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- PDB-8s9q: HIV-1 Integrase Catalytic Core Domain (CCD) F185H Mutant Complexe... -

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Basic information

Entry
Database: PDB / ID: 8s9q
TitleHIV-1 Integrase Catalytic Core Domain (CCD) F185H Mutant Complexed with STP03-0404
ComponentsIntegrase
KeywordsVIRAL PROTEIN / Integrase
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding
Similarity search - Function
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. / Integrase core domain / Integrase, catalytic core ...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. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Chem-WBV / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsDinh, T. / Kvaratskhelia, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI143649 United States
CitationJournal: Biorxiv / Year: 2024
Title: The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir.
Authors: Dinh, T. / Tber, Z. / Rey, J.S. / Mengshetti, S. / Annamalai, A.S. / Haney, R. / Briganti, L. / Amblard, F. / Fuchs, J.R. / Cherepanov, P. / Kim, K. / Schinazi, R.F. / Perilla, J.R. / Kim, B. / Kvaratskhelia, M.
History
DepositionMar 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4162
Polymers17,9211
Non-polymers4951
Water1,20767
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8334
Polymers35,8432
Non-polymers9902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area3540 Å2
ΔGint-20 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.991, 71.991, 65.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Integrase


Mass: 17921.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76353
#2: Chemical ChemComp-WBV / (2S)-tert-butoxy{4-(4-chlorophenyl)-2,3,6-trimethyl-1-[(1-methyl-1H-pyrazol-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-5-yl}acetic acid / Pirmitegravir


Mass: 495.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31ClN4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M (NH4)2SO4, 0.1 M sodium cacodylate (pH = 6.5), 10% PEG 8000, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.26→31.59 Å / Num. obs: 9580 / % possible obs: 99.94 % / Redundancy: 20 % / Biso Wilson estimate: 36.03 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.05948 / Rrim(I) all: 0.2942 / Net I/σ(I): 8.67
Reflection shellResolution: 2.26→2.341 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 0.82 / Num. unique obs: 941 / CC1/2: 0.506 / CC star: 0.82 / Rpim(I) all: 0.5318 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NUJ

6nuj


Resolution: 2.26→31.59 Å / SU ML: 0.2927 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2931 946 9.87 %
Rwork0.2552 8634 -
obs0.2588 9580 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.19 Å2
Refinement stepCycle: LAST / Resolution: 2.26→31.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 35 67 1130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021086
X-RAY DIFFRACTIONf_angle_d0.39931477
X-RAY DIFFRACTIONf_chiral_restr0.0404166
X-RAY DIFFRACTIONf_plane_restr0.0015179
X-RAY DIFFRACTIONf_dihedral_angle_d13.108374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.380.29941350.29071204X-RAY DIFFRACTION99.85
2.38-2.530.30141330.27961204X-RAY DIFFRACTION100
2.53-2.720.33461380.28761225X-RAY DIFFRACTION100
2.72-30.27491300.2521224X-RAY DIFFRACTION100
3-3.430.29411330.25141228X-RAY DIFFRACTION99.93
3.43-4.310.27491330.22241236X-RAY DIFFRACTION100
4.32-31.590.29821440.26311313X-RAY DIFFRACTION100

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