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- PDB-7r7q: Immature HIV-1 CACTD-SP1 lattice with Inositol hexakisphosphate (IP6) -

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Basic information

Entry
Database: PDB / ID: 7r7q
TitleImmature HIV-1 CACTD-SP1 lattice with Inositol hexakisphosphate (IP6)
ComponentsGag polyprotein
KeywordsPROTEIN BINDING / HIV-1 capsid / maturation inhibitors / HIV-AIDS
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / 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 / Retroviral matrix protein ...Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / 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 / 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.
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLID-STATE NMR / simulated annealing
AuthorsSarkar, S. / Zadrozny, K.K. / Zadorozhnyi, R. / Russell, R.W. / Quinn, C.M. / Kleinpeter, A. / Ablan, S. / Meshkin, H. / Perilla, J.R. / Ganser-Pornillos, B.K. ...Sarkar, S. / Zadrozny, K.K. / Zadorozhnyi, R. / Russell, R.W. / Quinn, C.M. / Kleinpeter, A. / Ablan, S. / Meshkin, H. / Perilla, J.R. / Ganser-Pornillos, B.K. / Pornillos, O. / Freed, E.O. / Gronenborn, A.M. / Polenova, T.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5P50AI1504817 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5P30GM110758 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5P50GM082251 United States
National Science Foundation (NSF, United States)CHE0959496 United States
National Institutes of Health/Office of the DirectorS10-OD012213 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM104316 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI129678 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of HIV-1 maturation inhibitor binding and activity.
Authors: Sarkar, S. / Zadrozny, K.K. / Zadorozhnyi, R. / Russell, R.W. / Quinn, C.M. / Kleinpeter, A. / Ablan, S. / Meshkin, H. / Perilla, J.R. / Freed, E.O. / Ganser-Pornillos, B.K. / Pornillos, O. ...Authors: Sarkar, S. / Zadrozny, K.K. / Zadorozhnyi, R. / Russell, R.W. / Quinn, C.M. / Kleinpeter, A. / Ablan, S. / Meshkin, H. / Perilla, J.R. / Freed, E.O. / Ganser-Pornillos, B.K. / Pornillos, O. / Gronenborn, A.M. / Polenova, T.
History
DepositionJun 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: 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 1.2May 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
G: Gag polyprotein
H: Gag polyprotein
I: Gag polyprotein
J: Gag polyprotein
K: Gag polyprotein
L: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2287
Polymers66,5686
Non-polymers6601
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9870 Å2
ΔGint-68 kcal/mol
Surface area32000 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
Gag polyprotein


Mass: 11094.672 Da / Num. of mol.: 6 / Mutation: P241T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72497
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D CORD 50 ms
121isotropic12D CORD 100 ms
131isotropic12D NCACX 50 ms
241isotropic12D NCACX 50 ms
151isotropic13D NCOCX 25 ms
161isotropic22D CORD 25 ms
171isotropic22D CORD 50 ms
181isotropic22D NCACX 25 ms
191isotropic22D NCOCX 25 ms
1101isotropic23D NCACX 25 ms
3111isotropic32D NCACX 25 ms
3121isotropic32D NCOCX 25 ms
5132isotropic12D CORD 50 ms
4142isotropic12D HC CP HETCOR
4152isotropic12D doubleREDOR HETCOR
4162isotropic11D 31P direct polarization
4172isotropic11D 31P cross polarization
4182isotropic11D doubleREDOR
6193isotropic12D hNH HETCOR
6203isotropic12D HC CP HETCOR
NMR detailsText: magic angle spinning

