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- PDB-1jma: CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jma | |||||||||
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Title | CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM | |||||||||
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![]() | VIRAL PROTEIN / V-type Ig molecule and TNFR superfamily | |||||||||
Function / homology | ![]() negative regulation of adaptive immune memory response / negative regulation of alpha-beta T cell proliferation / tumor necrosis factor receptor activity / positive regulation of cytokine production involved in immune response / TNFs bind their physiological receptors / Costimulation by the CD28 family / cytokine binding / positive regulation of T cell migration / T cell costimulation / positive regulation of peptidyl-tyrosine phosphorylation ...negative regulation of adaptive immune memory response / negative regulation of alpha-beta T cell proliferation / tumor necrosis factor receptor activity / positive regulation of cytokine production involved in immune response / TNFs bind their physiological receptors / Costimulation by the CD28 family / cytokine binding / positive regulation of T cell migration / T cell costimulation / positive regulation of peptidyl-tyrosine phosphorylation / virus receptor activity / host cell Golgi apparatus / defense response to Gram-negative bacterium / adaptive immune response / entry receptor-mediated virion attachment to host cell / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / symbiont entry into host cell / immune response / external side of plasma membrane / innate immune response / viral envelope / ubiquitin protein ligase binding / virion membrane / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Carfi, A. / Willis, S.H. / Whitbeck, J.C. / Krummenacker, C. / Cohen, G.H. / Eisenberg, R.J. / Wiley, D.C. | |||||||||
![]() | ![]() Title: Herpes simplex virus glycoprotein D bound to the human receptor HveA. Authors: Carfi, A. / Willis, S.H. / Whitbeck, J.C. / Krummenacher, C. / Cohen, G.H. / Eisenberg, R.J. / Wiley, D.C. #1: ![]() Title: Herpes simplex virus-1 entry into cells mediated by a novel member of the TNF/NGF receptor family Authors: Montgomery, R.I. / Warner, M.S. / Lurn, B.J. / Spear, P.G. | |||||||||
History |
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Remark 11 | Residues 1 to 3, 93,94 and 106 to 167 including 5 C-terminus HIS tag residues in chain B, and ...Residues 1 to 3, 93,94 and 106 to 167 including 5 C-terminus HIS tag residues in chain B, and residues 260 to 290 that includes 5 C-terimus HIS tag residues were not visible in the electron density maps due to disorder | |||||||||
Remark 12 | Weak or no electron density was observed for the side chains of the following residues: Chain B ...Weak or no electron density was observed for the side chains of the following residues: Chain B residues: 5, 6, 18, 31, 71, 95 and 96. Chain A residues: 16, 18, 20, 21, 35, 89, 91, 186, 196 and 259 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.1 KB | Display | ![]() |
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PDB format | ![]() | 65.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17767.955 Da / Num. of mol.: 1 / Fragment: HVEA-162 / Mutation: ECTODOMAIN OF THE FULL PROTEIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Genus: Simplexvirus / Production host: ![]() ![]() | ||
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#2: Protein | Mass: 32315.697 Da / Num. of mol.: 1 / Fragment: GD-285 / Mutation: C-TERMINAL TRUNCATION AT RESIDUE 285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#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: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.36 % | ||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.8M Ammonium Sulfate and 5% Peg400 and Tris-HCL 100mM pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 19, 2000 / Details: monochromator |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9196 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→25 Å / Num. all: 24279 / Num. obs: 24260 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.65→20 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5 / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 272205 |
Reflection shell | *PLUS % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 16.177 Å2
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Refine analyze | Luzzati sigma a obs: 0.35 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.236 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.008 |