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- PDB-8ct5: Catalytic Core Domain of HIV-1 Integrase (F185K) -

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Basic information

Entry
Database: PDB / ID: 8ct5
TitleCatalytic Core Domain of HIV-1 Integrase (F185K)
ComponentsIntegrase
KeywordsVIRAL PROTEIN / VIRAL DNA INTEGRATION / DNA BINDING / LEDGF BINDING
Function / homology
Function and homology information


exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsGupta, K. / Van Duyne, G.D. / Eilers, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 AI 052845 United States
CitationJournal: Plos Pathog. / Year: 2023
Title: Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 angstrom resolution: Routes to inhibitor optimization.
Authors: Eilers, G. / Gupta, K. / Allen, A. / Montermoso, S. / Murali, H. / Sharp, R. / Hwang, Y. / Bushman, F.D. / Van Duyne, G.
History
DepositionMay 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2785
Polymers17,8941
Non-polymers3844
Water59433
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,55710
Polymers35,7882
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area4320 Å2
ΔGint-128 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.973, 72.973, 66.097
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
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: 17894.152 Da / Num. of mol.: 1 / Mutation: F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Variant: F185K / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72498
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7% PEG 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5, 5 mM manganese chloride, 5 mM magnesium chloride, and 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.97→29.3 Å / Num. obs: 14661 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 37.8 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.018 / Rpim(I) all: 0.018 / Rrim(I) all: 0.026 / Net I/σ(I): 27.3
Reflection shellResolution: 1.97→2.044 Å / Redundancy: 2 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1422 / CC1/2: 0.942 / CC star: 0.985 / Rpim(I) all: 0.151 / Rrim(I) all: 0.213 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L3U

3l3u


Resolution: 1.97→29.3 Å / SU B: 6.454 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23648 1460 10 %RANDOM
Rwork0.20069 ---
obs0.20435 13200 99.8 %-
Displacement parametersBiso mean: 50.797 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å2-0 Å2
2---0.12 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.97→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 20 33 1166

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