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- PDB-9ona: Immature HIV-1 CACTD-SP1 lattice with Maturation inhibitor PF-463... -

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Basic information

Entry
Database: PDB / ID: 9ona
TitleImmature HIV-1 CACTD-SP1 lattice with Maturation inhibitor PF-46396 (S) and Inositol hexakisphosphate (IP6)
ComponentsCapsid protein p24
KeywordsPROTEIN BINDING / HIV-1 / maturation inhibitors / PF-46396
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / INOSITOL HEXAKISPHOSPHATE / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodSOLID-STATE NMR / simulated annealing
AuthorsZadorozhnyi, R. / Quinn, C.M. / Zadrozny, K.K. / Ablan, S.D. / Kennedy, B.J. / Yap, G.P.A. / Sanner, D. / Kraml, C. / Freed, E.O. / Ganser-Pornillos, B.K. ...Zadorozhnyi, R. / Quinn, C.M. / Zadrozny, K.K. / Ablan, S.D. / Kennedy, B.J. / Yap, G.P.A. / Sanner, D. / Kraml, C. / Freed, E.O. / Ganser-Pornillos, B.K. / Pornillos, O. / Gronenborn, A.M. / Polenova, T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U54AI170791 United States
National Science Foundation (NSF, United States)CHE0959496 United States
National Institutes of Health/Office of the DirectorS10-OD026896A United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structural Basis for HIV-1 Maturation Inhibition by PF-46396 Determined by MAS NMR.
Authors: Zadorozhnyi, R. / Quinn, C.M. / Zadrozny, K.K. / Ablan, S.D. / Kennedy, B.J. / Yap, G.P.A. / Sanner, D. / Kraml, C. / Freed, E.O. / Ganser-Pornillos, B.K. / Pornillos, O. / Gronenborn, A.M. / Polenova, T.
History
DepositionMay 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
J: Capsid protein p24
K: Capsid protein p24
L: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6838
Polymers66,5686
Non-polymers1,1152
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
Capsid protein p24 / Pr160Gag-Pol


Mass: 11094.672 Da / Num. of mol.: 6 / Fragment: residues 278-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12497
#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
#3: Chemical ChemComp-A1CCZ / 1-{(2S)-2-(4-tert-butylphenyl)-2-[(2,3-dihydro-1H-inden-2-yl)amino]ethyl}-3-(trifluoromethyl)pyridin-2(1H)-one


Mass: 454.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29F3N2O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D CORD 50 ms
121isotropic12D CORD 50 ms
131isotropic22D CORD 100 ms
141isotropic22D CORD 250 ms
151isotropic22D CORD 500 ms
161isotropic22D NCACX 50 ms
171isotropic22D PAIN-CP
281isotropic31D 19F-13C TEDOR
391isotropic22D hNH dREDOR-HETCOR
3101isotropic22D 1H-1H RFDR-dREDOR
4111isotropic11D 1H-31P CP
4121isotropic11D 1H-31P direct
4131isotropic12D 1H-31P HETCOR
5142isotropic12D 1H-13C HETCOR
4152isotropic12D 1H-13C HETCOR
1163isotropic22D CORD 50 ms
1173isotropic22D CORD 500 ms
4183isotropic12D 1H-31P HETCOR
4193isotropic11D 1H-31P direct
4203isotropic11D 1H-31P CP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solid1400 uM [U-100% 13C; U-100% 15N] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (racemic), 400 uM INOSITOL HEXAKISPHOSPHATE, protein bufferU-13C,15N HIV-1 CACTD-SP1/PF-46396(racem)/IP6protein buffer
solid2400 uM [U-13C; U-15N; U-2H] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (racemic), 400 uM INOSITOL HEXAKISPHOSPHATE, protein bufferFD-13C,15N HIV-1 CACTD-SP1/PF-46396(racem)/IP6protein buffer
solid3400 uM [U-100% 13C; U-100% 15N] HIV-1 capsid C-terminal domain, 360 uM PF-46396 (S), 400 uM INOSITOL HEXAKISPHOSPHATE, protein bufferU-13C,15N HIV-1 CACTD-SP1/PF-46396(S)/IP6protein buffer
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMHIV-1 capsid C-terminal domain[U-100% 13C; U-100% 15N]1
360 uMPF-46396 (racemic)natural abundance1
400 uMINOSITOL HEXAKISPHOSPHATEnatural abundance1
400 uMHIV-1 capsid C-terminal domain[U-13C; U-15N; U-2H]2
360 uMPF-46396 (racemic)natural abundance2
400 uMINOSITOL HEXAKISPHOSPHATEnatural abundance2
400 uMHIV-1 capsid C-terminal domain[U-100% 13C; U-100% 15N]3
360 uMPF-46396 (S)natural abundance3
400 uMINOSITOL HEXAKISPHOSPHATEnatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1250 mM4C81 atm277 K
2250 mM37C81 atm310 K
3250 mM33C81 atm306 K
4250 mM15C81 atm288 K
5250 mM-10C81 atm263 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE III HDBrukerAVANCE III HD6002
Bruker AVANCE IIIBrukerAVANCE III5003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKYLee, Tonelli and Markleychemical shift assignment
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
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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