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
gel solid1400 uM [U-100% 13C; U-100% 15N] HIV-1 CACTD-SP1, 400 uM IP6, Protein bufferImmature HIV-1 CACTD-SP1 lattice with Inositol hexakisphosphate (IP6). Protein is uniformly 13C, 15N labeled, IP6 is in natural abundance form.100% [U-13C; U-15N] HIV-1 CACTD-SP1/IP6Protein buffer
gel solid2400 uM [U-100% 13C; U-100% 15N; 99.9%-2H] HIV-1 CACTD-SP1, 400 uM IP6, Protein bufferImmature HIV-1 CACTD-SP1 crystalline array with Inositol hexakisphosphate (IP6). Protein is uniformly 13C, 15N labeled, deuterium exchanged, IP6 is in natural abundance form.100% [U-13C; U-15N], 99.9%-2H HIV-1 CACTD-SP1/IP6Protein buffer
gel solid3400 uM [U-100% 13C; U-100% 15N; 99.9%-2H] HIV-1 CACTD-SP1, 400 uM IP6 S2, Protein bufferImmature HIV-1 CACTD-SP1 crystalline array with Inositol hexakisphosphate (IP6). Protein is uniformly 13C, 15N labeled, deuterium exchanged, IP6 is in natural abundance form. (IP6 was dissolved in water)100% [U-13C; U-15N], 99.9%-2H HIV-1 CACTD-SP1/IP6 S2Protein buffer
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMHIV-1 CACTD-SP1[U-100% 13C; U-100% 15N]1
400 uMIP6natural abundance1
400 uMHIV-1 CACTD-SP1[U-100% 13C; U-100% 15N; 99.9%-2H]2
400 uMIP6natural abundance2
400 uMHIV-1 CACTD-SP1[U-100% 13C; U-100% 15N; 99.9%-2H]3
400 uMIP6 S2natural abundance3
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1Immature HIV-1 CACTD-SP1 lattice with Inositol hexakisphosphate (IP6). Protein is uniformly 13C, 15N labeled, IP6 is in natural abundance form. 4 degree C.250 mM100% [U-13C; U-15N] HIV-1 CACTD-SP1/IP6 (4C)8 1 atm277.15 K
2Immature HIV-1 CACTD-SP1 lattice with Inositol hexakisphosphate (IP6). Protein is uniformly 13C, 15N labeled, IP6 is in natural abundance form. -10 degree C.250 mM100% [U-13C; U-15N] HIV-1 CACTD-SP1/IP6 (-10C)8 1 atm263.15 K
3Immature HIV-1 CACTD-SP1 lattice with Inositol hexakisphosphate (IP6). Protein is uniformly 13C, 15N labeled, IP6 is in natural abundance form. -79 degree C.250 mM100% [U-13C; U-15N] HIV-1 CACTD-SP1/IP6 (-79C)8 1 atm194.15 K
4Immature HIV-1 CACTD-SP1 crystalline array with Inositol hexakisphosphate (IP6). Protein is uniformly 13C, 15N labeled, deuterium exchanged, IP6 is in natural abundance form. 4 degree C.250 mM100% [U-13C; U-15N], 99.9%-2H HIV-1 CACTD-SP1/IP6 (4C)8 1 atm277.15 K
5Immature HIV-1 CACTD-SP1 crystalline array with Inositol hexakisphosphate (IP6). Protein is uniformly 13C, 15N labeled, deuterium exchanged, IP6 is in natural abundance form. -5 degree C.250 mM100% [U-13C; U-15N], 99.9%-2H HIV-1 CACTD-SP1/IP6 (-5C)8 1 atm268.15 K
6Immature HIV-1 CACTD-SP1 crystalline array with Inositol hexakisphosphate (IP6). Protein is uniformly 13C, 15N labeled, deuterium exchanged, IP6 is in natural abundance form. (IP6 was dissolved in water). 4 degree C.250 mM100% [U-13C; U-15N], 99.9%-2H HIV-1 CACTD-SP1/IP6 S28 1 atm277.15 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 III7503

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKY3.115Lee, Tonellli, Markleychemical shift assignment
CcpNmr Analysis2.4CCPNchemical shift assignment
NMRFAM-SPARKY3.115Lee, Tonellli and Markleydata analysis
TALOS-NShen and Baxstructure calculation
X-PLOR NIH2.53Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH2.53Schwieters, 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: 5

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