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- PDB-1a6s: M-DOMAIN FROM GAG POLYPROTEIN OF ROUS SARCOMA VIRUS, NMR, 20 STRU... -

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Basic information

Entry
Database: PDB / ID: 1a6s
TitleM-DOMAIN FROM GAG POLYPROTEIN OF ROUS SARCOMA VIRUS, NMR, 20 STRUCTURES
ComponentsGAG POLYPROTEINGroup-specific antigen
KeywordsVIRAL PROTEIN / CORE PROTEIN / VIRUS STRUCTURE / MEMBRANE BINDING
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 / host cell plasma membrane / proteolysis ...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 / host cell plasma membrane / proteolysis / zinc ion binding / membrane
Similarity search - Function
Immunodeficiency lentiviruses, gag gene matrix protein p17 / Retroviral Gag polyprotein, M / Retroviral M domain / 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. / DNA polymerase; domain 1 ...Immunodeficiency lentiviruses, gag gene matrix protein p17 / Retroviral Gag polyprotein, M / Retroviral M domain / 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. / DNA polymerase; domain 1 / 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 - Prague C
MethodSOLUTION NMR / distance geometry
AuthorsMcdonnell, J.M. / Fushman, D. / Cahill, S.M. / Zhou, W. / Wolven, A. / Wilson, C.B. / Nelle, T.D. / Resh, M.D. / Wills, J. / Cowburn, D.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Solution structure and dynamics of the bioactive retroviral M domain from Rous sarcoma virus
Authors: McDonnell, J.M. / Fushman, D. / Cahill, S.M. / Zhou, W. / Wolven, A. / Wilson, C.B. / Nelle, T.D. / Resh, M.D. / Wills, J. / Cowburn, D.
#1: Journal: J.Virol. / Year: 1996
Title: A Large Region within the Rous Sarcoma Virus Matrix Protein is Dispensable for Budding and Infectivity
Authors: Nelle, T.D. / Wills, J.W.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Three-Dimensional Structure of the Htlv-II Matrix Protein and Comparative Analysis of Matrix Proteins from the Different Classes of Pathogenic Human Retroviruses
Authors: Christensen, A.M. / Massiah, M.A. / Turner, B.G. / Sundquist, W.I. / Summers, M.F.
#3: Journal: Embo J. / Year: 1996
Title: The Solution Structure of the Bovine Leukaemia Virus Matrix Protein and Similarity with Lentiviral Matrix Proteins
Authors: Matthews, S. / Mikhailov, M. / Burny, A. / Roy, P.
#4: Journal: Nature / Year: 1995
Title: Crystal Structure of Siv Matrix Antigen and Implications for Virus Assembly
Authors: Rao, Z. / Belyaev, A.S. / Fry, E. / Roy, P. / Jones, I.M. / Stuart, D.I.
#5: Journal: J.Mol.Biol. / Year: 1994
Title: Three-Dimensional Structure of the Human Immunodeficiency Virus Type 1 Matrix Protein
Authors: Massiah, M.A. / Starich, M.R. / Paschall, C. / Summers, M.F. / Christensen, A.M. / Sundquist, W.I.
History
DepositionMar 2, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAG POLYPROTEIN


Theoretical massNumber of molelcules
Total (without water)9,1801
Polymers9,1801
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 / 1000LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein GAG POLYPROTEIN / Group-specific antigen


Mass: 9179.745 Da / Num. of mol.: 1 / Fragment: M-DOMAIN / Mutation: M1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus - Prague C / Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: PRAGUE C / Cell line: BL21 / Gene: GAG / Plasmid: PATV-8 / Species (production host): Escherichia coli / Gene (production host): GAG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03322

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N)HSQC
121(1H-13C)HSQC
131HSQC-J
1412D AND 3D 15N-NOESY-HMQC AND TOCSY-HMQC
15113C-NOESY-HMQC
161(H)CCH-TOCSY
171HNCA
181HN(CO)CA
191CBCANH
1101CBCA(CO)NH
1111(1H)15N-NOE
1121H2O-SELECTIVE 15N-EDITED NOESY AND ROESY
1131HYDROGEN-DEUTERIUM EXCHANGE
NMR detailsText: COORDINATES WERE CALCULATED FROM SOLUTION NMR DATA USING THE PROGRAM DYANA.

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Sample preparation

DetailsContents: H20
Sample conditionsIonic strength: 100 mM / pH: 6.0 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX500 / Manufacturer: Bruker / Model: DMX500 / Field strength: 500 MHz

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Processing

Software
NameClassification
DYANAmodel building
XWINNMRmodel building
DYANArefinement
XWINNMRrefinement
NMR software
NameVersionDeveloperClassification
DYANAGUNTERT,WUTHRICHrefinement
XwinNMRstructure solution
XEASYstructure solution
DIANAstructure solution
DYANAstructure solution
THE ECEPP LIBRARY WAS USEDUSEDstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: STRUCTURES WERE CALCULATED USING THE DISTANCE GEOMETRY PROGRAM DYANA. NO FURTHER REFINEMENT WAS PERFORMED. AN ANALYSIS OF THE QUALITY OF STRUCTURES PRODUCED WAS CARRIED OUT USING PROCHECK-NMR.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 1000 / Conformers submitted total number: 20

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