[English] 日本語
Yorodumi
- PDB-4pc0: Structure of the human RbAp48-MTA1(670-711) complex -

+
Open data


ID or keywords:

Loading...

-
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 / NURF complex / NuRD 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 / Transcription of E2F targets under negative control by DREAM complex ...CAF-1 complex / NURF complex / NuRD 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 / Transcription of E2F targets under negative control by DREAM complex / positive regulation of protein autoubiquitination / Polo-like kinase mediated events / response to ionizing radiation / negative regulation of gene expression, epigenetic / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / ATPase complex / entrainment of circadian clock by photoperiod / Sin3-type complex / 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 / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of cell migration / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / 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 / double-strand break repair / nucleosome assembly / nuclear envelope / histone binding / Oxidative Stress Induced Senescence / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / microtubule / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / transcription coactivator activity / chromatin remodeling / 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 / 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 / nucleoplasm / nucleus / metal ion binding / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more