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- PDB-7ue1: HIV-1 Integrase Catalytic Core Domain Mutant (KGD) in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 7ue1
TitleHIV-1 Integrase Catalytic Core Domain Mutant (KGD) in Complex with Inhibitor GRL-142
ComponentsIntegrase
KeywordsVIRAL PROTEIN / Inhibitor
Function / homology
Function and homology information


DNA integration / RNA stem-loop binding / RNA-directed DNA polymerase activity / 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-7OA / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAoki, M. / Aoki-Ogata, H. / Bulut, H. / Hayashi, H. / Davis, D. / Hasegawa, K. / Yarchoan, R. / Ghosh, A.K. / Pau, A.K. / Mitsuya, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Sci Adv / Year: 2023
Title: GRL-142 binds to and impairs HIV-1 integrase nuclear localization signal and potently suppresses highly INSTI-resistant HIV-1 variants.
Authors: Aoki, M. / Aoki-Ogata, H. / Bulut, H. / Hayashi, H. / Takamune, N. / Kishimoto, N. / Tanaka, H. / Higashi-Kuwata, N. / Hattori, S.I. / Das, D. / Venkateswara Rao, K. / Iwama, K. / Davis, D.A. ...Authors: Aoki, M. / Aoki-Ogata, H. / Bulut, H. / Hayashi, H. / Takamune, N. / Kishimoto, N. / Tanaka, H. / Higashi-Kuwata, N. / Hattori, S.I. / Das, D. / Venkateswara Rao, K. / Iwama, K. / Davis, D.A. / Hasegawa, K. / Murayama, K. / Yarchoan, R. / Ghosh, A.K. / Pau, A.K. / Machida, S. / Misumi, S. / Mitsuya, H.
History
DepositionMar 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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 / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1444
Polymers36,3412
Non-polymers8032
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-25 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.368, 111.368, 137.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-302-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 57 through 187 or resid 193 through 208))
21(chain B and (resid 57 through 138 or resid 151 through 208))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERARGARG(chain A and (resid 57 through 187 or resid 193 through 208))AA57 - 18711 - 141
12GLYGLYLEULEU(chain A and (resid 57 through 187 or resid 193 through 208))AA193 - 208147 - 162
21SERSERGLUGLU(chain B and (resid 57 through 138 or resid 151 through 208))BB57 - 13811 - 92
22VALVALLEULEU(chain B and (resid 57 through 138 or resid 151 through 208))BB151 - 208105 - 162

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Components

#1: Protein Integrase


Mass: 18170.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YUI7
#2: Chemical ChemComp-7OA / (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate


Mass: 706.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40F2N4O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestY

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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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 8.5, 2% polyethylene glycol (PEG) 400, and 2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→86.49 Å / Num. obs: 8978 / % possible obs: 99.81 % / Redundancy: 14.07 % / Biso Wilson estimate: 89.87 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 15.86
Reflection shellResolution: 3→3.05 Å / Redundancy: 13.52 % / Rmerge(I) obs: 1.307 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 875 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L3U

3l3u


Resolution: 3→86.49 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3174 420 4.69 %RANDOM
Rwork0.2233 8541 --
obs0.2274 8961 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 524.18 Å2 / Biso mean: 112.4495 Å2 / Biso min: 45.1 Å2
Refinement stepCycle: final / Resolution: 3→86.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 93 0 2317
Biso mean--119.39 --
Num. residues----288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A800X-RAY DIFFRACTION12.664TORSIONAL
12B800X-RAY DIFFRACTION12.664TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3-3.430.42041430.341327732916
3.43-4.330.31681450.22828032948
4.33-86.490.28831320.19529653097

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