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Yorodumi- PDB-2ghw: Crystal structure of SARS spike protein receptor binding domain i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ghw | ||||||
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Title | Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R | ||||||
Components |
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Keywords | VIRUS/VIRAL PROTEIN/ANTIBIOTIC / SARS / S protein / neutralizing antibody / VIRUS-VIRAL PROTEIN-ANTIBIOTIC COMPLEX | ||||||
Function / homology | Function and homology information Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | SARS coronavirus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hwang, W.C. / Lin, Y. / Santelli, E. / Sui, J. / Jaroszewski, L. / Stec, B. / Farzan, M. / Marasco, W.A. / Liddington, R.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural basis of neutralization by a human anti-severe acute respiratory syndrome spike protein antibody, 80R. Authors: Hwang, W.C. / Lin, Y. / Santelli, E. / Sui, J. / Jaroszewski, L. / Stec, B. / Farzan, M. / Marasco, W.A. / Liddington, R.C. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF ANTI-SARS SCFV ANTIBODY, 80R IS NOT AVAILABLE AT UNIPROT SEQUENCE DATABASE ...SEQUENCE THE SEQUENCE OF ANTI-SARS SCFV ANTIBODY, 80R IS NOT AVAILABLE AT UNIPROT SEQUENCE DATABASE AT THE TIME OF PROCESSING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ghw.cif.gz | 185.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ghw.ent.gz | 145.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ghw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ghw_validation.pdf.gz | 461.2 KB | Display | wwPDB validaton report |
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Full document | 2ghw_full_validation.pdf.gz | 479.2 KB | Display | |
Data in XML | 2ghw_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 2ghw_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/2ghw ftp://data.pdbj.org/pub/pdb/validation_reports/gh/2ghw | HTTPS FTP |
-Related structure data
Related structure data | 2ghvC 1dzbS 2ajfS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 2
NCS ensembles :
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-Components
#1: Protein | Mass: 22883.830 Da / Num. of mol.: 2 / Fragment: RBD of spike protein S1 (318-510) Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Gene: S / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59594 #2: Antibody | Mass: 26454.303 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q65ZC9 #3: Chemical | ChemComp-CL / #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: 2.87 Å3/Da / Density % sol: 57.21 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 12.5% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→50 Å / Num. all: 51915 / Num. obs: 51915 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 3.1 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.29→2.38 Å / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.9 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AJF CHAIN F, 1DZB CHAIN A Resolution: 2.3→45.55 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.848 / SU B: 37.1 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.106 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→45.55 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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