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- PDB-8cta: Minimal 2:2 Ternary Complex between BI-224436 bound HIV-1 Integra... -

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Basic information

Entry
Database: PDB / ID: 8cta
TitleMinimal 2:2 Ternary Complex between BI-224436 bound HIV-1 Integrase Catalytic Core Domain Dimer and Carboxy Terminal Domains
Components(Integrase) x 2
KeywordsVIRAL PROTEIN / VIRAL DNA INTEGRATION / DNA BINDING / LEDGF BINDING
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...RNA-directed DNA polymerase activity / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / 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
Integrase, C-terminal domain superfamily, retroviral / Ribonuclease H-like superfamily/Ribonuclease H / 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 / Ribonuclease H-like superfamily/Ribonuclease H / 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 / SH3 type barrels. / 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. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-L3D / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsGupta, K. / Van Duyne, G.D. / Eilers, G. / Bushman, F.D.
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 22, 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_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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: Integrase
F: Integrase
G: Integrase
H: Integrase
I: Integrase
J: Integrase
K: Integrase
L: Integrase
M: Integrase
N: Integrase
O: Integrase
P: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,68251
Polymers190,46616
Non-polymers5,21635
Water1,17165
1
A: Integrase
B: Integrase
C: Integrase
D: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,81211
Polymers47,6174
Non-polymers1,1957
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Integrase
F: Integrase
G: Integrase
H: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,12216
Polymers47,6174
Non-polymers1,50612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Integrase
J: Integrase
K: Integrase
L: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,93613
Polymers47,6174
Non-polymers1,3199
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Integrase
N: Integrase
O: Integrase
P: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,81211
Polymers47,6174
Non-polymers1,1957
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.510, 116.510, 112.800
Angle α, β, γ (deg.)90.00, 103.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Integrase


Mass: 17580.045 Da / Num. of mol.: 8 / Fragment: Catalytic Core Domain / Mutation: F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: pol / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72498
#2: Protein
Integrase


Mass: 6228.216 Da / Num. of mol.: 8 / Fragment: Carboxy Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72498
#3: Chemical
ChemComp-L3D / (2S)-tert-butoxy[4-(2,3-dihydropyrano[4,3,2-de]quinolin-7-yl)-2-methylquinolin-3-yl]acetic acid


Mass: 442.506 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H26N2O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20 mM Tris pH 7.4, 250-300 mM NaCl, 1 mM DTT, 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.93→19.85 Å / Num. obs: 48717 / % possible obs: 90.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 53.5 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.043 / Rrim(I) all: 0.09 / Net I/σ(I): 10.8
Reflection shellResolution: 2.93→3.04 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2000 / CC1/2: 0.915 / CC star: 0.999 / Rpim(I) all: 0.59 / Rrim(I) all: 1.25 / % possible all: 41.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XDSdata scaling
PHENIX1.17.1.3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L3U

