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- PDB-1ncv: DETERMINATION CC-CHEMOKINE MCP-3, NMR, 7 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1ncv
TitleDETERMINATION CC-CHEMOKINE MCP-3, NMR, 7 STRUCTURES
ComponentsMONOCYTE CHEMOATTRACTANT PROTEIN 3
KeywordsCYTOKINE / MCP-3 / BETA-CHEMOKINE / CHEMOTAXIS / HEPARIN-BINDING / GLYCOPROTEIN
Function / homology
Function and homology information


CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity ...CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / cytoskeleton organization / neutrophil chemotaxis / response to gamma radiation / cellular response to type II interferon / intracellular calcium ion homeostasis / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / heparin binding / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space / extracellular region
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 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
AuthorsMeunier, S. / Bernassau, J.M. / Guillemot, J.C. / Ferrara, P. / Darbon, H.
CitationJournal: Biochemistry / Year: 1997
Title: Determination of the three-dimensional structure of CC chemokine monocyte chemoattractant protein 3 by 1H two-dimensional NMR spectroscopy.
Authors: Meunier, S. / Bernassau, J.M. / Guillemot, J.C. / Ferrara, P. / Darbon, H.
History
DepositionFeb 5, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MONOCYTE CHEMOATTRACTANT PROTEIN 3
B: MONOCYTE CHEMOATTRACTANT PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)17,9492
Polymers17,9492
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)7 / 50NOE VIOLATION
Representative

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Components

#1: Protein MONOCYTE CHEMOATTRACTANT PROTEIN 3


Mass: 8974.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: OVARY / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P80098
Compound detailsCHAINS A AND B ARE THE TWO MONOMERS CONSTITUTING THE DIMER.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121CLTOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED BY STANDARD 1H 2D NMR EXPERIMENTS

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Sample preparation

Sample conditionspH: 5.0 / Temperature: 290 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker DMX600BrukerDMX6006002

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
DIANAstructure solution
XPLORstructure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: NOE VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 7

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