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

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Basic information

Entry
Database: PDB / ID: 8buv
TitleHIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor LEDGIN 3
ComponentsIntegrase
KeywordsVIRAL PROTEIN / Integrase / HIV / ALLINI / LEDGIN 3 / Allosteric Inhibitor / Inhibitor / Retrovirus / INLAI / NCINI / MINI / LEDGIN
Function / homology
Function and homology information


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 ...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 / telomerase activity / 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-723 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSinger, M.R. / Pye, V.E. / Cook, N.J. / Cherepanov, P.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Cancer Research UKFC001061 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001061 United Kingdom
Wellcome TrustFC001061 United Kingdom
The Francis Crick InstituteFC001061 United Kingdom
CitationJournal: To Be Published
Title: HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor LEDGIN 3
Authors: Singer, M.R. / Cherepanov, P.
History
DepositionNov 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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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)104,66714
Polymers103,6184
Non-polymers1,04810
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.840, 65.160, 69.790
Angle α, β, γ (deg.)90.000, 99.900, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_1ens_2(chain "B" and (resid 57 through 76 or resid 78...
d_2ens_2(chain "D" and (resid 57 through 76 or resid 78...

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_1ASNASNALAALAAA222 - 2764 - 58
d_21ens_1ASNASNALAALACC222 - 2764 - 58
d_11ens_2SERSERALAALABB57 - 7678 - 97
d_12ens_2HISHISVALVALBB78 - 11399 - 134
d_13ens_2THRTHRGLYGLYBB115 - 140136 - 161
d_14ens_2GLYGLYGLUGLUBB140 - 170161 - 191
d_15ens_2LEULEUTHRTHRBB172 - 206193 - 227
d_21ens_2SERSERALAALADD57 - 7678 - 97
d_22ens_2HISHISVALVALDD78 - 11399 - 134
d_23ens_2THRTHRGLUGLUDD115 - 170136 - 191
d_24ens_2LEULEUTHRTHRDD172 - 206193 - 227

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.327514946708, 0.271229383021, -0.905079323302), (0.0615128630814, -0.962000654527, -0.266028021766), (-0.942841517625, 0.0314541328795, -0.331753689002)15.2965256784, 34.3369521657, 31.7265305718
2given(0.464768176801, 0.128912907978, -0.875997719169), (0.133545481925, -0.988232789977, -0.0745758477802), (-0.87530345943, -0.0823250567655, -0.476514888475)18.0313355296, 34.6523833485, 35.4295676211

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Components

#1: Protein
Integrase / IN


Mass: 25904.537 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The construct is of HIV-1 integrase with the following domain swap: The C-Terminal Domain of HIV-1 integrase (from residues 220 to 288) is followed by the Catalytic Core Domain of HIV-1 ...Details: The construct is of HIV-1 integrase with the following domain swap: The C-Terminal Domain of HIV-1 integrase (from residues 220 to 288) is followed by the Catalytic Core Domain of HIV-1 integrase (from residues 50 to 212). In addition, there are the following mutations: F185K and W243E. The residue numbers are correct in the structure. Because the linker is not defined in the electron density map, we do not know for sure which CTD is linked to which CCD in the lattice formation. We have therefore kept each domain as a separate chain. This chain is CTD There are 2 copies of CTD and CCD in the asymmetric unit. We cannot determine how they are connected in the crystal lattice.,The construct is of HIV-1 integrase with the following domain swap: The C-Terminal Domain of HIV-1 integrase (from residues 220 to 288) is followed by the Catalytic Core Domain of HIV-1 integrase (from residues 50 to 212). In addition, there are the following mutations: F185K and W243E. The residue numbers are correct in the structure. Because the linker is not defined in the electron density map, we do not know for sure which CTD is linked to which CCD in the lattice formation. We have therefore kept each domain as a separate chain. This chain is CTD There are 2 copies of CTD and CCD in the asymmetric unit. We cannot determine how they are connected in the crystal lattice.
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-723 / (6-chloro-2-oxo-4-phenyl-1,2-dihydroquinolin-3-yl)acetic acid


