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- PDB-8t5b: HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Co... -

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Basic information

Entry
Database: PDB / ID: 8t5b
TitleHIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor EKC-110
Components(Integrase) x 2
KeywordsVIRAL PROTEIN / Integrase
Function / homology
Function and homology information


telomerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...telomerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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
Chem-QD6 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
C: Integrase
D: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1838
Polymers47,1724
Non-polymers1,0114
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.954, 69.984, 63.858
Angle α, β, γ (deg.)90.00, 100.73, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 57 through 68 or (resid 69...
d_2ens_1(chain "B" and (resid 57 through 86 or resid 88...
d_1ens_2(chain "C" and (resid 221 through 223 or resid 225 through 268 or resid 270 through 276))
d_2ens_2(chain "D" and (resid 221 through 223 or resid 225...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERALAALAAA57 - 861 - 30
d_12ens_1VALVALGLYGLYAA88 - 10632 - 50
d_13ens_1TRPTRPGLYGLYAA108 - 14052 - 84
d_14ens_1GLYGLYALAALAAA149 - 16993 - 113
d_15ens_1HISHISTHRTHRAA171 - 210115 - 154
d_16ens_1QD6QD6QD6QD6AE301
d_21ens_1SERSERALAALABB57 - 861 - 30
d_22ens_1VALVALGLYGLYBB88 - 10632 - 50
d_23ens_1TRPTRPGLYGLYBB108 - 14052 - 84
d_24ens_1GLYGLYALAALABB149 - 16993 - 113
d_25ens_1HISHISTHRTHRBB171 - 210115 - 154
d_26ens_1QD6QD6QD6QD6BG301
d_11ens_2GLNGLNPHEPHECC221 - 2231 - 3
d_12ens_2VALVALILEILECC225 - 2685 - 48
d_13ens_2ASPASPALAALACC270 - 27650 - 56
d_21ens_2GLNGLNPHEPHEDD221 - 2231 - 3
d_22ens_2VALVALILEILEDD225 - 2685 - 48
d_23ens_2ASPASPALAALADD270 - 27650 - 56

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.215191036733, 0.00523971019743, -0.97655791592), (-0.00687015924213, -0.999952738192, -0.00687912016233), (-0.976547806624, 0.00818943339108, -0.215144868772)21.5300101429, 9.42042970047, 26.7274012227
2given(0.196085353563, -0.00108179402297, -0.98058623478), (0.0324263923429, -0.999445330766, 0.00758682340071), (-0.980050541144, -0.033284538924, -0.195941512373)21.1136409915, 9.46168895408, 26.7849118389

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Components

#1: Protein Integrase / IN


Mass: 17011.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: Protein Integrase / IN


Mass: 6574.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#3: 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.: 2 / Source method: obtained synthetically / Formula: C26H29ClN4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% (wt/vol) PEG 8,000, 20% ethylene glycol, 30 mM MgCl2, 30 mM CaCl2, and 0.1 M imidazole-MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9774 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.08→46.72 Å / Num. obs: 31574 / % possible obs: 97.17 % / Redundancy: 1.9 % / Biso Wilson estimate: 35.79 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.06936 / Rpim(I) all: 0.06936 / Rrim(I) all: 0.09809 / Net I/σ(I): 6.22
Reflection shellResolution: 2.08→2.154 Å / Rmerge(I) obs: 0.9956 / Mean I/σ(I) obs: 0.52 / Num. unique obs: 2807 / CC1/2: 0.32 / CC star: 0.696 / Rpim(I) all: 0.9956 / Rrim(I) all: 1.408 / % possible all: 84.72

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A1Q

8a1q


Resolution: 2.08→46.72 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 1998 6.35 %
Rwork0.24 --
obs0.2416 31455 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 2 82 3348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033384
X-RAY DIFFRACTIONf_angle_d0.6034579
X-RAY DIFFRACTIONf_dihedral_angle_d14.5921240
X-RAY DIFFRACTIONf_chiral_restr0.046496
X-RAY DIFFRACTIONf_plane_restr0.007576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.40441170.36891794X-RAY DIFFRACTION83
2.13-2.190.33981291981X-RAY DIFFRACTION92
2.19-2.250.42361340.39311993X-RAY DIFFRACTION93
2.25-2.330.3511500.30782090X-RAY DIFFRACTION98
2.33-2.410.32721420.27742130X-RAY DIFFRACTION99
2.41-2.510.29791460.26622144X-RAY DIFFRACTION100
2.51-2.620.29051460.24432165X-RAY DIFFRACTION100
2.62-2.760.26921470.25382152X-RAY DIFFRACTION100
2.76-2.930.28631510.2492157X-RAY DIFFRACTION100
2.93-3.160.24061380.22742163X-RAY DIFFRACTION100
3.16-3.480.23591460.2162172X-RAY DIFFRACTION100
3.48-3.980.25171490.20592139X-RAY DIFFRACTION99
3.98-5.010.20451540.19532177X-RAY DIFFRACTION100
5.01-46.720.26741490.24272200X-RAY DIFFRACTION99

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