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- PDB-6wap: Atomic-Resolution Structure of HIV-1 Capsid Tubes by Magic Angle ... -

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Basic information

Entry
Database: PDB / ID: 6wap
TitleAtomic-Resolution Structure of HIV-1 Capsid Tubes by Magic Angle Spinning NMR
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / magic angle spinning NMR / HIV-1 capsid / CA protein assemblies / HIV-AIDS
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding ...viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) ...Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodSOLID-STATE NMR / simulated annealing
AuthorsLu, M. / Russell, R.W. / Bryer, A. / Quinn, C.M. / Hou, G. / Zhang, H. / Schwieters, C.D. / Perilla, J.R. / Gronenborn, A.M. / Polenova, T.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50AI1504817 United States
National Science Foundation (NSF, United States)CHE0959496 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110758 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD012213 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR.
Authors: Lu, M. / Russell, R.W. / Bryer, A.J. / Quinn, C.M. / Hou, G. / Zhang, H. / Schwieters, C.D. / Perilla, J.R. / Gronenborn, A.M. / Polenova, T.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 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 1.3May 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

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Assembly

Deposited unit
A: HIV-1 capsid protein


Theoretical massNumber of molelcules
Total (without water)25,6301
Polymers25,6301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein HIV-1 capsid protein


Mass: 25630.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: Gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P12493

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1Exp1 CORD50ms
121isotropic2Exp2 CORD500ms
131isotropic4Exp3 DARR50ms
141isotropic1Exp4 NCA
151isotropic4Exp5 NCA
161isotropic1Exp6 NCACX
171isotropic4Exp7 NCACX
181isotropic1Exp8 NCOCX
191isotropic2Exp9 NCOCX3d
1101isotropic2Exp10 CONCA3d
1111isotropic4Exp11 NCACX3d
1121isotropic4Exp12 NCOCX3d
1132isotropic1Exp13 CORD10ms
1142isotropic1Exp14 CORD20ms
1152isotropic1Exp15 CORD50ms
1162isotropic1Exp16 CORD100ms
1172isotropic1Exp17 CORD200ms
1182isotropic1Exp18 CORD300ms
1192isotropic1Exp19 CORD400ms
1202isotropic1Exp20 CORD500ms
1212isotropic2Exp21 CORD500ms
1222isotropic1Exp22 NCACX
1233isotropic3Exp23 CORD25ms
1243isotropic3Exp24 CORD500ms
1253isotropic1Exp25 CORD500ms
1263isotropic1Exp26 PAINCP
1274isotropic2Exp27 CORD25ms
1285isotropic2Exp28 R211
1295isotropic2Exp29 REDOR1ms
1305isotropic2Exp30 REDOR1.6ms
1315isotropic2Exp31 REDOR2ms
1326isotropic1Exp32 CORD50ms
1336isotropic1Exp33 PDSD1s
1347isotropic1Exp34 CORD50ms
1358isotropic2Exp35 CORD500ms
1369isotropic1Exp36 NHHC3ms
1379isotropic1Exp37 NHHC5ms

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
gel solid1100 % [U-13C; U-15N] HIV-1 capsid protein, solidU-13C,15N-CAsolid
gel solid2100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein, solid1,6-13C-Glu,U-15N-CAsolid
gel solid3100 % [2-13C]-Glucose,U-15N HIV-1 capsid protein, solid2-13C-Glu,U-15N-CAsolid
gel solid4100 % 13C,15N-His HIV-1 capsid protein, solid13C,15N-His-CAsolid
gel solid5100 % 13C,15N-Tyr HIV-1 capsid protein, solid13C,15N-Tyr-CAsolid
gel solid650 % 13C,15N-Ala HIV-1 capsid protein, 50 % 13C,15N-Ile HIV-1 capsid protein, solidmixed-Ala/Ile-CAsolid
gel solid750 % 13C,15N-Ala HIV-1 capsid protein, 50 % 13C,15N-Val HIV-1 capsid protein, solidmixed-Ala/Val-CAsolid
gel solid886 % HIV-1 capsid protein, 14 % U-13C,15N-CA HIV-1 capsid protein, solidDiluted-CAsolid
gel solid950 % [U-13C] HIV-1 capsid protein, 50 % [U-15N] HIV-1 capsid protein, solidmixed-13C/15N-CAsolid
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 %HIV-1 capsid protein[U-13C; U-15N]1
100 %HIV-1 capsid protein[1,6-13C]-Glucose,U-15N2
100 %HIV-1 capsid protein[2-13C]-Glucose,U-15N3
100 %HIV-1 capsid protein13C,15N-His4
100 %HIV-1 capsid protein13C,15N-Tyr5
50 %13C,15N-Ala HIV-1 capsid protein13C,15N-Ala6
50 %13C,15N-Ile HIV-1 capsid protein13C,15N-Ile6
50 %13C,15N-Ala HIV-1 capsid protein13C,15N-Ala7
50 %13C,15N-Val HIV-1 capsid protein13C,15N-Val7
86 %HIV-1 capsid proteinnatural abundance8
14 %U-13C,15N-CA HIV-1 capsid proteinU-13C,15N-CA8
50 %[U-13C] HIV-1 capsid protein[U-13C]9
50 %[U-15N] HIV-1 capsid protein[U-15N]9
Sample conditionsIonic strength: 2.4 M / Label: tubes / pH: 6 / Pressure: 1 atm / Temperature: 277 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III5003
NHMFL NHMFLNHMFLNHMFL9004

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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