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

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Basic information

Entry
Database: PDB / ID: 8cbt
TitleHIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor MUT872
ComponentsIntegrase
KeywordsVIRAL PROTEIN / Integrase / HIV / ALLINI / Allosteric Inhibitor / Inhibitor / Retrovirus / INLAI / NCINI / MINI / LEDGIN / Mutabilis / MUT872
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / viral penetration into host nucleus / RNA-directed DNA polymerase activity / 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 / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Integrase, C-terminal domain superfamily, retroviral / 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, C-terminal domain superfamily, retroviral / 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. / SH3 type barrels. / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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 / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-W2Q / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsSinger, M.R. / Pye, V.E. / Yu, Z. / 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: Antimicrob.Agents Chemother. / Year: 2023
Title: Biological and Structural Analyses of New Potent Allosteric Inhibitors of HIV-1 Integrase.
Authors: Bonnard, D. / Le Rouzic, E. / Singer, M.R. / Yu, Z. / Le Strat, F. / Batisse, C. / Batisse, J. / Amadori, C. / Chasset, S. / Pye, V.E. / Emiliani, S. / Ledoussal, B. / Ruff, M. / Moreau, F. ...Authors: Bonnard, D. / Le Rouzic, E. / Singer, M.R. / Yu, Z. / Le Strat, F. / Batisse, C. / Batisse, J. / Amadori, C. / Chasset, S. / Pye, V.E. / Emiliani, S. / Ledoussal, B. / Ruff, M. / Moreau, F. / Cherepanov, P. / Benarous, R.
History
DepositionJan 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Structure summary / Category: struct / struct_keywords / Item: _struct.title / _struct_keywords.text
Revision 1.2Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)105,19418
Polymers103,6184
Non-polymers1,57614
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-26 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.306, 64.470, 70.702
Angle α, β, γ (deg.)90.000, 101.660, 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

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 6 types, 172 molecules

#2: Chemical ChemComp-W2Q / (2~{S})-2-[3-cyclopropyl-2-(3,4-dihydro-2~{H}-chromen-6-yl)-6-methyl-phenyl]-2-cyclopropyloxy-ethanoic acid


Mass: 378.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H26O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

