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- PDB-1je4: Solution structure of the monomeric variant of the chemokine MIP-1beta -

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Basic information

Entry
Database: PDB / ID: 1je4
TitleSolution structure of the monomeric variant of the chemokine MIP-1beta
Componentsmacrophage inflammatory protein 1-beta
KeywordsANTIVIRAL PROTEIN / MIP-1beta / chemokine / macrophage inflammatory protein
Function / homology
Function and homology information


CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR5 chemokine receptor binding / CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / positive regulation of calcium ion transport / chemokine activity / Chemokine receptors bind chemokines / establishment or maintenance of cell polarity ...CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR5 chemokine receptor binding / CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / positive regulation of calcium ion transport / chemokine activity / Chemokine receptors bind chemokines / establishment or maintenance of cell polarity / Interleukin-10 signaling / host-mediated suppression of viral transcription / positive regulation of calcium-mediated signaling / cytokine activity / response to toxic substance / response to virus / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / G alpha (i) signalling events / cell adhesion / immune response / positive regulation of cell migration / inflammatory response / signal transduction / extracellular space / extracellular region / identical protein binding
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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / The initial fold was obtained by distance geometry, further refined by simulated annealing.
Model type detailsminimized average
AuthorsKim, S. / Jao, S. / Laurence, J.S. / LiWang, P.J.
Citation
Journal: Biochemistry / Year: 2001
Title: Structural comparison of monomeric variants of the chemokine MIP-1beta having differing ability to bind the receptor CCR5.
Authors: Kim, S. / Jao, S. / Laurence, J.S. / LiWang, P.J.
#1: Journal: Biochemistry / Year: 2000
Title: CC chemokine MIP-1beta can function as a monomer and depends on Phe13 for receptor binding
Authors: Laurence, J.S. / Blanpain, C. / Burgner, J.W. / Parmentier, M. / LiWang, P.J.
#2: Journal: Science / Year: 1994
Title: High-resolution solution structure of the beta chemokine hMIP-1beta by multidimensional NMR
Authors: Lodi, P.J. / Garrett, D.S. / Kuszewski, J. / Tsang, M.L. / Weatherbee, J.A. / Leonard, W.J. / Gronenborn, A.M. / Clore, G.M.
History
DepositionJun 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 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: macrophage inflammatory protein 1-beta


Theoretical massNumber of molelcules
Total (without water)7,7491
Polymers7,7491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein macrophage inflammatory protein 1-beta / MIP-1beta / T-CELL ACTIVATION PROTEIN 2 / ACT-2 / LYMPHOCYTE ACTIVATION GENE-1 PROTEIN / LAG-1


Mass: 7748.646 Da / Num. of mol.: 1 / Mutation: F13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13236
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
NMR detailsText: This structure was determined using standard 3D 15N or 13C edited NMR experiments.

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Sample preparation

DetailsContents: 1-2mM MIP-1b F13A U-15N, 13C; 20mM Na-phosphate buffer
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM sodium phosphate / pH: 2.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglioprocessing
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: The initial fold was obtained by distance geometry, further refined by simulated annealing.
Software ordinal: 1
Details: The structure is based on a total 940 restraints, 851 distance constraints, 69 dihedral angle restraints, 20 distance restraints for 10 hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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