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- PDB-1b50: NMR STRUCTURE OF HUMAN MIP-1A D26A, 10 STRUCTURES -

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Entry
Database: PDB / ID: 1b50
TitleNMR STRUCTURE OF HUMAN MIP-1A D26A, 10 STRUCTURES
ComponentsMIP-1A
KeywordsCHEMOKINE / CYTOKINE / CHEMOTAXIS
Function / homology
Function and homology information


lymphocyte chemotaxis / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / signaling / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation ...lymphocyte chemotaxis / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / signaling / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / regulation of sensory perception of pain / negative regulation of bone mineralization / CCR chemokine receptor binding / positive regulation of microglial cell activation / cell activation / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / phospholipase activator activity / macrophage chemotaxis / positive regulation of calcium ion import / chemoattractant activity / monocyte chemotaxis / negative regulation of osteoclast differentiation / Interleukin-10 signaling / exocytosis / cellular response to interleukin-1 / negative regulation by host of viral transcription / cytoskeleton organization / neutrophil chemotaxis / positive regulation of calcium-mediated signaling / positive regulation of interleukin-1 beta production / calcium-mediated signaling / cellular response to type II interferon / response to toxic substance / positive regulation of inflammatory response / intracellular calcium ion homeostasis / osteoblast differentiation / positive regulation of neuron apoptotic process / chemotaxis / calcium ion transport / positive regulation of tumor necrosis factor production / MAPK cascade / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / cellular response to tumor necrosis factor / kinase activity / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / positive regulation of cell migration / inflammatory response / negative regulation of gene expression / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / cytosol / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING STARTING FROM RANDOM ATOM POSITIONS
AuthorsWaltho, J.P. / Higgins, L.D. / Craven, C.J. / Tan, P. / Dudgeon, T.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Identification of amino acid residues critical for aggregation of human CC chemokines macrophage inflammatory protein (MIP)-1alpha, MIP-1beta, and RANTES. Characterization of active ...Title: Identification of amino acid residues critical for aggregation of human CC chemokines macrophage inflammatory protein (MIP)-1alpha, MIP-1beta, and RANTES. Characterization of active disaggregated chemokine variants.
Authors: Czaplewski, L.G. / McKeating, J. / Craven, C.J. / Higgins, L.D. / Appay, V. / Brown, A. / Dudgeon, T. / Howard, L.A. / Meyers, T. / Owen, J. / Palan, S.R. / Tan, P. / Wilson, G. / Woods, N.R. ...Authors: Czaplewski, L.G. / McKeating, J. / Craven, C.J. / Higgins, L.D. / Appay, V. / Brown, A. / Dudgeon, T. / Howard, L.A. / Meyers, T. / Owen, J. / Palan, S.R. / Tan, P. / Wilson, G. / Woods, N.R. / Heyworth, C.M. / Lord, B.I. / Brotherton, D. / Christison, R. / Craig, S. / Cribbes, S. / Edwards, R.M. / Evans, S.J. / Gilbert, R. / Morgan, P. / Randle, E. / Schofield, N. / Varley, P.G. / Fisher, J. / Waltho, J.P. / Hunter, M.G.
History
DepositionJan 11, 1999Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.5Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MIP-1A
B: MIP-1A


Theoretical massNumber of molelcules
Total (without water)15,3572
Polymers15,3572
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 / 30CONVERGED LOW ENERGY 'PLATEAU' OF ENERGY DISTRIBUTION
Representative

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Components

#1: Protein MIP-1A


Mass: 7678.577 Da / Num. of mol.: 2 / Mutation: D26A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P10147
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111ST
121ARD HETERONUCLEAR TECHNIQUES
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELLED MIP-1A. ADDITIONAL INTERMONOMER CONSTRAINTS WERE ACQUIRED USING A MIXED 13C/ 15N-12C/14N SAMPLE.

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Sample preparation

DetailsContents: 10% H2O/90% D2O
Sample conditionsIonic strength: NO ADDED SALT / pH: 3.5 / Pressure: 1 atm / Temperature: 318 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING STARTING FROM RANDOM ATOM POSITIONS
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: CONVERGED LOW ENERGY 'PLATEAU' OF ENERGY DISTRIBUTION
Conformers calculated total number: 30 / Conformers submitted total number: 10

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