Mass: 313.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H12ClNO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, ethylene glycol, magnesium chloride, calcium chloride, imidazole, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Aug 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→47.29 Å / Num. obs: 30313 / % possible obs: 99.53 % / Redundancy: 12.12 % / Biso Wilson estimate: 44.24 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.063 / Net I/σ(I): 8
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 8.18 % / Rmerge(I) obs: 3.512 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1506 / CC1/2: 0.367 / Rpim(I) all: 1.263 / % possible all: 97.73

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Processing

Software
NameVersionClassification
PHENIXdev_4694refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A1P

8a1p


Resolution: 2.04→47.29 Å / SU ML: 0.3686 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2469 1483 4.91 %
Rwork0.2154 28712 -
obs0.2169 30195 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.94 Å2
Refinement stepCycle: LAST / Resolution: 2.04→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 70 164 3369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00173301
X-RAY DIFFRACTIONf_angle_d0.45614446
X-RAY DIFFRACTIONf_chiral_restr0.0423485
X-RAY DIFFRACTIONf_plane_restr0.0029557
X-RAY DIFFRACTIONf_dihedral_angle_d10.68731208
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.1619515202
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.02321221442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.110.4181430.40062483X-RAY DIFFRACTION95.18
2.11-2.180.35191480.33872595X-RAY DIFFRACTION99.1
2.18-2.270.32121200.31022577X-RAY DIFFRACTION99.15
2.27-2.370.2941280.29572606X-RAY DIFFRACTION99.38
2.37-2.50.28761260.27292631X-RAY DIFFRACTION99.57
2.5-2.650.32081220.25812614X-RAY DIFFRACTION99.2
2.65-2.860.28371510.25092594X-RAY DIFFRACTION99.64
2.86-3.140.26451400.23112633X-RAY DIFFRACTION99.78
3.15-3.60.21671310.19962634X-RAY DIFFRACTION99.89
3.6-4.530.20471250.17092656X-RAY DIFFRACTION99.78
4.54-47.290.21951490.1822689X-RAY DIFFRACTION99.75
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)
10.98085002381-0.279496108246-0.7055018083620.2027527300160.2152124225310.537556473866-0.325623961179-0.228292924384-0.7325748925320.282470340642-0.2377311427770.4884756491790.1337454093980.0774333955236-0.02747078771330.4094072394280.004963712794040.03895170446680.6422734914430.01079209725790.495357772183-20.357864530310.38388458234.65712587179
20.291350295789-0.137369224154-0.0173207148570.499272901162-0.2969686066150.4925140763250.138354111733-0.03804920848070.425045363988-0.429665529244-0.2283303225580.1074108532730.3631007036430.03534699814060.0002261087689830.4276368935640.0179679522807-0.02251642651350.637428884952-0.01792547558240.415928406075-23.317717965216.28288533360.396142785487
30.02599122975670.0109500629330.01076995814820.0178878431915-0.0005317996914880.00766130077345-0.06721290111640.1491459862190.642945906526-0.0230888215609-0.3672414431770.177591931828-0.1995336579780.00926192838384-0.002402813711120.765025962552-0.269650550637-0.01613917461181.178660827020.3560738084510.812915757544-3.4930393847421.44177378391.9972158427
40.5998738822530.0268514224074-0.1447711971791.28999589849-0.0919481944960.8495331077860.07065478956560.326915448479-0.0692032194544-0.1817256713730.001079736595410.1120263911730.284535953553-0.0638514528496-1.65009795485E-50.3796106151250.01374633471760.001032944466490.38405784971-0.0336133614160.382361862615-1.79569730037.9305432347216.3397205106