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, sitting 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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.14→64.47 Å / Num. obs: 26052 / % possible obs: 100 % / Redundancy: 36.95 % / Biso Wilson estimate: 46.91 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.027 / Net I/σ(I): 13.6
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 27.51 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1265 / CC1/2: 0.931 / Rpim(I) all: 0.32 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→52.21 Å / SU ML: 0.2876 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.1406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2534 1258 4.83 %
Rwork0.2073 24765 -
obs0.2096 26023 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.49 Å2
Refinement stepCycle: LAST / Resolution: 2.14→52.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 107 158 3237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00153196
X-RAY DIFFRACTIONf_angle_d0.40234312
X-RAY DIFFRACTIONf_chiral_restr0.0418480
X-RAY DIFFRACTIONf_plane_restr0.0028530
X-RAY DIFFRACTIONf_dihedral_angle_d13.34291185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.230.35321480.28842728X-RAY DIFFRACTION99.93
2.23-2.330.311240.26622733X-RAY DIFFRACTION99.97
2.33-2.450.28791220.24462760X-RAY DIFFRACTION99.97
2.45-2.60.26921430.22982708X-RAY DIFFRACTION99.96
2.6-2.80.29711550.23592753X-RAY DIFFRACTION100
2.8-3.090.30211450.22632742X-RAY DIFFRACTION100
3.09-3.530.24191330.2022766X-RAY DIFFRACTION99.97
3.53-4.450.2171360.18112777X-RAY DIFFRACTION100
4.45-52.210.23571520.1942798X-RAY DIFFRACTION99.76
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)
10.842527401158-0.274989229237-0.5959184967351.592180508320.2388888397151.28364940582-0.01472485181440.01901416906370.150415284005-0.265193022597-0.07325383990870.188701239043-0.192098450737-0.2343239875223.56398182644E-60.3864538159280.0346133871504-0.01573230776720.3345644434780.0436906634250.430395178817.7259208223-9.409286532197.24090376798
20.4099265675820.15370961291-0.1723915178540.3920547761630.064804526260.03870474559740.212458665881.002617018750.129817603331-0.863868058527-0.262044755350.413999819344-0.531815575895-0.4264011214840.009216603454090.4884942650410.0688874880903-0.08784360193220.4885519464750.03534190591050.47400593099810.2861362135-10.5307548202-2.05049777844
30.531575100234-0.08817011739910.4302292951020.849616951849-0.3831865478231.628763881150.155675869396-0.2718633906720.3516539851590.276733344911-0.0802315410548-0.0470229410328-0.235238302992-0.0613430125678-9.23095543274E-60.380696315899-0.02852734238390.04206175189510.36848103356-0.08109423876370.37853258630819.1481276537-9.1734262375221.3250261922
40.169824115069-0.0588424817235-0.0203668642701-0.1451301628710.1310811676120.290947706553-0.168171793747-0.596686153926-0.0689914266030.09055941397410.486891207203-0.09205671197890.3102892608950.1699098561010.001106560475490.4252603846590.03869965846190.04819493958370.3978436255330.05931584350820.53972138701217.9624026794-32.349768907816.0035133214
50.737881369622-0.413013485465-0.5756452961030.4039167101850.08742408517030.441172041788-1.89894278112E-5-0.215185663311-0.05438791114920.2054257240.0167092043722-0.04731896741910.196361658251-0.0289185003735-6.31771497014E-60.4393459015510.01536181363110.03376334973480.3677422534390.03416278005860.38461114417521.4803833939-27.810110263916.0481395698
60.0301681975680.0353647745928-0.07956814312250.0327589417072-0.06627138249490.0425579300840.64754508773-0.967805295635-0.2109646400420.273927140163-0.274737618291-0.631630674230.2014878309420.1778165372020.000296502245480.5627705065860.00380335254447-0.04330900431090.5316660973870.06068967714260.39312151050328.832305313-24.158581492226.756334847
70.288186333148-0.0471934961308-0.0270087774520.10396170681-0.015547397101-0.0117416914009-0.112319875209-0.4476949986370.3584191063620.105830502224-0.07840378189720.4865619027350.6808163558270.171330596459-0.01290398310740.5280623144290.05764527840160.02698004037360.6523795063870.08942507802070.384411878420.5538232694-32.592263776126.378366025
80.1587214349260.0712061944706-0.04190689635570.2407411573880.1991887105230.1320583372330.1880657016290.156319118173-0.272416209254-0.3163502077220.2300277452230.6712830541450.568382867313-0.5552674127420.0004890450745710.555460220048-0.169514741356-0.009667804231670.465931662383-0.04781911454420.54627569046913.1492152938-34.36164900043.62785334137
