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- PDB-4pc0: Structure of the human RbAp48-MTA1(670-711) complex -

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Basic information

Entry
Database: PDB / ID: 4pc0
TitleStructure of the human RbAp48-MTA1(670-711) complex
Components
  • Histone-binding protein RBBP4
  • Metastasis-associated protein MTA1
KeywordsCELL CYCLE / MTA1-NuRD subcomplex
Function / homology
Function and homology information


CAF-1 complex / NuRD complex / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / 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 ...CAF-1 complex / NuRD complex / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / 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 / Transcription of E2F targets under negative control by DREAM complex / response to ionizing radiation / ATPase complex / negative regulation of gene expression, epigenetic / entrainment of circadian clock by photoperiod / Sin3-type complex / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / locomotor rhythm / Transcriptional Regulation by E2F6 / SUMOylation of transcription factors / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin E associated events during G1/S transition / 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 / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / brain development / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / HCMV Early Events / transcription corepressor activity / nuclear envelope / double-strand break repair / nucleosome assembly / Oxidative Stress Induced Senescence / RNA polymerase II-specific DNA-binding transcription factor binding / histone binding / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transcription coactivator activity / chromosome, telomeric region / DNA replication / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / 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 ...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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAlqarni, S.S.M. / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Histone-binding protein RBBP4
C: Metastasis-associated protein MTA1
D: Metastasis-associated protein MTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8967
Polymers104,7244
Non-polymers1723
Water6,485360
1
A: Histone-binding protein RBBP4
C: Metastasis-associated protein MTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4944
Polymers52,3622
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-13 kcal/mol
Surface area19200 Å2
MethodPISA
2
B: Histone-binding protein RBBP4
D: Metastasis-associated protein MTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4023
Polymers52,3622
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-13 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.250, 123.230, 87.340
Angle α, β, γ (deg.)90.000, 103.390, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPTYRTYRAA10 - 40910 - 409
21ASPASPTYRTYRBB10 - 40910 - 409
12LEULEULEULEUCC671 - 6902 - 21
22LEULEULEULEUDD671 - 6902 - 21

NCS ensembles :
ID
1
2

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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 / human MTA1


Mass: 4652.402 Da / Num. of mol.: 2 / Fragment: Residues 653-694 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13330
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M calcium acetate and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→61.61 Å / Num. obs: 33957 / % possible obs: 91.1 % / Redundancy: 6.9 % / Net I/σ(I): 11.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xu7

2xu7


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.318 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.749 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1705 5.1 %RANDOM
Rwork0.2037 32008 --
obs0.2065 33713 90.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.17 Å2 / Biso mean: 33.568 Å2 / Biso min: 11.98 Å2
Baniso -1Baniso -2Baniso -3
1-3.32 Å20 Å2-3.51 Å2
2---1.57 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6726 0 8 360 7094
Biso mean--50.81 30.09 -
Num. residues----846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196914
X-RAY DIFFRACTIONr_bond_other_d0.0010.026316
X-RAY DIFFRACTIONr_angle_refined_deg1.0411.9349412
X-RAY DIFFRACTIONr_angle_other_deg2.341314621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17624.985337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.166151131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7611528
X-RAY DIFFRACTIONr_chiral_restr0.0610.21019
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217849
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021575
X-RAY DIFFRACTIONr_mcbond_it1.2943.3373380
X-RAY DIFFRACTIONr_mcbond_other1.2933.3363379
X-RAY DIFFRACTIONr_mcangle_it2.2824.9984218
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A238850.07
12B238850.07
21C10170.04
22D10170.04
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 138 -
Rwork0.257 2545 -
all-2683 -
obs--99.89 %

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