[English] 日本語
Yorodumi
- PDB-6bw4: Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bw4
TitleCrystal structure of RBBP4 in complex with PRDM16 N-terminal peptide
Components
  • Histone-binding protein RBBP4
  • PR domain zinc finger protein 16
KeywordsGENE REGULATION / NuRD / Complex / Epigenetics / Structural Genomics / Structural Genomics Consortium / SGC / Histone-binding protein / Chromatin regulator / Nucleus / Repressor / WD repeat
Function / homology
Function and homology information


negative regulation of white fat cell differentiation / negative regulation of muscle cell differentiation / negative regulation of granulocyte differentiation / [histone H3]-lysine9 N-methyltransferase / CAF-1 complex / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9 monomethyltransferase activity / tolerance induction in gut-associated lymphoid tissue / regulation of cellular respiration ...negative regulation of white fat cell differentiation / negative regulation of muscle cell differentiation / negative regulation of granulocyte differentiation / [histone H3]-lysine9 N-methyltransferase / CAF-1 complex / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9 monomethyltransferase activity / tolerance induction in gut-associated lymphoid tissue / regulation of cellular respiration / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / regulatory T cell differentiation / DNA replication-dependent chromatin assembly / regulation of stem cell differentiation / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Polo-like kinase mediated events / Transcription of E2F targets under negative control by DREAM complex / beige fat cell differentiation / chromatin-protein adaptor activity / histone H3 methyltransferase activity / Sin3-type complex / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / histone deacetylase complex / Transcriptional Regulation by E2F6 / brown fat cell differentiation / RNA Polymerase I Transcription Initiation / 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 / Regulation of TP53 Activity through Acetylation / transcription repressor complex / protein localization to chromatin / 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 / brain development / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / protein maturation / transcription coregulator activity / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / 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 / HCMV Early Events / Regulation of PD-L1(CD274) transcription / transcription corepressor activity / nucleosome assembly / positive regulation of cold-induced thermogenesis / heterochromatin formation / methylation / DNA-binding transcription activator activity, RNA polymerase II-specific / histone binding / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / sequence-specific DNA binding / Potential therapeutics for SARS / nuclear body / chromosome, telomeric region / DNA replication / transcription coactivator activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA repair / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
PRDM16, PR/SET domain / PR domain zinc finger protein 2, PR domain / : / C2H2-type zinc finger / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain profile. / SET domain superfamily ...PRDM16, PR/SET domain / PR domain zinc finger protein 2, PR domain / : / C2H2-type zinc finger / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain profile. / SET domain superfamily / SET domain / 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 / Histone-lysine N-methyltransferase PRDM16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsIvanochko, D. / Halabelian, L. / Hutchinson, A. / Seitova, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex.
Authors: Ivanochko, D. / Halabelian, L. / Henderson, E. / Savitsky, P. / Jain, H. / Marcon, E. / Duan, S. / Hutchinson, A. / Seitova, A. / Barsyte-Lovejoy, D. / Filippakopoulos, P. / Greenblatt, J. / ...Authors: Ivanochko, D. / Halabelian, L. / Henderson, E. / Savitsky, P. / Jain, H. / Marcon, E. / Duan, S. / Hutchinson, A. / Seitova, A. / Barsyte-Lovejoy, D. / Filippakopoulos, P. / Greenblatt, J. / Lima-Fernandes, E. / Arrowsmith, C.H.
History
DepositionDec 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Histone-binding protein RBBP4
B: PR domain zinc finger protein 16
A: Histone-binding protein RBBP4
D: PR domain zinc finger protein 16


Theoretical massNumber of molelcules
Total (without water)98,55116
Polymers98,5514
Non-polymers012
Water2,018112
1
C: Histone-binding protein RBBP4
B: PR domain zinc finger protein 16


Theoretical massNumber of molelcules
Total (without water)49,2752
Polymers49,2752
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histone-binding protein RBBP4
D: PR domain zinc finger protein 16


Theoretical massNumber of molelcules
Total (without water)49,27514
Polymers49,2752
Non-polymers012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.034, 59.862, 101.843
Angle α, β, γ (deg.)90.000, 94.550, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11C
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 9 - 410 / Label seq-ID: 11 - 412

Dom-IDAuth asym-IDLabel asym-ID
1CA
2AC

-
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: 47853.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028
#2: Protein/peptide PR domain zinc finger protein 16 / PR domain-containing protein 16 / Transcription factor MEL1 / MDS1/EVI1-like gene 1


Mass: 1421.801 Da / Num. of mol.: 2 / Fragment: N-terminal residues 1-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9HAZ2
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 22% PEG3350, 0.2 M Sodium malonate, 0.1 M BisTris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→19.87 Å / Num. obs: 61417 / % possible obs: 99.2 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.033 / Rrim(I) all: 0.067 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.054.10.7381816544830.90.4110.8472.499.3
8.94-19.873.70.02224976770.9990.0120.0264791.3

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6bw3

6bw3


Resolution: 2→19.87 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 13.237 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 2961 4.8 %RANDOM
Rwork0.1987 ---
obs0.2004 58442 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.26 Å2 / Biso mean: 52.505 Å2 / Biso min: 29.57 Å2
Baniso -1Baniso -2Baniso -3
1-3.23 Å2-0 Å2-0.31 Å2
2---2.88 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 2→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5877 0 12 112 6001
Biso mean--58 47.94 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196040
X-RAY DIFFRACTIONr_bond_other_d0.0020.025199
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9238260
X-RAY DIFFRACTIONr_angle_other_deg0.953312062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7965760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64524.737266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21515896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7931520
X-RAY DIFFRACTIONr_chiral_restr0.090.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216795
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021197
Refine LS restraints NCS

Ens-ID: 1 / Number: 23256 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1C
2A
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 217 -
Rwork0.298 4211 -
all-4428 -
obs--99.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.53050.26970.2772.57260.59891.95490.08080.10130.02650.09980.0145-0.2463-0.0595-0.0115-0.09530.33960.0119-0.19140.01980.01370.1483-6.082618.4541-15.5305
22.18950.1014-1.02481.8506-3.64648.7491-0.2177-0.03130.17420.0376-0.001-0.0946-0.106-0.10470.21870.3146-0.0098-0.01310.3080.04370.3427-8.292834.0806-22.3211
31.65290.31890.24162.7253-0.34672.0897-0.0469-0.1947-0.04880.48490.06980.0525-0.1262-0.1856-0.02290.48460.0323-0.17230.03730.0070.0909-32.6399-8.7304-34.381
41.252-0.1432-1.30210.26150.634711.7149-0.12210.1403-0.04910.0609-0.0646-0.1239-0.1325-0.48960.18670.26530.0056-0.01230.2342-0.0320.2817-33.84265.6404-28.5792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C9 - 410
2X-RAY DIFFRACTION2B1 - 10
3X-RAY DIFFRACTION3A4 - 410
4X-RAY DIFFRACTION4D1 - 10

+
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