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Yorodumi- PDB-1je4: Solution structure of the monomeric variant of the chemokine MIP-1beta -
+Open data
-Basic information
Entry | Database: PDB / ID: 1je4 | ||||||
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Title | Solution structure of the monomeric variant of the chemokine MIP-1beta | ||||||
Components | macrophage inflammatory protein 1-beta | ||||||
Keywords | ANTIVIRAL 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 / positive regulation of calcium ion transport / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / 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 / positive regulation of calcium ion transport / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / establishment or maintenance of cell polarity / Interleukin-10 signaling / negative regulation by host of viral transcription / positive regulation of calcium-mediated signaling / cytokine activity / response to virus / response to toxic substance / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / G alpha (i) signalling events / cell adhesion / positive regulation of cell migration / inflammatory response / immune response / signal transduction / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / The initial fold was obtained by distance geometry, further refined by simulated annealing. | ||||||
Model type details | minimized average | ||||||
Authors | Kim, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1je4.cif.gz | 30.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1je4.ent.gz | 23.4 KB | Display | PDB format |
PDBx/mmJSON format | 1je4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1je4_validation.pdf.gz | 243.1 KB | Display | wwPDB validaton report |
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Full document | 1je4_full_validation.pdf.gz | 242.8 KB | Display | |
Data in XML | 1je4_validation.xml.gz | 2.6 KB | Display | |
Data in CIF | 1je4_validation.cif.gz | 2.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/1je4 ftp://data.pdbj.org/pub/pdb/validation_reports/je/1je4 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 3D 15N or 13C edited NMR experiments. |
-Sample preparation
Details | Contents: 1-2mM MIP-1b F13A U-15N, 13C; 20mM Na-phosphate buffer Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 20mM sodium phosphate / pH: 2.5 / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: minimized average structure | ||||||||||||||||
NMR ensemble | Conformers submitted total number: 1 |