[English] 日本語
Yorodumi- PDB-1d1d: NMR SOLUTION STRUCTURE OF THE CAPSID PROTEIN FROM ROUS SARCOMA VIRUS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d1d | ||||||
---|---|---|---|---|---|---|---|
Title | NMR SOLUTION STRUCTURE OF THE CAPSID PROTEIN FROM ROUS SARCOMA VIRUS | ||||||
Components | PROTEIN (CAPSID PROTEIN) | ||||||
Keywords | VIRAL PROTEIN / TWO INDEPENDENT DOMAINS HELICAL BUNDLES / VIRUS/VIRAL PROTEIN | ||||||
Function / homology | Function and homology information host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / aspartic-type endopeptidase activity / nucleic acid binding / structural constituent of virion / zinc ion binding Similarity search - Function | ||||||
Biological species | Rous sarcoma virus | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS SIMULATED ANNEALING | ||||||
Authors | Campos-Olivas, R. / Newman, J.L. / Summers, M.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Solution structure and dynamics of the Rous sarcoma virus capsid protein and comparison with capsid proteins of other retroviruses. Authors: Campos-Olivas, R. / Newman, J.L. / Summers, M.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1d1d.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1d1d.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 1d1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d1d_validation.pdf.gz | 354.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1d1d_full_validation.pdf.gz | 627.9 KB | Display | |
Data in XML | 1d1d_validation.xml.gz | 108.2 KB | Display | |
Data in CIF | 1d1d_validation.cif.gz | 133.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/1d1d ftp://data.pdbj.org/pub/pdb/validation_reports/d1/1d1d | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 28443.596 Da / Num. of mol.: 1 / Mutation: N-TERMINAL HIS-TAGGED Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Strain: SCHMIDT RUPPIN A-2 Description: THE SOURCE OF THE CA_RSV GENE IS PLASMID PSRA-2 OF ATCC 45000, WHICH IS A PLASMID CLONE CONTAINING FULL LENGTH ROUS SARCOMA VIRUS, STRAIN SCHMIDT RUPPIN A-2, DERIVED FROM UNINTEGRATED ...Description: THE SOURCE OF THE CA_RSV GENE IS PLASMID PSRA-2 OF ATCC 45000, WHICH IS A PLASMID CLONE CONTAINING FULL LENGTH ROUS SARCOMA VIRUS, STRAIN SCHMIDT RUPPIN A-2, DERIVED FROM UNINTEGRATED DNA FROM AN ACUTE INFECTION OF QT-6 CELLS Plasmid: PET-16B (NOVAGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) PLYSS / References: UniProt: O92954 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||
NMR details | Text: THE 1H, 13C, AND 15N CHEMICAL SHIFT ASSIGNMENTS HAVE BEEN DEPOSITED ATTHE BIOMOLECULAR RESONANCE DATABANK (BMRB ENTRY 4384). |
-Sample preparation
Details |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Sample conditions | Ionic strength: 10 mM PHOSPHATE / pH: 6 / Pressure: 1 atm / Temperature: 303.00 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: TORSION ANGLE DYNAMICS SIMULATED ANNEALING / Software ordinal: 1 Details: 20 CONFORMERS COMPATIBLE WITH THE NMR CONSTRAINTS WERE CALCULATED USING DYANA 1.5 AND THE STANDARD TORSION ANGLE SIMULATED ANHEALING PROTOCOL. PRELIMINARY CALCULATIONS WERE CARRIED OUT ...Details: 20 CONFORMERS COMPATIBLE WITH THE NMR CONSTRAINTS WERE CALCULATED USING DYANA 1.5 AND THE STANDARD TORSION ANGLE SIMULATED ANHEALING PROTOCOL. PRELIMINARY CALCULATIONS WERE CARRIED OUT INDEPENDENTLY FOR EACH OF THE TWO N- AND C- TERMINAL DOMAINS OF THE PROTEIN. INITIALLY ONLY NOE DISTANCE CONSTRAINTS WERE IMPOSED. THE INITIAL STRUCTURES WERE THEN USED TO ASSES THE ACCURACY OF THE TORSION ANGLE CONSTRAINTS GENERATED BY ANALYSIS OF HA, CA, CB, CO AND N CHEMICAL SHIFTS WITH THE PROGRAM TALOS. FINALLY, UPPER AND LOWER LIMIT DISTANCE CONSTRAINTS WERE IMPOSED FOR UNAMBIGUOUS INTRAHELICAL H-BONDS. | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20 |