[English] 日本語
Yorodumi
- PDB-2rvm: Solution structure of the chromodomain of HP1alpha with the phosp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rvm
TitleSolution structure of the chromodomain of HP1alpha with the phosphorylated N-terminal tail
ComponentsChromobox protein homolog 5
KeywordsTRANSCRIPTION / chromodomain / hp1alpha
Function / homology
Function and homology information


chromocenter / Factors involved in megakaryocyte development and platelet production / histone methyltransferase complex / site of DNA damage / histone deacetylase complex / heterochromatin / ribonucleoprotein complex binding / pericentric heterochromatin / methylated histone binding / transcription repressor complex ...chromocenter / Factors involved in megakaryocyte development and platelet production / histone methyltransferase complex / site of DNA damage / histone deacetylase complex / heterochromatin / ribonucleoprotein complex binding / pericentric heterochromatin / methylated histone binding / transcription repressor complex / PML body / kinetochore / histone deacetylase binding / protein-macromolecule adaptor activity / chromatin organization / DNA-binding transcription factor binding / chromosome, telomeric region / ribonucleoprotein complex / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain ...Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily
Similarity search - Domain/homology
Chromobox protein homolog 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsKawaguchi, A. / Nishimura, Y.
CitationJournal: Sci Rep / Year: 2016
Title: Extended string-like binding of the phosphorylated HP1 alpha N-terminal tail to the lysine 9-methylated histone H3 tail
Authors: Shimojo, H. / Kawaguchi, A. / Oda, T. / Hashiguchi, N. / Omori, S. / Moritsugu, K. / Kidera, A. / Hiragami-Hamada, K. / Nakayama, J. / Sato, M. / Nishimura, Y.
History
DepositionDec 18, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn / struct_ref / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chromobox protein homolog 5


Theoretical massNumber of molelcules
Total (without water)10,1691
Polymers10,1691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 600structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein Chromobox protein homolog 5 / Heterochromatin protein 1 homolog alpha / HP1 alpha


Mass: 10169.046 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: For phosphorylation of Ser the expression with pRSFduet (CK2)
Gene: Cbx5, Hp1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q61686

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HN(CO)CA
1913D HBHA(CO)NH
11013D C(CO)NH
11113D H(CCO)NH
11223D (H)CCH-TOCSY
11313D 1H-15N NOESY
11423D 1H-13C NOESY aliphatic
11523D 1H-13C NOESY aromatic

-
Sample preparation

Details
Solution-IDContentsSolvent system
110 mM [U-99% 13C; U-99% 15N] potassium phosphate-1, 20 mM [U-99% 13C; U-99% 15N] sodium chloride-2, 5 mM [U-99% 13C; U-99% 15N] DTT-3, 90% H2O/10% D2O90% H2O/10% D2O
210 mM [U-99% 13C; U-99% 15N] potassium phosphate-4, 20 mM [U-99% 13C; U-99% 15N] sodium chloride-5, 5 mM [U-99% 13C; U-99% 15N] DTT-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMpotassium phosphate-1[U-99% 13C; U-99% 15N]1
20 mMsodium chloride-2[U-99% 13C; U-99% 15N]1
5 mMDTT-3[U-99% 13C; U-99% 15N]1
10 mMpotassium phosphate-4[U-99% 13C; U-99% 15N]2
20 mMsodium chloride-5[U-99% 13C; U-99% 15N]2
5 mMDTT-6[U-99% 13C; U-99% 15N]2
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
OliviaYokochi, M., Sekiguchi, S. and Inagaki, F.chemical shift assignment
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 600 / Conformers submitted total number: 20 / Representative conformer: 1

+
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