[English] 日本語
Yorodumi
- PDB-5vtb: Crystal structure of RBBP4 bound to BCL11a peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vtb
TitleCrystal structure of RBBP4 bound to BCL11a peptide
Components
  • B-cell lymphoma/leukemia 11A
  • Histone-binding protein RBBP4
KeywordsPROTEIN BINDING / RBBP4 / Histone Binding protein / WD40 domain
Function / homology
Function and homology information


negative regulation of neuron remodeling / transcription regulatory region nucleic acid binding / negative regulation of branching morphogenesis of a nerve / negative regulation of dendrite extension / positive regulation of collateral sprouting / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / CAF-1 complex / regulation of dendrite development / negative regulation of axon extension ...negative regulation of neuron remodeling / transcription regulatory region nucleic acid binding / negative regulation of branching morphogenesis of a nerve / negative regulation of dendrite extension / positive regulation of collateral sprouting / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / CAF-1 complex / regulation of dendrite development / negative regulation of axon extension / negative regulation of dendrite development / NURF complex / NuRD complex / regulation of cell fate specification / Formation of the embryonic stem cell BAF (esBAF) complex / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / cellular response to L-glutamate / regulation of stem cell differentiation / ALK mutants bind TKIs / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Polo-like kinase mediated events / Transcription of E2F targets under negative control by DREAM complex / paraspeckles / SWI/SNF complex / Sin3-type complex / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / histone deacetylase complex / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / G0 and Early G1 / protein sumoylation / 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 / negative regulation of cell migration / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of transforming growth factor beta receptor signaling pathway / Regulation of PTEN gene transcription / brain development / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / positive regulation of neuron projection development / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / negative regulation of neuron projection development / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Negative Regulation of CDH1 Gene Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / transcription coregulator activity / nuclear matrix / HCMV Early Events / Signaling by ALK fusions and activated point mutants / Regulation of PD-L1(CD274) transcription / nucleosome assembly / heterochromatin formation / histone binding / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / Potential therapeutics for SARS / nuclear body / DNA replication / chromosome, telomeric region / postsynapse / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of cell population proliferation / protein heterodimerization activity / negative regulation of DNA-templated transcription / DNA repair / positive regulation of gene expression / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / BCL-11A-like CCHC zinc finger / : / C2H2 zinc finger / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / Zinc finger, C2H2 type / zinc finger ...: / : / BCL-11A-like CCHC zinc finger / : / C2H2 zinc finger / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / Zinc finger C2H2 type domain signature. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger C2H2-type / 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 / BCL11 transcription factor A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMeagher, J.L. / Stuckey, J.A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Probing the interaction between the histone methyltransferase/deacetylase subunit RBBP4/7 and the transcription factor BCL11A in epigenetic complexes.
Authors: Moody, R.R. / Lo, M.C. / Meagher, J.L. / Lin, C.C. / Stevers, N.O. / Tinsley, S.L. / Jung, I. / Matvekas, A. / Stuckey, J.A. / Sun, D.
History
DepositionMay 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone-binding protein RBBP4
B: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3923
Polymers50,2992
Non-polymers921
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-0 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.301, 85.264, 87.968
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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: 48457.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Production host: unidentified baculovirus / References: UniProt: Q09028
#2: Protein/peptide B-cell lymphoma/leukemia 11A / BCL-11A / B-cell CLL/lymphoma 11A / COUP-TF-interacting protein 1 / Ecotropic viral integration ...BCL-11A / B-cell CLL/lymphoma 11A / COUP-TF-interacting protein 1 / Ecotropic viral integration site 9 protein homolog / EVI-9 / Zinc finger protein 856


Mass: 1842.134 Da / Num. of mol.: 1 / Fragment: UNP residues 2-16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H165
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.89 Å3/Da / Density % sol: 35.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG2000 MME, 0.1 M potassium thiocyanate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 15853 / % possible obs: 99.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.043 / Rrim(I) all: 0.123 / Χ2: 0.963 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4480.5660.9250.2090.6040.83198.7
2.44-2.498.20.5910.9080.2170.6310.84399.3
2.49-2.538.30.4970.9170.1810.530.86999.3
2.53-2.598.20.4310.9470.1590.460.88599.9
2.59-2.648.40.4030.9430.1480.430.84899.5
2.64-2.78.20.3450.9680.1270.3680.91899.7
2.7-2.778.30.3140.9630.1150.3350.92599.7
2.77-2.858.20.2550.9710.0940.2730.87499.9
2.85-2.938.20.2350.9770.0870.2510.89399.7
2.93-3.028.30.2090.9830.0760.2220.93399.9
3.02-3.138.30.1710.9870.0630.1820.95399.9
3.13-3.268.20.1390.9910.0520.1480.979100
3.26-3.418.30.1110.9940.0420.1191.008100
3.41-3.588.20.0970.9930.0360.1041.104100
3.58-3.818.30.0820.9940.0310.0881.208100
3.81-4.18.30.0690.9970.0250.0741.117100
4.1-4.528.40.0570.9970.0210.0611.11699.9
4.52-5.178.40.050.9970.0190.0541.112100
5.17-6.518.40.0540.9970.020.0580.89599.8
6.51-507.60.0470.9970.0180.0510.91199.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4R7A

4r7a


Resolution: 2.4→44.32 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.462 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.532 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.263
RfactorNum. reflection% reflectionSelection details
Rfree0.244 702 4.71 %RANDOM
Rwork0.201 ---
obs0.203 14917 94 %-
Displacement parametersBiso max: 116.42 Å2 / Biso mean: 36.06 Å2 / Biso min: 12.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.5918 Å20 Å20 Å2
2---2.6279 Å20 Å2
3---0.0361 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.4→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2766 0 6 140 2912
Biso mean--46.89 42.41 -
Num. residues----363
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1243SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes417HARMONIC5
X-RAY DIFFRACTIONt_it2848HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion384SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3194SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2848HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3896HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.45
X-RAY DIFFRACTIONt_other_torsion2.41
LS refinement shellResolution: 2.39→2.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.264 92 4.25 %
Rwork0.196 2071 -
all0.199 2163 -
obs--75.92 %

+
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