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- PDB-8t52: HIV-1 Integrase Catalytic Core Domain (CCD) F185H/Y99H/A128T Muta... -

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Basic information

Entry
Database: PDB / ID: 8t52
TitleHIV-1 Integrase Catalytic Core Domain (CCD) F185H/Y99H/A128T Mutant Complexed with EKC-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
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-QD6 / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 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 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _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)19,3832
Polymers18,9021
Non-polymers4811
Water79344
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7654
Polymers37,8032
Non-polymers9622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area3520 Å2
ΔGint-17 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.243, 72.243, 66.423
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: 18901.572 Da / Num. of mol.: 1 / Mutation: F185H, Y99H, A128T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2WR52
#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.: 44 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
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: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.07→31.73 Å / Num. obs: 11041 / % possible obs: 87.16 % / Redundancy: 1.9 % / Biso Wilson estimate: 27.21 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02927 / Rpim(I) all: 0.02927 / Rrim(I) all: 0.0414 / Net I/σ(I): 28.93
Reflection shellResolution: 2.07→2.149 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.5911 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 284 / CC1/2: 0.365 / CC star: 0.731 / Rpim(I) all: 0.5911 / Rrim(I) all: 0.8359 / % possible all: 22.95

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8D3S

8d3s


Resolution: 2.07→31.73 Å / SU ML: 0.4035 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.6501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3141 1104 10.15 %
Rwork0.2637 9777 -
obs0.2688 10881 87.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.93 Å2
Refinement stepCycle: LAST / Resolution: 2.07→31.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 34 44 1106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341085
X-RAY DIFFRACTIONf_angle_d0.61081475
X-RAY DIFFRACTIONf_chiral_restr0.0422167
X-RAY DIFFRACTIONf_plane_restr0.0034179
X-RAY DIFFRACTIONf_dihedral_angle_d11.7795374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.170.3613450.3586380X-RAY DIFFRACTION28.03
2.17-2.280.50241120.4747947X-RAY DIFFRACTION68.28
2.28-2.430.32781530.29931363X-RAY DIFFRACTION99.67
2.43-2.610.3221560.2711388X-RAY DIFFRACTION99.94
2.61-2.880.32151580.26611396X-RAY DIFFRACTION100
2.88-3.290.31021610.25241402X-RAY DIFFRACTION100
3.29-4.150.27581560.23741417X-RAY DIFFRACTION99.68
4.15-31.730.29711630.23491484X-RAY DIFFRACTION100

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