RBAP48 / Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48


Mass: 47709.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Plasmid: PFBDM / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028
#2: Protein/peptide Metastasis-associated protein MTA1 / MTA1


Mass: 3741.347 Da / Num. of mol.: 2 / Fragment: Residues 639-669 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13330
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 20000, 20% v/v PEGMME 550, 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, and 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9809 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9809 Å / Relative weight: 1
ReflectionResolution: 2.5→52.31 Å / Num. obs: 35120 / % possible obs: 99.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 10.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RbAp48

Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.891 / SU B: 9.318 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.481 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1746 5 %RANDOM
Rwork0.1785 33113 --
obs0.1809 34859 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.29 Å2 / Biso mean: 25.706 Å2 / Biso min: 3.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å21.11 Å2
2---1.06 Å20 Å2
3---0.94 Å2
Refinement stepCycle: final / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6487 0 4 251 6742
Biso mean--22.42 19.78 -
Num. residues----812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196691
X-RAY DIFFRACTIONr_bond_other_d0.0010.026116
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9329115
X-RAY DIFFRACTIONr_angle_other_deg2.378314158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8285815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47225.03332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.153151103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2881528
X-RAY DIFFRACTIONr_chiral_restr0.0860.2986
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217602
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021528
X-RAY DIFFRACTIONr_mcbond_it1.9212.483251
X-RAY DIFFRACTIONr_mcbond_other1.9212.483250
X-RAY DIFFRACTIONr_mcangle_it3.3083.7064057
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 124 -
Rwork0.253 2389 -
all-2513 -
obs--99.64 %

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