[English] 日本語
![](img/lk-miru.gif)
- PDB-2c3a: Structure of unliganded HSV gD reveals a mechanism for receptor- ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2c3a | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of unliganded HSV gD reveals a mechanism for receptor- mediated activation of virus entry | |||||||||
![]() | GLYCOPROTEIN D | |||||||||
![]() | VIRAL PROTEIN / VIRUS / HERPES SIMPLEX VIRUS / HSV-1 / GLYCOPROTEIN D | |||||||||
Function / homology | ![]() host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / viral envelope / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Krummenacher, C. / Supekar, V.M. / Whitbeck, J.C. / Lazear, E. / Connolly, S.A. / Eisenberg, R.J. / Cohen, G.H. / Wiley, D.C. / Carfi, A. | |||||||||
![]() | ![]() Title: Structure of Unliganded Hsv Gd Reveals a Mechanism for Receptor-Mediated Activation of Virus Entry. Authors: Krummenacher, C. / Supekar, V.M. / Whitbeck, J.C. / Lazear, E. / Connolly, S.A. / Eisenberg, R.J. / Cohen, G.H. / Wiley, D.C. / Carfi, A. | |||||||||
History |
| |||||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 120.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 91.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1010.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1019.4 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c36C ![]() 1l2gS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
2 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 100 - 200 / Label seq-ID: 79 - 179
NCS oper: (Code: given Matrix: (0.96045, 0.27667, 0.03155), Vector: |
-
Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 31743.059 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: N-ACETYL-D-GLUCOSAMINE LINKED TO ASN94 FOR BOTH CHAINS A AND B Source: (gene. exp.) ![]() ![]() Strain: PATTON / Plasmid: PDL485 / Cell line (production host): SF9 / Production host: ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 4 types, 62 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-ZN / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, VAL 62 TO CYS ENGINEERED RESIDUE IN CHAIN A, ALA 327 TO CYS ...ENGINEERED |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % |
---|---|
Crystal grow | pH: 4.6 / Details: 100MM NA ACETATE PH 4.6, 10MM ZNCL2, 24% PEG &K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 23602 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.07 / % possible all: 98.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L2G Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.386 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.517 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FIRST 22 RESIDUES DISORDERED FOR BOTH CHAINS A,B. RESIDUES 256-267 DISORDERED FOR BOTH CHAINS A,B
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|