[English] 日本語
Yorodumi
- PDB-1rjt: NMR Structure of CXC Chemokine CXCL11/ITAC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rjt
TitleNMR Structure of CXC Chemokine CXCL11/ITAC
ComponentsSmall inducible cytokine B11
KeywordsCYTOKINE / chemokine
Function / homology
Function and homology information


CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / T cell chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / neutrophil chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / adenylate cyclase-activating G protein-coupled receptor signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide ...CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / T cell chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / neutrophil chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / adenylate cyclase-activating G protein-coupled receptor signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / cell-cell signaling / heparin binding / regulation of cell population proliferation / G alpha (i) signalling events / cellular response to lipopolysaccharide / inflammatory response / signal transduction / extracellular space / extracellular region
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-X-C motif chemokine 11
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsBooth, V. / Clark-Lewis, I. / Sykes, B.D.
CitationJournal: Protein Sci. / Year: 2004
Title: NMR structure of CXCR3 binding chemokine CXCL11 (ITAC).
Authors: Booth, V. / Clark-Lewis, I. / Sykes, B.D.
History
DepositionNov 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small inducible cytokine B11


Theoretical massNumber of molelcules
Total (without water)8,3241
Polymers8,3241
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)10 / 20structures with the lowest energy
RepresentativeModel #2closest to the average

-
Components

#1: Protein Small inducible cytokine B11 / CXCL11 / Interferon-inducible T-cell alpha chemoattractant / I-TAC / Interferon-gamma-inducible ...CXCL11 / Interferon-inducible T-cell alpha chemoattractant / I-TAC / Interferon-gamma-inducible protein-9 / IP-9 / H174 / Beta-R1


Mass: 8324.064 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthesized with N15 isotope labels on all leucine and valine residues. Sequence is naturally found in Homo sapiens (human).
References: UniProt: O14625

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY
141DQF-COSY
NMR detailsText: Assignments were made for all three sample conditions. Structure was calculated using data from all three conditions.

-
Sample preparation

DetailsContents: 2 mM CXCL11, partial N15
Solvent system: 20 mM deuterated sodium acetate, 1 mM sodium azide, 1 mM DSS, 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 4.5 ambient 318 K
20 5.0 ambient 303 K
30 5.0 ambient 313 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglioprocessing
NMRView5.0.4Johnsondata analysis
CNS1.2Brungerrefinement
ARIA1.2Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

+
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://pdbjlvh1.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