+Open data
-Basic information
Entry | Database: PDB / ID: 1mq8 | |||||||||
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Title | Crystal structure of alphaL I domain in complex with ICAM-1 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig superfamily / Rossmann fold / metal mediated protein interface | |||||||||
Function / homology | Function and homology information regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / memory T cell extravasation / T cell antigen processing and presentation / 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 / membrane to membrane docking ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / memory T cell extravasation / T cell antigen processing and presentation / 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 / membrane to membrane docking / adhesion of symbiont to host / RUNX3 Regulates Immune Response and Cell Migration / establishment of endothelial barrier / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / leukocyte migration / receptor clustering / Interleukin-10 signaling / immunological synapse / Integrin cell surface interactions / specific granule membrane / phagocytosis / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cell adhesion molecule binding / cell-matrix adhesion / cellular response to leukemia inhibitory factor / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cellular response to glucose stimulus / cell-cell adhesion / cellular response to amyloid-beta / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / integrin binding / virus receptor activity / signaling receptor activity / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / membrane raft / external side of plasma membrane / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Shimaoka, M. / Xiao, T. / Liu, J.-H. / Yang, Y. / Dong, Y. / Jun, C.-D. / McCormack, A. / Zhang, R. / Joachimiak, A. / Takagi, J. ...Shimaoka, M. / Xiao, T. / Liu, J.-H. / Yang, Y. / Dong, Y. / Jun, C.-D. / McCormack, A. / Zhang, R. / Joachimiak, A. / Takagi, J. / Wang, J.-H. / Springer, T.A. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: Structures of the aL 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. / Dong, Y. / Jun, C.-D. / McCormack, A. / Zhang, R. / 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 | 1mq8.cif.gz | 143.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mq8.ent.gz | 117.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mq8_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1mq8_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1mq8_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 1mq8_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/1mq8 ftp://data.pdbj.org/pub/pdb/validation_reports/mq/1mq8 | HTTPS FTP |
-Related structure data
Related structure data | 1mjnC 1mq9C 1mqaC 1ic1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | chain A and B form a biological complex, so do chain C and D. Chain A and C also form a biological dimer. |
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 31623.771 Da / Num. of mol.: 2 / Fragment: domains 1 and 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ICAM-1 / Plasmid: pMT/BiP/V5-His / Production host: Schneider S2 insect cells / Strain (production host): Schneider S2 insect cells / References: UniProt: P05362 #2: Protein | Mass: 20191.178 Da / Num. of mol.: 2 / Fragment: Integrin alphaL I domain / Mutation: L186C, F324C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LFA-1 (AlphaLbeta2) / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20701 |
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-Sugars , 2 types, 8 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 6 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.78 Å3/Da / Density % sol: 55.3 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 25% PEG 4000, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 0.91 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jan 1, 2001 / Details: mirrors |
Radiation | Monochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 25280 / Num. obs: 23330 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 1 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.5 / Num. unique all: 469 / Rsym value: 0.412 / % possible all: 70.7 |
Reflection | *PLUS Highest resolution: 3.3 Å / Lowest resolution: 50 Å / Num. obs: 12338 / Num. measured all: 23330 |
Reflection shell | *PLUS % possible obs: 70.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IC1 Resolution: 3.3→50 Å / Rfactor Rfree error: 0.013 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood refinement target
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Displacement parameters | Biso mean: 67 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→50 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3.3 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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