[English] 日本語
Yorodumi
- PDB-3cfs: Structural basis of the interaction of RbAp46/RbAp48 with histone H4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cfs
TitleStructural basis of the interaction of RbAp46/RbAp48 with histone H4
Components
  • Histone H4
  • Histone-binding protein RBBP7
KeywordsHISTONE/CHAPERONE / RbAp46/RbAp48 / Chromatin / Histone / WD-40 repeat protein / chaperone / Acetylation / Chromatin regulator / DNA replication / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / WD repeat / Chromosomal protein / Nucleosome core / HISTONE-CHAPERONE COMPLEX
Function / homology
Function and homology information


cellular heat acclimation / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / ESC/E(Z) complex / regulation of stem cell differentiation / response to steroid hormone / ATPase complex / positive regulation of stem cell population maintenance ...cellular heat acclimation / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / ESC/E(Z) complex / regulation of stem cell differentiation / response to steroid hormone / ATPase complex / positive regulation of stem cell population maintenance / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Regulation of TP53 Activity through Acetylation / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / negative regulation of cell migration / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / negative regulation of transforming growth factor beta receptor signaling pathway / Formation of the beta-catenin:TCF transactivating complex / brain development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / negative regulation of cell growth / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold ...Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
ARSENIC / Histone H4 / Histone-binding protein RBBP7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMurzina, N.V. / Pei, X.-Y. / Pratap, J.V. / Sparkes, M. / Vicente-Garcia, J. / Ben-Shahar, T.R. / Verreault, A. / Luisi, B.F. / Laue, E.D.
CitationJournal: Structure / Year: 2008
Title: Structural Basis for the Recognition of Histone H4 by the Histone-Chaperone RbAp46.
Authors: Murzina, N.V. / Pei, X.Y. / Zhang, W. / Sparkes, M. / Vicente-Garcia, J. / Pratap, J.V. / McLaughlin, S.H. / Ben-Shahar, T.R. / Verreault, A. / Luisi, B.F. / Laue, E.D.
History
DepositionMar 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Histone-binding protein RBBP7
E: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7113
Polymers48,6362
Non-polymers751
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-4.2 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.665, 85.725, 117.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Histone-binding protein RBBP7 / Retinoblastoma-binding protein 7 / RBBP-7 / Retinoblastoma-binding protein p46 / Histone ...Retinoblastoma-binding protein 7 / RBBP-7 / Retinoblastoma-binding protein p46 / Histone acetyltransferase type B subunit 2 / Nucleosome-remodeling factor subunit RBAP46


Mass: 46937.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP7 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16576
#2: Protein/peptide Histone H4 /


Mass: 1698.050 Da / Num. of mol.: 1 / Fragment: UNP residues 28 to 42
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H4A / Cell line (production host): Tuner(DE3)LacI / Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Chemical ChemComp-ARS / ARSENIC / Arsenic


Mass: 74.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: As
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 18% PEG8000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2006 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→19.5 Å / Num. obs: 18615 / % possible obs: 99.8 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.13 / Rsym value: 0.127 / Net I/σ(I): 16
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.409 / % possible all: 98

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD data phased model

Resolution: 2.4→19.53 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.405 / SU ML: 0.108 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24862 935 5.1 %RANDOM
Rwork0.18418 ---
obs0.18745 17375 99.95 %-
all-17375 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--1.2 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.268 Å0.094 Å
Luzzati d res low-6 Å
Luzzati sigma a0.229 Å0.251 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3186 0 1 210 3397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0213273
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.751.9264458
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46324.845161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71515538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7731514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022515
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.31397
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.52143
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.5346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.331
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.83622030
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.54233223
X-RAY DIFFRACTIONr_scbond_it5.49121421
X-RAY DIFFRACTIONr_scangle_it7.29531235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 69 -
Rwork0.192 1251 -
obs--99.7 %

+
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