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- PDB-6wa4: Solution NMR structure of the unmyristoylated feline immunodefici... -

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Basic information

Entry
Database: PDB / ID: 6wa4
TitleSolution NMR structure of the unmyristoylated feline immunodeficiency virus matrix protein
ComponentsMatrix protein
KeywordsVIRAL PROTEIN / FIV
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / viral capsid / viral nucleocapsid / nucleic acid binding / structural constituent of virion / zinc ion binding
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Gag polyprotein / GAG protein
Similarity search - Component
Biological speciesFeline immunodeficiency virus
MethodSOLUTION NMR / na
AuthorsBrown, J.B. / Summers, H.R. / Brown, L.A. / Marchant, J. / Canova, P.N. / O'Hern, C.T. / Abbott, S.T. / Nyaunu, C. / Maxwell, S. / Johnson, T. ...Brown, J.B. / Summers, H.R. / Brown, L.A. / Marchant, J. / Canova, P.N. / O'Hern, C.T. / Abbott, S.T. / Nyaunu, C. / Maxwell, S. / Johnson, T. / Moser, M.B. / Carter, H. / Ablan, S. / Freed, E.O. / Summers, M.F.
Funding support United States, 9items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM066706 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM042561 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)IMSD R25 GM-055036-18 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM103297 United States
National Science Foundation (NSF, United States)DGE-1144243 United States
National Science Foundation (NSF, United States)1460653 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 AI30917 United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural and Mechanistic Studies of the Rare Myristoylation Signal of the Feline Immunodeficiency Virus.
Authors: Brown, J.B. / Summers, H.R. / Brown, L.A. / Marchant, J. / Canova, P.N. / O'Hern, C.T. / Abbott, S.T. / Nyaunu, C. / Maxwell, S. / Johnson, T. / Moser, M.B. / Ablan, S.D. / Carter, H. / ...Authors: Brown, J.B. / Summers, H.R. / Brown, L.A. / Marchant, J. / Canova, P.N. / O'Hern, C.T. / Abbott, S.T. / Nyaunu, C. / Maxwell, S. / Johnson, T. / Moser, M.B. / Ablan, S.D. / Carter, H. / Freed, E.O. / Summers, M.F.
History
DepositionMar 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein


Theoretical massNumber of molelcules
Total (without water)13,9881
Polymers13,9881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 160target function
RepresentativeModel #1target function

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Components

#1: Protein Matrix protein / MA


Mass: 13988.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus / Gene: GAG / Production host: Escherichia coli (E. coli) / References: UniProt: Q66971, UniProt: P16087*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
212isotropic12D 1H-1H NOESY
422isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
341isotropic12D 1H-15N HSQC
3111isotropic22D 1H-15N HSQC
153isotropic13D CBCA(CO)NH
3103isotropic13D CBCA(CO)NH
193isotropic13D HN(CA)CB
383isotropic13D HN(CA)CB
173isotropic13D HNCO
363isotropic13D HNCO
1203isotropic13D HN(CA)CO
3193isotropic13D HN(CA)CO
1181isotropic13D 1H-15N NOESY
3171isotropic23D 1H-15N NOESY
1163isotropic14D HSQC-NOESY-HMQC
2154isotropic14D HMQC-NOESY-HMQC
2144isotropic12D 1H-13 HMQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution150 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O1H/15N90% H2O/10% D2O
solution450 mM sodium phosphate, 10 mM [U-98% 2H] DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L ammonium chloride, 300 uM [U-13C] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 100% D2O1H/13C100% D2O
solution350 mM sodium phosphate, 10 mM DTT, 5 mM sodium chloride, 4 g/L [U-99% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-13C; U-15N] Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 90% H2O/10% D2O1H/15N/13C90% H2O/10% D2O
solution250 mM sodium phosphate, 10 mM [U-98% 2H] DTT, 5 mM sodium chloride, 300 uM Unmyristoylated Feline Immunodeficiency Virus Matrix Protein, 100% D2O1H100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphatenatural abundance1
10 mMDTTnatural abundance1
5 mMsodium chloridenatural abundance1
4 g/Lglucosenatural abundance1
1 g/Lammonium chloride[U-99% 15N]1
300 uMUnmyristoylated Feline Immunodeficiency Virus Matrix Protein[U-15N]1
50 mMsodium phosphatenatural abundance4
10 mMDTT[U-98% 2H]4
5 mMsodium chloridenatural abundance4
4 g/Lglucose[U-99% 13C]4
1 g/Lammonium chloridenatural abundance4
300 uMUnmyristoylated Feline Immunodeficiency Virus Matrix Protein[U-13C]4
50 mMsodium phosphatenatural abundance3
10 mMDTTnatural abundance3
5 mMsodium chloridenatural abundance3
4 g/Lglucose[U-99% 13C]3
1 g/Lammonium chloride[U-99% 15N]3
300 uMUnmyristoylated Feline Immunodeficiency Virus Matrix Protein[U-13C; U-15N]3
50 mMsodium phosphatenatural abundance2
10 mMDTT[U-98% 2H]2
5 mMsodium chloridenatural abundance2
300 uMUnmyristoylated Feline Immunodeficiency Virus Matrix Proteinnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
15 mMconditions_18 1 atm298 K
25 mMconditions_28 pD1 atm298 K
35 mMconditions_35 1 atm298 K
45 mMconditions_45 pD1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRFxJohnson, One Moon Scientificprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: na / Software ordinal: 8
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 160 / Conformers submitted total number: 20

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