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- PDB-1d1d: NMR SOLUTION STRUCTURE OF THE CAPSID PROTEIN FROM ROUS SARCOMA VIRUS -

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Basic information

Entry
Database: PDB / ID: 1d1d
TitleNMR SOLUTION STRUCTURE OF THE CAPSID PROTEIN FROM ROUS SARCOMA VIRUS
ComponentsPROTEIN (CAPSID PROTEIN)
KeywordsVIRAL 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 / structural constituent of virion / nucleic acid binding / aspartic-type endopeptidase activity / zinc ion binding
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Retroviral Gag polyprotein, M / Retroviral M domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal ...Retroviral nucleocapsid Gag protein p24, N-terminal / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Retroviral Gag polyprotein, M / Retroviral M domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRous sarcoma virus
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS SIMULATED ANNEALING
AuthorsCampos-Olivas, R. / Newman, J.L. / Summers, M.F.
CitationJournal: 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
DepositionSep 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CAPSID PROTEIN)


Theoretical massNumber of molelcules
Total (without water)28,4441
Polymers28,4441
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #7

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Components

#1: Protein PROTEIN (CAPSID 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C-SEPARATED NOESY
1214D 13C/15N-SEPARATED NOESY
1314D 15N-SEPARATED NOESY
1413D 15N- SEPARATED NOESY
NMR detailsText: THE 1H, 13C, AND 15N CHEMICAL SHIFT ASSIGNMENTS HAVE BEEN DEPOSITED ATTHE BIOMOLECULAR RESONANCE DATABANK (BMRB ENTRY 4384).

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Sample preparation

Details
Solution-IDContentsSolvent system
1~1 MM CA_RSV, 10 MM PHOSPHATE (PH 6.0), 0.2 MM N3NA, 0.1 MM EDTA, 0.1 MM PMSF, 1 MG/L PEPSTATIN A, 5 MM BETA-MERCAPTOETHANOL90% H2O/10% D2O
2~1 MM CA_RSV, 10 MM PHOSPHATE (PH 6.0), 0.2 MM N3NA, 0.1 MM EDTA, 0.1 MM PMSF, 1 MG/L PEPSTATIN A, 5 MM BETA-MERCAPTOETHANOL100% D2O
Sample conditionsIonic strength: 10 mM PHOSPHATE / pH: 6.00 / Pressure: 1 atm / Temperature: 303.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5P.GUNTHER, ETH-ZURICHrefinement
XwinNMR2.5structure solution
NMRPipe1999structure solution
NMRView3structure solution
TALOS1999.019.15.47structure solution
RefinementMethod: 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 ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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