[English] 日本語
Yorodumi
- PDB-2a05: The cysteine-rich secretory protein domain of Tpx-1 is related to... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a05
TitleThe cysteine-rich secretory protein domain of Tpx-1 is related to ion channel toxins and regulates Ryanodine receptor Ca2+ signaling
ComponentsCysteine-rich secretory protein-2
KeywordsSIGNALING PROTEIN / 3 Alpha Helices / 5 Disulphide bonds / 2 domains
Function / homology
Function and homology information


cell-cell adhesion / extracellular space
Similarity search - Function
Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / ShKT domain ...Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / ShKT domain / ShKT domain profile. / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cysteine-rich secretory protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Automated Resonance assignment using Torsion Angle Dynamics (CANDID), Further refinement with CA, CB chem shifts, database potentials
AuthorsGibbs, G.M. / Scanlon, M.J. / Swarbrick, J. / Curtis, S. / Dulhunty, A.F. / O'Bryan, M.K.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The cysteine-rich secretory protein domain of Tpx-1 is related to ion channel toxins and regulates ryanodine receptor Ca2+ signaling.
Authors: Gibbs, G.M. / Scanlon, M.J. / Swarbrick, J. / Curtis, S. / Gallant, E. / Dulhunty, A.F. / O'Bryan, M.K.
History
DepositionJun 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine-rich secretory protein-2


Theoretical massNumber of molelcules
Total (without water)6,1221
Polymers6,1221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 49violations <0.2A NOE, total energy
RepresentativeModel #1lowest target function

-
Components

#1: Protein Cysteine-rich secretory protein-2 / Tpx-1 Crisp / CRISP-2 / Testis-specific protein TPX-1


Mass: 6121.932 Da / Num. of mol.: 1 / Fragment: residues 189-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pTriEx4 / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B(DE3) pLacI / References: UniProt: P16563
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 15N-separated TOCSY
1322D NOESY
1432D TOCSY
153DQF-COSY
1632D NOESY
NMR detailsText: Standard 2D/3D methods

-
Sample preparation

Details
Solution-IDContents
11mM TpX-1 U-15N 90% H2O 10% D2O
21mM TpX-1 90% H2O 10% D2O
31mM TpX-1 100% D2O
Sample conditionsIonic strength: 1mM / pH: 5.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX5003

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1Brukercollection
XwinNMR1Brukerprocessing
Sparky3.101Goddard Kellerdata analysis
CYANA1.06Guntertrefinement
XPLOR-NIH2.9.9Clore Schwieters Kuszewski Tjandrarefinement
RefinementMethod: Automated Resonance assignment using Torsion Angle Dynamics (CANDID), Further refinement with CA, CB chem shifts, database potentials
Software ordinal: 1
Details: NOES: 187 intra 251 short 253 med 188 long. 78 Chem shifts
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: violations <0.2A NOE, total energy / Conformers calculated total number: 49 / Conformers submitted total number: 23

+
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