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- PDB-7snl: Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhi... -

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Entry
Database: PDB / ID: 7snl
TitleDisulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor N-(1-(3-(4-chloro-1-methyl-3-(methylsulfonamido)-1H-indazol-7-yl)-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl)-2-(3,5-difluorophenyl)ethyl)-2-(3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl)acetamide
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / 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
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / 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 ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-9VI / IODIDE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsBester, S.M. / Kvaratskhelia, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI157802 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54-AI150472 United States
CitationJournal: To Be Published
Title: Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor N-(1-(3-(4-chloro-1-methyl-3-(methylsulfonamido)-1H-indazol-7-yl)-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl)-2-(3,5- ...Title: Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor N-(1-(3-(4-chloro-1-methyl-3-(methylsulfonamido)-1H-indazol-7-yl)-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl)-2-(3,5-difluorophenyl)ethyl)-2-(3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl)acetamide
Authors: Adu-Ampratwum, D. / Haney, R. / Bester, S.M. / Annamalai, A.S. / Wei, G. / Fuchs, J.R. / Kvaratskhelia, M.
History
DepositionOct 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,00513
Polymers25,4611
Non-polymers1,54412
Water2,198122
1
A: Capsid protein p24
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)162,03178
Polymers152,7686
Non-polymers9,26472
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area25110 Å2
ΔGint-573 kcal/mol
Surface area57620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.260, 92.260, 57.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z

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Components

#1: Protein Capsid protein p24 / CA


Mass: 25461.271 Da / Num. of mol.: 1 / Mutation: A14C, E45C, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03366
#2: Chemical ChemComp-9VI / N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-methyl-1H-indazol-7-yl}-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-6,7-dihydro-1H-indazol-1-yl]acetamide


Mass: 788.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H27ClF5N9O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M NaI, 9% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→46.93 Å / Num. obs: 11261 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 31.21 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.2
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1120 / CC1/2: 0.532 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VKV

6vkv


Resolution: 2.39→46.93 Å / SU ML: 0.291 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261 574 5.1 %
Rwork0.2426 10685 -
obs0.2436 11259 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.67 Å2
Refinement stepCycle: LAST / Resolution: 2.39→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 65 122 1801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261710
X-RAY DIFFRACTIONf_angle_d0.51782335
X-RAY DIFFRACTIONf_chiral_restr0.0374254
X-RAY DIFFRACTIONf_plane_restr0.0039297
X-RAY DIFFRACTIONf_dihedral_angle_d14.086632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.630.35711270.30612666X-RAY DIFFRACTION99.89
2.63-3.010.31071540.26742649X-RAY DIFFRACTION100
3.01-3.790.2381350.25132657X-RAY DIFFRACTION99.25
3.79-46.930.2321580.20742713X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.507812226791.97514897877-2.842601221772.77370938122-0.01748620826235.884253991590.0343787892293-1.09239707238-1.185442601330.365071403115-0.2023587224630.08934747772090.7121473201740.6956930081430.2019779167980.3384097310880.0187167040928-0.002127181599790.3498087687260.1222490809210.418509251075-8.563463472728.666264029433.76473075728
22.08578794255-0.4064178191120.5744870772272.277564509020.3105710808662.25208331869-0.0913070696246-0.306248591615-0.01272886791350.2243202347690.001328404292710.0928701838448-0.117617169229-0.3061098649320.09057381952660.1993459318640.0123551386309-0.01272890449920.188192505128-0.01603821741410.192258875467-20.324365804817.8732618712-6.00238882459
33.464232623710.9938496857431.137721915053.962311401270.1973611799312.436425924620.01153066750940.0465313373157-0.124923214627-0.231049188292-0.08798777308580.03253499384440.0221010185118-0.05358247974210.09879763932980.1538333097610.006729005978940.03186225851190.244270345227-0.02569516193570.206330961806-37.6185936438-5.88456374691-28.6368137136
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 16 )1 - 161 - 16
22chain 'A' and (resid 17 through 144 )17 - 14417 - 144
33chain 'A' and (resid 145 through 220 )145 - 220145 - 210

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