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Yorodumi- PDB-1mhp: Crystal structure of a chimeric alpha1 integrin I-domain in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mhp | ||||||
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Title | Crystal structure of a chimeric alpha1 integrin I-domain in complex with the Fab fragment of a humanized neutralizing antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / integrin / cell adhesion / receptor / antibody | ||||||
Function / homology | Function and homology information Integrin cell surface interactions / Smooth Muscle Contraction / cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / positive regulation of phosphoprotein phosphatase activity ...Integrin cell surface interactions / Smooth Muscle Contraction / cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / basal part of cell / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / positive regulation of phosphoprotein phosphatase activity / collagen binding / cell chemotaxis / cell-matrix adhesion / neutrophil chemotaxis / neuron projection morphogenesis / acrosomal vesicle / integrin-mediated signaling pathway / cell-cell adhesion / vasodilation / positive regulation of neuron apoptotic process / integrin binding / perikaryon / protein phosphatase binding / positive regulation of MAPK cascade / cell adhesion / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / focal adhesion / cell surface / metal ion binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Karpusas, M. / Taylor, F. / Ferrant, J. / Weinreb, P. / Garber, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structure of the alpha 1 beta 1 Integrin I Domain in Complex with an Antibody Fab Fragment Authors: Karpusas, M. / Ferrant, J. / Weinreb, P. / Carmillo, A. / Taylor, F. / Garber, E. | ||||||
History |
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Remark 999 | SEQUENCE AN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING FOR ...SEQUENCE AN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING FOR CHAINS H AND X (Fab fragment, heavy chain) AND FOR CHAINS L AND Y (FAB FRAGMENT, light chain). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mhp.cif.gz | 198.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mhp.ent.gz | 164.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/1mhp ftp://data.pdbj.org/pub/pdb/validation_reports/mh/1mhp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21629.518 Da / Num. of mol.: 2 / Fragment: alpha1 I-domain / Mutation: G217V, R218Q, Q219R, L222R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P18614 #2: Antibody | Mass: 23141.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster) #3: Antibody | Mass: 23201.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster) #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 1500, Tris, NaCl, beta-mercaptoethanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→35 Å / Num. all: 36501 / Num. obs: 35275 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.92 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.29 / % possible all: 87.7 |
Reflection | *PLUS Lowest resolution: 500 Å |
Reflection shell | *PLUS % possible obs: 87.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→35 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→35 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 500 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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