[English] 日本語
Yorodumi
- PDB-2l9h: Oligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l9h
TitleOligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, and SAXS Data
ComponentsC-C motif chemokine 5
KeywordsIMMUNE SYSTEM / Chemokine / Oligomer
Function / homology
Function and homology information


regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / : / receptor signaling protein tyrosine kinase activator activity / CCR5 chemokine receptor binding / positive regulation of T cell chemotaxis / positive regulation of homotypic cell-cell adhesion / CCR chemokine receptor binding / neutrophil activation / positive regulation of G protein-coupled receptor signaling pathway / phosphatidylinositol phospholipase C activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / positive regulation of calcium ion transport / eosinophil chemotaxis / positive regulation of innate immune response / cellular response to fibroblast growth factor stimulus / positive regulation of monocyte chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / regulation of T cell activation / dendritic cell chemotaxis / negative regulation of G protein-coupled receptor signaling pathway / leukocyte cell-cell adhesion / negative regulation of viral genome replication / phospholipase activator activity / positive regulation of macrophage chemotaxis / macrophage chemotaxis / positive regulation of smooth muscle cell migration / chemoattractant activity / exocytosis / monocyte chemotaxis / Interleukin-10 signaling / regulation of insulin secretion / positive regulation of cell adhesion / cellular response to interleukin-1 / negative regulation by host of viral transcription / positive regulation of T cell migration / positive regulation of translational initiation / positive regulation of viral genome replication / positive regulation of T cell proliferation / positive regulation of phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / cell chemotaxis / positive regulation of epithelial cell proliferation / epithelial cell proliferation / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / response to virus / response to toxic substance / cellular response to virus / cellular response to type II interferon / intracellular calcium ion homeostasis / chemotaxis / calcium ion transport / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / 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-C motif chemokine 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SOLUTION SCATTERING / molecular dynamics, SAXS-potential guided scoring within grid search
Model detailsbest agreement with data, model 1
AuthorsWang, X. / Watson, C.M. / Sharp, J.S. / Handel, T.M. / Prestegard, J.H.
CitationJournal: Structure / Year: 2011
Title: Oligomeric Structure of the Chemokine CCL5/RANTES from NMR, MS, and SAXS Data.
Authors: Wang, X. / Watson, C. / Sharp, J.S. / Handel, T.M. / Prestegard, J.H.
History
DepositionFeb 9, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-C motif chemokine 5
B: C-C motif chemokine 5
C: C-C motif chemokine 5
D: C-C motif chemokine 5


Theoretical massNumber of molelcules
Total (without water)31,4484
Polymers31,4484
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)1 / 1target function based on SAXS & knowledge-based potential
RepresentativeModel #1best agreement with data

-
Components

#1: Protein
C-C motif chemokine 5 / EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific ...EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific protein P228 / TCP228 / T-cell-specific protein RANTES


Mass: 7862.011 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P13501

-
Experimental details

-
Experiment

Experiment
MethodDetails
SOLUTION NMRTetrameric model of the inflammatory chemokine CCL5/RANTES
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N J-mod TROSY
1222D 1H-15N TROSY
1322D 1H-15N HSQC
1422D 1H-15N J-mod TROSY
1512D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] ccl5, 50 mM sodium acetate, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] ccl5, 50 mM sodium acetate, 5 % polyacrylamide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMccl5-1[U-100% 15N]1
50 mMsodium acetate-21
1 mMccl5-3[U-100% 15N]2
50 mMsodium acetate-42
5 %polyacrylamide-52
Sample conditionsIonic strength: 0.05 / pH: 4.4 / Pressure: ambient / Temperature: 297 K

-
Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002
Soln scatterType: x-ray / Buffer name: ACETATE / Conc. range: 7 - 10 / Data analysis software list: GNOM, OLIGOMER / Data reduction software list: SAXS for Windows XP / Detector specific: Bruker / Detector type: AXS Vantec 2000 / Mean guiner radius: 31 nm / Mean guiner radius esd: 0.01 nm / Num. of time frames: 10 / Protein length: 121 / Sample pH: 4.5 / Source beamline instrument: Bruker NanostarU / Source class: N / Source type: Bruker NanostarU TXS / Temperature: 288 K

-
Processing

NMR software
NameDeveloperClassification
NAMDPhillips, Braun, Wang, Gumbart, Tajkhorshid, Villa, Chipot, Skeel, Kale, and Schulterefinement
NMRViewJohnson, One Moon Scientificdata analysis
VNMRJVariancollection
VMDHumphrey, Dalke & Schulten.refinement
RefinementMethod: molecular dynamics, SAXS-potential guided scoring within grid search
Software ordinal: 1
NMR representativeSelection criteria: best agreement with data
NMR ensembleConformer selection criteria: target function based on SAXS & knowledge-based potential
Conformers calculated total number: 1 / Conformers submitted total number: 1
Soln scatter modelMethod: CONSTRAINED SCATTERING FITTING INCORPORATING NMR RDC DATA.
Conformer selection criteria: THE MODELS WERE GENERATED USING GRID SEARCH, CONTRAINING THE ORIENTATION BETWEEN THE DIMERS ACCORDING TO NMR RDC DATA. MODELS WERE THEN SCORED BASED ON AGREEMENT BETWEEN ...Conformer selection criteria: THE MODELS WERE GENERATED USING GRID SEARCH, CONTRAINING THE ORIENTATION BETWEEN THE DIMERS ACCORDING TO NMR RDC DATA. MODELS WERE THEN SCORED BASED ON AGREEMENT BETWEEN THEORETICAL AND EXPERIMENTAL SCATTERING CURVE AND SOUNDNESS OF THE INTERFACE AS DEFINED BY A RESIDUE PAIRING SCORE.
Details: PDB CODE 1U4L / Num. of conformers calculated: 5953 / Num. of conformers submitted: 1 / Representative conformer: 1 / Software author list: UIUC, EMBL / Software list: VMD, GNOM, OLIGOMER

+
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://pdbjlc1.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