3l3u


Resolution: 2.93→19.85 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 39.239 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26129 4441 10 %RANDOM
Rwork0.21569 ---
obs0.22023 39969 90.34 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.007 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å20.12 Å2
2--0.21 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.93→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12031 0 368 65 12464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01712644
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611993
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.81617073
X-RAY DIFFRACTIONr_angle_other_deg0.4731.57227804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3545.2411553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.241102192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1870.21864
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022480
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4672.1476017
X-RAY DIFFRACTIONr_mcbond_other3.4672.1476017
X-RAY DIFFRACTIONr_mcangle_it5.5543.2017460
X-RAY DIFFRACTIONr_mcangle_other5.5543.2017461
X-RAY DIFFRACTIONr_scbond_it4.2192.5796627
X-RAY DIFFRACTIONr_scbond_other4.2192.586628
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2353.6939614
X-RAY DIFFRACTIONr_long_range_B_refined13.62841.59751334
X-RAY DIFFRACTIONr_long_range_B_other13.62741.59651329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.931→3.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 125 -
Rwork0.352 1123 -
obs--35.08 %
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)
15.5051-1.1129-1.13094.9519-0.02173.9584-0.08170.0939-0.2512-0.1215-0.0744-1.44110.91260.7840.15620.6282-0.01740.19050.71840.05330.9086-20.268-9.81835.846
24.214-0.3162-1.13523.1335-0.39854.9770.09310.75860.6875-0.7809-0.1978-0.676-0.22520.10960.10470.4033-0.17840.13920.58210.16990.4964-29.7643.8927.717
30.1528-0.6641-0.22043.17031.07580.37580.11620.0497-0.0172-0.0084-0.08620.1640.0071-0.049-0.031.14120.02990.53821.74050.03551.0418-7.943-13.1167.191
49.13430.2824-1.68093.02190.11924.1106-0.3160.392-0.0717-0.37790.25030.6547-0.1794-0.34260.06570.285-0.13080.00570.33630.0370.3835-53.047-6.65945.063
55.5541-0.0681-1.26374.10970.04133.8223-0.0933-0.0445-0.6760.0945-0.0592-0.8910.67350.71670.15250.3176-0.05530.08530.52760.01350.42725.0818.94235.433
65.11480.0515-1.71672.07180.27694.75160.14320.91590.6754-0.6103-0.133-0.2032-0.5351-0.1242-0.01020.3941-0.15260.08540.52030.08810.233915.58132.50226.654
71.4567-1.4762-2.7836.07571.99585.61370.13870.1143-0.08520.0688-0.22360.61590.0793-0.13150.08490.9688-0.06010.34351.4771-0.20070.791135.77713.8356.239
810.8784-1.56730.04873.2753-1.49653.9878-0.23110.1584-0.46290.00110.31541.1387-0.3312-0.462-0.08420.3297-0.07170.05460.40340.02680.4933-7.42922.83845.245
96.2774-1.9048-2.26243.33881.04952.9513-0.2556-0.0119-0.04310.21480.1614-0.68180.52650.61510.09420.2889-0.0479-0.03040.4650.06910.274328.197-41.46338.588
104.7864-0.9305-1.55663.84860.48054.5230.24651.14040.9148-0.7929-0.2332-0.223-0.3223-0.2016-0.01330.3339-0.11480.00250.56030.27550.384318.258-28.14529.162
110.9-1.1999-1.26829.20233.7442.85240.21020.32650.04950.2767-0.4289-0.00660.3348-0.42370.21870.8265-0.03230.29651.35190.30050.48640.422-45.6629.797
129.13730.294-1.71162.92640.04823.5747-0.16390.3753-0.0362-0.2530.12530.819-0.2713-0.11970.03860.2298-0.1354-0.01390.2058-0.01780.4091-5.743-36.9746.166
135.185-1.2015-2.45133.24310.83663.9517-0.233-0.0688-0.26020.33510.1812-0.56780.57720.62430.05170.3128-0.0554-0.01120.4321-0.0130.207873.777-12.35438.251
144.7083-0.7168-1.2493.90490.08663.82250.04351.24491.0975-0.7312-0.08620.1957-0.2183-0.33050.04270.3557-0.1784-0.00710.67760.26150.486863.6170.61428.346
150.1557-0.8841-0.206711.16663.11831.61870.11710.23160.04090.7086-0.28140.71010.6325-0.1340.16430.7613-0.0070.1931.19630.12270.241884.258-18.4688.722
168.6884-0.2054-4.56183.6906-2.19424.4998-0.2970.1215-0.36730.02830.41790.8901-0.3364-0.5098-0.12090.46610.0057-0.03470.3879-0.04560.454640.222-7.63746.71
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 208
2X-RAY DIFFRACTION2B56 - 210
3X-RAY DIFFRACTION3C221 - 271
4X-RAY DIFFRACTION4D222 - 271
5X-RAY DIFFRACTION5E57 - 208
6X-RAY DIFFRACTION6F57 - 210
7X-RAY DIFFRACTION7G221 - 271
8X-RAY DIFFRACTION8H222 - 271
9X-RAY DIFFRACTION9I57 - 208
10X-RAY DIFFRACTION10J57 - 210
11X-RAY DIFFRACTION11K221 - 271
12X-RAY DIFFRACTION12L221 - 271
13X-RAY DIFFRACTION13M56 - 209
14X-RAY DIFFRACTION14N55 - 210
15X-RAY DIFFRACTION15O221 - 271
16X-RAY DIFFRACTION16P220 - 271

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