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- PDB-6g16: Structure of the human RBBP4:MTA1(464-546) complex showing loop e... -

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Basic information

Entry
Database: PDB / ID: 6g16
TitleStructure of the human RBBP4:MTA1(464-546) complex showing loop exchange
Components
  • Histone-binding protein RBBP4
  • Metastasis-associated protein MTA1
KeywordsTRANSCRIPTION / WD40 / corepressor / metastasis
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMillard, C.J. / Varma, N. / Fairall, L. / Schwabe, J.W.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT100237 United Kingdom
Citation
Journal: Elife / Year: 2016
Title: The structure of the core NuRD repression complex provides insights into its interaction with chromatin.
Authors: Christopher J Millard / Niranjan Varma / Almutasem Saleh / Kyle Morris / Peter J Watson / Andrew R Bottrill / Louise Fairall / Corinne J Smith / John W R Schwabe /
Abstract: The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure ...The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin.
#1: Journal: Elife / Year: 2016
Title: The structure of the core NuRD repression complex provides insights into its interaction with chromatin.
Authors: Christopher J Millard / Niranjan Varma / Almutasem Saleh / Kyle Morris / Peter J Watson / Andrew R Bottrill / Louise Fairall / Corinne J Smith / John W R Schwabe /
Abstract: The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure ...The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin.
History
DepositionMar 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 13, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.4Jan 17, 2024Group: 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 RBBP4
B: Metastasis-associated protein MTA1
C: Histone-binding protein RBBP4
D: Metastasis-associated protein MTA1
E: Histone-binding protein RBBP4
F: Metastasis-associated protein MTA1
G: Histone-binding protein RBBP4
H: Metastasis-associated protein MTA1


Theoretical massNumber of molelcules
Total (without water)229,9328
Polymers229,9328
Non-polymers00
Water00
1
A: Histone-binding protein RBBP4
B: Metastasis-associated protein MTA1


Theoretical massNumber of molelcules
Total (without water)57,4832
Polymers57,4832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-22 kcal/mol
Surface area21030 Å2
MethodPISA
2
C: Histone-binding protein RBBP4
D: Metastasis-associated protein MTA1


Theoretical massNumber of molelcules
Total (without water)57,4832
Polymers57,4832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-23 kcal/mol
Surface area20980 Å2
MethodPISA
3
E: Histone-binding protein RBBP4
F: Metastasis-associated protein MTA1


Theoretical massNumber of molelcules
Total (without water)57,4832
Polymers57,4832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-21 kcal/mol
Surface area20970 Å2
MethodPISA
4
G: Histone-binding protein RBBP4
H: Metastasis-associated protein MTA1


Theoretical massNumber of molelcules
Total (without water)57,4832
Polymers57,4832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-22 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.232, 150.352, 95.694
Angle α, β, γ (deg.)90.00, 94.99, 90.00
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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Plasmid: PCDNA3 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q09028
#2: Protein
Metastasis-associated protein MTA1


Mass: 9773.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTA1 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q13330

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.21 M AMMONIUM CITRATE, 19% PEG 3350, 15 mM MALTOSE pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.8→95.4 Å / Num. obs: 51450 / % possible obs: 95 % / Redundancy: 9.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.5
Reflection shellResolution: 2.8→2.88 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 3.4 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLM7.2.1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FXY

5fxy


Resolution: 2.8→95.33 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.876 / SU B: 17.132 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26328 2719 5 %RANDOM
Rwork0.22443 ---
obs0.2264 51450 94.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.404 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å2-2.06 Å2
2---2.31 Å20 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 2.8→95.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14642 0 0 0 14642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915033
X-RAY DIFFRACTIONr_bond_other_d0.0060.0213475
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.93620468
X-RAY DIFFRACTIONr_angle_other_deg0.989331381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71651815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.71524.234725
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.194152469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9511587
X-RAY DIFFRACTIONr_chiral_restr0.0970.22235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116652
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023011
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7545.677308
X-RAY DIFFRACTIONr_mcbond_other2.7515.6697307
X-RAY DIFFRACTIONr_mcangle_it4.4928.4949107
X-RAY DIFFRACTIONr_mcangle_other4.4928.4959108
X-RAY DIFFRACTIONr_scbond_it2.6455.8597725
X-RAY DIFFRACTIONr_scbond_other2.6455.867726
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3328.68711362
X-RAY DIFFRACTIONr_long_range_B_refined7.12664.82215966
X-RAY DIFFRACTIONr_long_range_B_other7.12564.8215966
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 180 -
Rwork0.335 3868 -
obs--96.89 %

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