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- PDB-4pbz: Structure of the human RbAp48-MTA1(670-695) complex -

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Basic information

Entry
Database: PDB / ID: 4pbz
TitleStructure of the human RbAp48-MTA1(670-695) complex
Components
  • Histone-binding protein RBBP4
  • Metastasis-associated protein MTA1
KeywordsCELL CYCLE / NuRD / sub-complex
Function / homology
Function and homology information


CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / ESC/E(Z) complex / regulation of stem cell differentiation / positive regulation of protein autoubiquitination ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / ESC/E(Z) complex / regulation of stem cell differentiation / positive regulation of protein autoubiquitination / Polo-like kinase mediated events / Transcription of E2F targets under negative control by DREAM complex / response to ionizing radiation / ATPase complex / entrainment of circadian clock by photoperiod / negative regulation of gene expression, epigenetic / Sin3-type complex / G1/S-Specific Transcription / Transcriptional Regulation by E2F6 / locomotor rhythm / positive regulation of stem cell population maintenance / SUMOylation of transcription factors / histone deacetylase complex / RNA Polymerase I Transcription Initiation / G0 and Early G1 / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / PKMTs methylate histone lysines / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / nuclear envelope / double-strand break repair / nucleosome assembly / Oxidative Stress Induced Senescence / histone binding / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromosome, telomeric region / DNA replication / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
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 ...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 domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / 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 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Histone-binding protein RBBP4 / Metastasis-associated protein MTA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMurthy, A. / Pei, X.Y. / Watson, A.A. / Silva, A.P.G. / 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
Revision 1.2Feb 4, 2015Group: Other
Revision 1.3Dec 20, 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
A: Histone-binding protein RBBP4
B: Metastasis-associated protein MTA1


Theoretical massNumber of molelcules
Total (without water)50,6732
Polymers50,6732
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-6 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.800, 59.820, 68.070
Angle α, β, γ (deg.)90.000, 99.190, 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.: 1
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


Mass: 2963.462 Da / Num. of mol.: 1 / Fragment: Residues 653-678 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13330
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v 2-Methyl-2,4-pentanediol (MPD), 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. ...Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v 2-Methyl-2,4-pentanediol (MPD), 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→33.6 Å / Num. obs: 26112 / % possible obs: 97.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 39.99 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.035 / Net I/σ(I): 13 / Num. measured all: 94637
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
2.15-2.212.90.5382.1459815930.38880.8
9.62-33.63.20.02334.39492930.01590.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
Aimless0.1.16data scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XU7

2xu7


Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.027 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1326 5.1 %RANDOM
Rwork0.1865 24747 --
obs0.189 24747 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.65 Å2 / Biso mean: 61.125 Å2 / Biso min: 20.16 Å2
Baniso -1Baniso -2Baniso -3
1-6.19 Å20 Å20.61 Å2
2---3.82 Å20 Å2
3----2.44 Å2
Refinement stepCycle: final / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 1 119 3379
Biso mean--104.26 52.35 -
Num. residues----408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193345
X-RAY DIFFRACTIONr_bond_other_d0.0010.023087
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9364554
X-RAY DIFFRACTIONr_angle_other_deg2.34337143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7115405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70124.938162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1315558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7011515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213772
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02753
X-RAY DIFFRACTIONr_mcbond_it4.5085.8851629
X-RAY DIFFRACTIONr_mcbond_other4.5025.8831628
X-RAY DIFFRACTIONr_mcangle_it6.8258.8042031
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 66 -
Rwork0.328 1507 -
all-1573 -
obs--80.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7540.0916-0.414.35910.23664.46220.01280.16480.0364-0.4641-0.04110.4980.3438-0.7769-0.0430.1538-0.0209-0.05030.2268-0.00890.198817.15988.76739.3112
25.68230.6636-1.97822.4448-2.97993.87090.4479-1.00020.21891.2255-0.0347-0.781-0.18210.90980.43910.56220.0687-0.2570.5104-0.08510.45735.536910.571431.7353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain BB670 - 691
2X-RAY DIFFRACTION2chain EE0

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