50.5115208052980.627807804242-0.4082999605980.763072518388-0.5038983903010.344543017266-0.0005510827635660.4464000849920.0227354062921-0.07352462444960.1598762463820.1225606411240.6916262169420.02874918472030.005378235089260.6396968206620.004545140009590.05649095678730.537332136464-0.1160060313090.386913462795-0.6428665775772.162082890027.54820621825
60.82286353774-0.01538020720340.249587649110.483622088689-0.1809608466340.3608403483920.0367659490439-0.197325573609-0.1538977808470.335153097628-0.0130992587272-0.3538046563740.08893733482590.502730533963-0.0001400759040060.410397002060.0536462723809-0.004957956254140.3547063258510.05184388171470.4481760137758.525619637635.9721427888929.7747196468
70.04706522083-0.01820304488370.03236794182710.533043398560.04694505526160.290470853887-0.3186516132590.656418271997-0.430106077994-0.472632152361-0.244874991532-0.5736119885430.2588060962860.713730132928-0.06343959883540.3582322060650.06512740586620.1321603891630.770148465651-0.03700967377350.55455911112617.011967829714.521056304610.2914956987
80.0843176027397-0.080851851546-0.09675793741290.1989813667560.08101928803690.260996760214-0.613652634038-0.07404139022850.2241669923660.8885956590920.3194931458420.12422415718-0.3934798708530.2212640365460.0001212182937110.8531018096860.10475644471-0.1021444652650.771980577726-0.01200833677780.5970266126778.6796682315620.555376894450.8398253882
90.109736900758-0.148328828402-0.02363569768391.319367997940.4838161945020.2430820246170.03697993928460.3475246089610.2389257529330.783075112987-0.0111506055758-0.3420256257630.2503760546370.854753946544-0.008085696969470.7301547236940.0940757226459-0.1472576386590.6952499523450.001763765543070.55545949024312.198451477216.501029958549.8304189054
100.584975263617-0.75007132841-0.08635581492041.541423813330.4360715578991.929814649260.08128673490790.0439833788341-0.01342009291960.23636658565-0.0543790980978-0.103065209722-0.2263882043020.2797330452467.55739413219E-60.357581484618-0.0378650812766-0.008735466748570.2884507893340.02663568690650.3654512377853.9705347846625.473657145428.5629884733
110.503030953083-0.258950440257-0.1300747657421.405703782140.1870808343970.807239545860.0276938224462-0.01509509510510.227025574819-0.184702386146-0.07806258650080.0567239083761-0.441782412651-0.102033044733-4.10229890165E-50.3954174402130.03233287484850.006030013596960.3646810071630.03055119624330.349480147715-1.268870500628.086148259216.1390796013
120.222226606805-0.322879404973-0.05673815534820.5109841752260.1021757821080.09631063524750.2511551151820.343380114325-0.285058133665-0.6214216800060.0790824843715-0.704338626093-0.05716016731710.5266578904070.1111763127980.315902137745-0.03414280024820.09504732781830.682323542452-0.00665368473370.61809049599118.334557979621.847934698914.4818300234
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 221 through 239 )AA221 - 2391 - 19
22chain 'A' and (resid 240 through 269 )AA240 - 26920 - 49
33chain 'A' and (resid 270 through 276 )AA270 - 27650 - 56
44chain 'B' and (resid 57 through 133 )BB57 - 1331 - 77
55chain 'B' and (resid 134 through 149 )BB134 - 14978 - 86
66chain 'B' and (resid 150 through 195 )BB150 - 19587 - 128
77chain 'B' and (resid 196 through 211 )BB196 - 211129 - 144
88chain 'C' and (resid 222 through 244 )CC222 - 2441 - 23
99chain 'C' and (resid 245 through 276 )CC245 - 27624 - 55
1010chain 'D' and (resid 57 through 133 )DD57 - 1332 - 78
1111chain 'D' and (resid 134 through 195 )DD134 - 19579 - 128
1212chain 'D' and (resid 196 through 210 )DD196 - 210129 - 143

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