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- PDB-1qa9: Structure of a Heterophilic Adhesion Complex Between the Human CD... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qa9 | ||||||
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Title | Structure of a Heterophilic Adhesion Complex Between the Human CD2 and CD58(LFA-3) Counter-Receptors | ||||||
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![]() | IMMUNE SYSTEM / CELL ADHESION / IG-LIKE DOMAIN / CD2 / CD58 | ||||||
Function / homology | ![]() positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / ficolin-1-rich granule membrane / T cell activation / secretory granule membrane / positive regulation of interleukin-8 production ...positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / ficolin-1-rich granule membrane / T cell activation / secretory granule membrane / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / cytoplasmic side of plasma membrane / receptor tyrosine kinase binding / cell-cell adhesion / cellular response to type II interferon / : / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cell-cell junction / cellular response to tumor necrosis factor / signaling receptor activity / cell surface receptor signaling pathway / external side of plasma membrane / signaling receptor binding / apoptotic process / Neutrophil degranulation / Golgi apparatus / cell surface / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Wang, J.-H. / Smolyar, A. / Tan, K. / Liu, J.-H. / Kim, M. / Sun, Z.J. / Wagner, G. / Reinherz, E.L. | ||||||
![]() | ![]() Title: Structure of a heterophilic adhesion complex between the human CD2 and CD58 (LFA-3) counterreceptors. Authors: Wang, J.H. / Smolyar, A. / Tan, K. / Liu, J.H. / Kim, M. / Sun, Z.Y. / Wagner, G. / Reinherz, E.L. #1: ![]() Title: Design and NMR Studies of a Functional Glycan-Free Adhesion Domain of the Human Cell Surface Receptor CD58 Authors: Sun, Z.-Y.J. / Dotsch, V. / Kim, M. / Li, J. / Reinherz, E.L. / Wagner, G. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.1 KB | Display | ![]() |
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PDB format | ![]() | 69.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.8 KB | Display | ![]() |
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Full document | ![]() | 404.7 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is each of the individual molecules |
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Components
#1: Protein | Mass: 12017.655 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ADHESION DOMAIN OF CD2 / Mutation: K61E, F63L, T67A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11003.180 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ADHESION DOMAIN OF CD58 / Mutation: F1S, V9K, V21Q, V58K, T85S, L93G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.17 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 400, (NH4)2SO4, NaCl, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 61 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→18 Å / Num. all: 9453 / Num. obs: 8196 / % possible obs: 86.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.2→3.31 Å / Rmerge(I) obs: 0.278 / Num. unique all: 8196 / % possible all: 87.6 |
Reflection | *PLUS Num. measured all: 41649 |
Reflection shell | *PLUS % possible obs: 87.6 % |
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Processing
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Refinement | Resolution: 3.2→18 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
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Refinement step | Cycle: LAST / Resolution: 3.2→18 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.2 Å / σ(F): 2 / Rfactor obs: 0.223 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.006 |