90.1032243043980.06392833204210.1451684985530.7678871094540.4923752962650.2277539418030.385253032729-0.4483648219330.227450989503-0.175398764909-0.07283772928970.145710687666-0.03411964189090.2403189701650.0003847616017990.34760331716-0.0344223445549-0.003992726993540.329098286849-0.0155856389050.3929349360169.96194232406-25.74755118234.41234926733
100.0197884604605-0.01192906508140.003543394272440.02230103338670.02718385598260.1790457530770.0537926646424-0.131822175149-0.346402837760.247574687768-0.2119922143920.3210951637650.954275931988-1.000276624710.0014135096640.399703130314-0.06180843047380.09037304059670.7462500880520.03854993206260.6045063542132.92614490426-21.426685374522.5840659288
110.7838527902680.606440523881-0.7102306367730.92578950315-0.5244391159050.63770923699-0.2775538722160.24843167180.02492086457170.1874291166220.0523339964502-0.479494351764-0.728755038892-0.594207126477-0.05159615880140.5058083996720.135372304933-0.1395766647251.08714848618-0.08297345566190.49458806806536.5869845373-21.558425614132.4178503506
120.0583694560146-0.02255820203780.009303882927870.127566342005-0.03287471595840.02385723432871.019502785580.1110995656260.7138224382920.208500364515-0.941091017793-0.5891816193770.8866361398340.341615929393-0.002759695121180.7039950327370.03670412699920.08584702330780.8002342138920.0298439637940.49760001915441.7662780663-27.560823904726.6356368479
131.395084737210.300762135261.071125790360.9035617157230.3045659558231.00213326033-0.359358040947-0.7705983299880.178268231020.435571756567-0.5886570221620.5123600273010.224453008127-1.76616909633-0.3088803425090.6042090234950.09768024943610.05866135122960.695892342991-0.1039928436060.39432103994143.358065176-18.651083505336.5733098423
140.378190576110.273423901435-0.2902063148940.623795202405-0.1917276140290.447809624476-0.2971448094170.03023931166750.535635470201-0.262020330588-0.5068940425990.0976151818418-0.143102302968-0.821034509676-0.005885163829770.4865269782640.16756416344-0.07138751802370.843152842099-0.04123058461850.50032099450942.9837849823-19.259221967330.750625588
150.0260551883658-0.0690030799222-0.002892202638890.713691797222-0.02191344889790.01922885836280.264039419008-0.265480858574-0.0554793646897-0.73960667388-0.5632874427740.0658926400173-0.579952289749-0.4731529550110.001506645836660.806820755019-0.0401963942502-0.1210886478091.039387392960.02996768521190.52005108230714.4229662305-14.3643970118-14.3931788059
160.963460262390.269540458129-0.7625665902180.334537582979-0.2889144045910.539929384481-0.4441263879030.137094437796-0.472820147198-1.05392676556-0.866364836172-0.1831047995790.0497081631853-0.485151347048-0.1066204731860.769522218879-0.0486655147499-0.1685096784380.95953006610.0219234505920.6005219140017.2771608688-17.6184296487-21.3115762807
170.296905946371-0.03927452780750.05160847474590.0363451117516-0.2282299155930.221728819308-0.536308648567-0.0597154840911-0.650629080996-0.4053554134070.06055432208160.006367232359861.082755181830.128835941787-0.006927181744840.838494586112-0.0553521493401-0.03786460128760.772792594731-0.02842707016740.68494141126310.486357657-19.5652677108-14.6874009099
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 57 through 123 )BC57 - 1231 - 67
22chain 'B' and (resid 124 through 149 )BC124 - 14968 - 84
33chain 'B' and (resid 150 through 208 )BC150 - 20885 - 140
44chain 'D' and (resid 57 through 68 )DJ57 - 681 - 12
55chain 'D' and (resid 69 through 123 )DJ69 - 12313 - 67
66chain 'D' and (resid 124 through 132 )DJ124 - 13268 - 76
77chain 'D' and (resid 133 through 149 )DJ133 - 14977 - 85
88chain 'D' and (resid 150 through 168 )DJ150 - 16886 - 104
99chain 'D' and (resid 169 through 195 )DJ169 - 195105 - 127
1010chain 'D' and (resid 196 through 210 )DJ196 - 210128 - 142
1111chain 'A' and (resid 223 through 227 )AA223 - 2271 - 5
1212chain 'A' and (resid 228 through 239 )AA228 - 2396 - 15
1313chain 'A' and (resid 240 through 255 )AA240 - 25516 - 31
1414chain 'A' and (resid 256 through 269 )AA256 - 26932 - 45
1515chain 'C' and (resid 222 through 239 )CF222 - 2391 - 16
1616chain 'C' and (resid 240 through 255 )CF240 - 25517 - 32
1717chain 'C' and (resid 256 through 273 )CF256 - 27333 - 50

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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