[English] 日本語
Yorodumi
- PDB-5ov3: Structure of the RbBP5 beta-propeller domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ov3
TitleStructure of the RbBP5 beta-propeller domain
Components(Retinoblastoma-binding protein 5) x 2
KeywordsSTRUCTURAL PROTEIN / WD40 beta-propeller
Function / homology
Function and homology information


Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / Formation of WDR5-containing histone-modifying complexes / Formation of the beta-catenin:TCF transactivating complex / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Neddylation / MLL3/4 complex / Set1C/COMPASS complex / histone methyltransferase complex / MLL1 complex ...Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / Formation of WDR5-containing histone-modifying complexes / Formation of the beta-catenin:TCF transactivating complex / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Neddylation / MLL3/4 complex / Set1C/COMPASS complex / histone methyltransferase complex / MLL1 complex / transcription initiation-coupled chromatin remodeling / response to estrogen / histone binding / transcription cis-regulatory region binding / DNA damage response / nucleolus / nucleoplasm / nucleus
Similarity search - Function
Retinoblastoma-binding protein 5/Swd1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Retinoblastoma-binding protein 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMittal, A. / Zhang, Y. / Gamblin, S.J. / Wilson, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Francis Crick InstituteFC001078 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The structure of the RbBP5 beta-propeller domain reveals a surface with potential nucleic acid binding sites.
Authors: Mittal, A. / Hobor, F. / Zhang, Y. / Martin, S.R. / Gamblin, S.J. / Ramos, A. / Wilson, J.R.
History
DepositionAug 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: 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: Retinoblastoma-binding protein 5
B: Retinoblastoma-binding protein 5
C: Retinoblastoma-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9945
Polymers85,6493
Non-polymers3442
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-2 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.809, 71.897, 178.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Retinoblastoma-binding protein 5 / RBBP-5


Mass: 42494.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbbp5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BX09
#2: Protein/peptide Retinoblastoma-binding protein 5 / RBBP-5


Mass: 659.708 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ambiguous fragment from either chain A or B / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbbp5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BX09
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.99 Å3/Da / Density % sol: 38.06 %
Crystal growTemperature: 300 K / Method: vapor diffusion / Details: 0.1M MES (pH 6.5), 40 % PEG 200

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→71.9 Å / Num. obs: 27559 / % possible obs: 99.8 % / Redundancy: 6.3 % / Net I/σ(I): 12.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XL2

2xl2


Resolution: 2.45→66.678 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.23
RfactorNum. reflection% reflection
Rfree0.271 1407 5.11 %
Rwork0.1959 --
obs0.1995 27559 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→66.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5093 0 23 37 5153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095222
X-RAY DIFFRACTIONf_angle_d1.0417083
X-RAY DIFFRACTIONf_dihedral_angle_d18.1383116
X-RAY DIFFRACTIONf_chiral_restr0.062805
X-RAY DIFFRACTIONf_plane_restr0.006901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.53760.34511460.29442530X-RAY DIFFRACTION98
2.5376-2.63920.3811520.2782558X-RAY DIFFRACTION100
2.6392-2.75930.36761310.2512576X-RAY DIFFRACTION100
2.7593-2.90480.28921460.23232579X-RAY DIFFRACTION100
2.9048-3.08680.34521340.23182591X-RAY DIFFRACTION100
3.0868-3.32510.27541350.20592606X-RAY DIFFRACTION100
3.3251-3.65970.28161460.18952607X-RAY DIFFRACTION100
3.6597-4.18920.2091430.17842640X-RAY DIFFRACTION100
4.1892-5.27770.26991230.15482674X-RAY DIFFRACTION100
5.2777-66.70310.2381510.19562791X-RAY DIFFRACTION99

+
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