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- PDB-8d3s: HIV-1 Integrase Catalytic Core Domain F185H Mutant Complexed with... -

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Basic information

Entry
Database: PDB / ID: 8d3s
TitleHIV-1 Integrase Catalytic Core Domain F185H Mutant Complexed with BKC-110
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
Ribonuclease H-like superfamily/Ribonuclease H / 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 ...Ribonuclease H-like superfamily/Ribonuclease H / 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. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-QD6 / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 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
DepositionJun 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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)18,4022
Polymers17,9211
Non-polymers4811
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.514, 72.514, 66.205
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-492-

HOH

21A-504-

HOH

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Components

#1: Protein Integrase


Mass: 17921.447 Da / Num. of mol.: 1 / Mutation: F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q76353
#2: Chemical ChemComp-QD6 / (2S)-tert-butoxy{4-(4-chlorophenyl)-2,6-dimethyl-1-[(1-methyl-1H-pyrazol-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-5-yl}acetic acid


Mass: 480.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29ClN4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M ammonium sulfate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 10% PEG8000, 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: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 21, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.84→45.56 Å / Num. obs: 17271 / % possible obs: 83.52 % / Redundancy: 8.8 % / Biso Wilson estimate: 29.75 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07834 / Rpim(I) all: 0.02764 / Rrim(I) all: 0.08324 / Net I/σ(I): 14.77
Reflection shellResolution: 1.84→1.921 Å / Rmerge(I) obs: 1.328 / Mean I/σ(I) obs: 0.74 / Num. unique obs: 240 / CC1/2: 0.773 / CC star: 0.934 / Rpim(I) all: 0.6903 / % possible all: 13.78

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6nuj

6nuj


Resolution: 1.84→45.56 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2736 1449 9.95 %
Rwork0.2437 13110 -
obs0.2467 14559 81.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.74 Å2 / Biso mean: 42.4886 Å2 / Biso min: 14.72 Å2
Refinement stepCycle: final / Resolution: 1.84→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 62 115 1205
Biso mean--37.86 34.77 -
Num. residues----132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.910.7575180.48751291478
1.91-1.980.4687570.491455060735
1.98-2.070.34521380.28891266140479
2.07-2.180.30971790.267115771756100
2.18-2.320.5241570.43131425158290
2.32-2.50.27361830.253616121795100
2.5-2.750.28871770.242315901767100
2.75-3.140.27531770.223616341811100
3.15-3.960.24291730.198816291802100
3.96-45.560.22161900.224516981888100
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)
11.84250.4014-0.54380.29-0.27891.50070.123-0.9495-0.19230.3304-0.21130.0388-0.1040.254-0.02520.02920.0722-0.09970.1427-0.04490.209723.9923-29.1184-12.4382
20.14380.0816-0.02350.0279-0.01780.2652-0.1222-0.2190.22560.0332-0.0819-0.0797-0.17180.29570.00010.2528-0.02940.00020.3354-0.01530.258630.384-24.9984-20.3636
32.24580.11130.89440.43770.30860.82610.269-1.43890.11910.343-0.1490.20340.1664-0.64580.09180.13490.06730.06990.363-0.13090.22212.8151-29.7774-10.6036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 93 )A56 - 93
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 153 )A94 - 153
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 208 )A154 - 208

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