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- PDB-5fxy: Structure of the human RBBP4:MTA1(464-546) complex -

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Basic information

Entry
Database: PDB / ID: 5fxy
TitleStructure of the human RBBP4:MTA1(464-546) complex
Components
  • HISTONE-BINDING PROTEIN RBBP4
  • METASTASIS-ASSOCIATED PROTEIN MTA1
KeywordsTRANSCRIPTION / TRANSCRIPTION REPRESSION COMPLEX METASTASIS ASSOCIATED COMPLEX MTA1 RBBP4 RBBP7 HISTONE BINDING PROTEIN
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 / 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 / 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 / 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 / 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 / Regulation of PTEN gene transcription / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / 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 / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / microtubule / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / 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: 3.2 Å
AuthorsMillard, C.J. / Varma, N. / Fairall, L. / Schwabe, J.W.R.
CitationJournal: 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 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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 area5610 Å2
ΔGint-27.5 kcal/mol
Surface area19380 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 area5400 Å2
ΔGint-23.9 kcal/mol
Surface area19780 Å2
MethodPISA
3
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 area5360 Å2
ΔGint-22.6 kcal/mol
Surface area19610 Å2
MethodPISA
4
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 area5290 Å2
ΔGint-26.1 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.294, 150.072, 95.591
Angle α, β, γ (deg.)90.00, 94.54, 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 / CHR OMATIN ASSEMBLY FACTOR I P48 SUBUNIT ...CHROMATIN ASSEMBLY FACTOR 1 SUBUNIT C / CAF-1 SUBUNIT C / CHR OMATIN ASSEMBLY FACTOR I P48 SUBUNIT / CAF-I 48 KDA SUBUNIT / CAF-I P48 / NUCLEOSOME-REMODELING FACTOR SUBUNIT RBAP48 / RETINOBLASTOMA-B INDING PROTEIN 4 / RBBP-4 / RETINOBLASTOMA-BINDING PROTEIN P48 / RBBP 4


Mass: 47709.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDNA3 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q09028
#2: Protein
METASTASIS-ASSOCIATED PROTEIN MTA1 / MTA1


Mass: 9773.559 Da / Num. of mol.: 4 / Fragment: RESIDUES 464-546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDNA3 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.34 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.21 M AMMONIUM CITRATE AND 19% PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Jul 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 3.2→95.3 Å / Num. obs: 35054 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.3
Reflection shellResolution: 3.2→3.34 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PC0

4pc0


Resolution: 3.2→95.29 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.844 / SU B: 35.296 / SU ML: 0.57 / Cross valid method: THROUGHOUT / ESU R Free: 0.611 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29084 1752 4.8 %RANDOM
Rwork0.24917 ---
obs0.25114 35054 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.709 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å20 Å2-2.13 Å2
2---2.95 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 3.2→95.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14366 0 0 0 14366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01914743
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213697
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.93620063
X-RAY DIFFRACTIONr_angle_other_deg0.856331583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57351767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.38724.169710
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.115152411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8721587
X-RAY DIFFRACTIONr_chiral_restr0.0680.22204
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02116518
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023405
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_it1.2999.1657155
X-RAY DIFFRACTIONr_mcbond_other1.2989.1647154
X-RAY DIFFRACTIONr_mcangle_it2.40313.7278893
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7339.1527588
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 136 -
Rwork0.338 2580 -
obs--97.66 %

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