+Open data
-Basic information
Entry | Database: PDB / ID: 1ic1 | |||||||||
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Title | THE CRYSTAL STRUCTURE FOR THE N-TERMINAL TWO DOMAINS OF ICAM-1 | |||||||||
Components | INTERCELLULAR ADHESION MOLECULE-1 | |||||||||
Keywords | CELL ADHESION / ICAM-1 / IMMUNOGLOBULIN FOLD / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / establishment of endothelial barrier / cell adhesion mediated by integrin ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / establishment of endothelial barrier / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / leukocyte migration / Interleukin-10 signaling / immunological synapse / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to leukemia inhibitory factor / cellular response to glucose stimulus / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / transmembrane signaling receptor activity / integrin binding / virus receptor activity / signaling receptor activity / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / cell adhesion / membrane raft / external side of plasma membrane / focal adhesion / cell surface / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SINGLE ISOMORPHOUS REPLACEMENT, MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Casasnovas, J.M. / Stehle, T. / Liu, J.-H. / Wang, J.-H. / Springer, T.A. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: A dimeric crystal structure for the N-terminal two domains of intercellular adhesion molecule-1. Authors: Casasnovas, J.M. / Stehle, T. / Liu, J.H. / 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 | 1ic1.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ic1.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ic1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/1ic1 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/1ic1 | HTTPS FTP |
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-Related 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.725335, -0.085912, -0.683014), Vector: |
-Components
#1: Protein | Mass: 20919.848 Da / Num. of mol.: 2 / Fragment: N-TERMINAL 190 RESIDUE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IC1-P191* / Plasmid: PBJ5-GS / Cell line (production host): CHO / Cellular location (production host): EXTRACELLULAR / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05362 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: 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: 3.89 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 17% PEG 4000, NA CACODYLATE, PH 6.5, AND 100 MM B-OCTYL-GLUCOPYRANOSIDE. | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 13176 / % possible obs: 95 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2 / % possible all: 97.4 |
Reflection shell | *PLUS % possible obs: 97.4 % |
-Processing
Software |
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Refinement | Method to determine structure: SINGLE ISOMORPHOUS REPLACEMENT, MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1ZXQ AND 1VSC Resolution: 3→15 Å / σ(F): 2 Details: THE AVERAGE B FACTOR FOR CHAIN A IS LOWER THAN FOR CHAIN B. THE ELECTRON DENSITY IS NOT WELL DEFINED FOR RESIDUE THR 190 IN BOTH CHAINS.
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Displacement parameters | Biso mean: 49.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.14 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.282 |