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Yorodumi- PDB-1mjn: Crystal Structure of the intermediate affinity aL I domain mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mjn | ||||||
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Title | Crystal Structure of the intermediate affinity aL I domain mutant | ||||||
Components | Integrin alpha-L | ||||||
Keywords | IMMUNE SYSTEM / Rossmann Fold | ||||||
Function / homology | Function and homology information memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering / Integrin cell surface interactions / specific granule membrane / phagocytosis / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / inflammatory response / external side of plasma membrane / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Shimaoka, M. / Xiao, T. / Liu, J.H. / Yang, Y.T. / Dong, Y.C. / Jun, C.D. / McCormack, A. / Zhang, R.G. / Wang, J.H. / Springer, T.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: Structures of the alphaL I Domain and its Complex with ICAM-1 reveal a Shape-shifting Pathway for Integrin Regulation Authors: Shimaoka, M. / Xiao, T. / Liu, J.H. / Yang, Y.T. / Dong, Y.C. / Jun, C.D. / McCormack, A. / Zhang, R.G. / Joachimiak, A. / Takagi, J. / Wang, J.H. / Springer, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mjn.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mjn.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/1mjn ftp://data.pdbj.org/pub/pdb/validation_reports/mj/1mjn | HTTPS FTP |
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-Related structure data
Related structure data | 1mq8C 1mq9C 1mqaC 1lfaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20362.336 Da / Num. of mol.: 1 / Fragment: Intermediate Affinity aL I Domain / Mutation: L161C, F299C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20701 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.38 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 |
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Detector | Type: SBC / Detector: CCD / Date: Dec 17, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 35329 / Num. obs: 33956 / % possible obs: 90.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2897 / Rsym value: 0.352 / % possible all: 47 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 35329 / Num. measured all: 197616 |
Reflection shell | *PLUS % possible obs: 47 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LFA Resolution: 1.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.38 Å /
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.3 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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