[English] 日本語
Yorodumi
- PDB-1b8t: SOLUTION STRUCTURE OF THE CHICKEN CRP1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b8t
TitleSOLUTION STRUCTURE OF THE CHICKEN CRP1
ComponentsPROTEIN (CRP1)
KeywordsCONTRACTILE / LIM DOMAIN / CRP / MUSCLE DIFFERENTIATION
Function / homology
Function and homology information


muscle tissue development / actinin binding / structural constituent of muscle / sarcomere organization / alpha-actinin binding / cell leading edge / stress fiber / phosphoprotein binding / Z disc / focal adhesion ...muscle tissue development / actinin binding / structural constituent of muscle / sarcomere organization / alpha-actinin binding / cell leading edge / stress fiber / phosphoprotein binding / Z disc / focal adhesion / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
Cysteine and glycine-rich protein 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / DYANA
AuthorsYao, X. / Perez-Alvarado, G.C. / Louis, H.A. / Pomies, P. / Hatt, C. / Summers, M.F. / Beckerle, M.C.
CitationJournal: Biochemistry / Year: 1999
Title: Solution structure of the chicken cysteine-rich protein, CRP1, a double-LIM protein implicated in muscle differentiation.
Authors: Yao, X. / Perez-Alvarado, G.C. / Louis, H.A. / Pomies, P. / Hatt, C. / Summers, M.F. / Beckerle, M.C.
History
DepositionFeb 2, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_ensemble ...database_2 / pdbx_nmr_ensemble / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (CRP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6105
Polymers20,3481
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)37 / 37structures with the least restraint violations
Representative

-
Components

#1: Protein PROTEIN (CRP1)


Mass: 20348.316 Da / Num. of mol.: 1 / Fragment: LIM-DOMAIN PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Tissue: MUSCLESkeletal muscle / Plasmid: PET5 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P67966
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HSQC
121NOESY
131COSY
141TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR DATA ON THE TWO INDIVIDUAL DOMAINS OF CRP1 AND N15-EDITED NOESY AND TOCSY DATA ON N15-LABELED CRP1.

-
Sample preparation

Sample conditionspH: 7.2 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: GE OMEGA PSG / Manufacturer: GE / Model: OMEGA PSG / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
DYANAGuntert, Braun and Wuthrichrefinement
NMRViewJohnson, One Moon Scientificstructure calculation
RefinementMethod: DYANA / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 37 / Conformers submitted total number: 37

+
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