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- PDB-8a1p: HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Co... -

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Basic information

Entry
Database: PDB / ID: 8a1p
TitleHIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor BI-D
ComponentsIntegrase
KeywordsVIRAL PROTEIN / Integrase / HIV / ALLINI / BI-D / Allosteric Inhibitor / Inhibitor / Retrovirus / INLAI / NCINI / MINI / LEDGIN
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-LF0 / DI(HYDROXYETHYL)ETHER / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Mbio / Year: 2023
Title: The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function.
Authors: Singer, M.R. / Dinh, T. / Levintov, L. / Annamalai, A.S. / Rey, J.S. / Briganti, L. / Cook, N.J. / Pye, V.E. / Taylor, I.A. / Kim, K. / Engelman, A.N. / Kim, B. / Perilla, J.R. / ...Authors: Singer, M.R. / Dinh, T. / Levintov, L. / Annamalai, A.S. / Rey, J.S. / Briganti, L. / Cook, N.J. / Pye, V.E. / Taylor, I.A. / Kim, K. / Engelman, A.N. / Kim, B. / Perilla, J.R. / Kvaratskhelia, M. / Cherepanov, P.
History
DepositionJun 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 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.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_src_gen / pdbx_initial_refinement_model / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_ec ..._entity.details / _entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num

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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)105,37918
Polymers103,6184
Non-polymers1,76114
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9540 Å2
ΔGint-16 kcal/mol
Surface area16860 Å2
Unit cell
Length a, b, c (Å)53.555, 65.210, 69.673
Angle α, β, γ (deg.)90.000, 100.170, 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.,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.
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, 194 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-LF0 / (2S)-tert-butoxy[4-(3,4-dihydro-2H-chromen-6-yl)-2-methylquinolin-3-yl]ethanoic acid


Mass: 405.486 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 180 / 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

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, ethylene glycol, magnesium chloride, calcium chloride, Tris-Bicine

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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: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→65.21 Å / Num. obs: 43655 / % possible obs: 99.42 % / Redundancy: 20.25 % / Biso Wilson estimate: 43.34 Å2 / CC1/2: 1 / Rpim(I) all: 0.009 / Rrim(I) all: 0.042 / Net I/σ(I): 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.830.621650.920.2691.23898.77
1.83-1.860.721470.9470.2090.9698.76
1.86-1.9121480.9690.1530.70498.71
1.9-1.941.321530.9680.1280.58398.99
1.94-1.981.921690.9840.0930.41998.95
1.98-2.032.421680.990.0740.3399.13
2.03-2.083.121370.9910.0630.28199.16
2.08-2.133.921920.9940.0520.22799.14
2.13-2.25.421600.9950.0420.18699.31
2.2-2.277.321800.9960.0350.15999.45
2.27-2.359.122000.9970.030.13799.55
2.35-2.4412.121720.9960.0250.11599.54
2.44-2.5515.821800.9980.0210.09499.59
2.55-2.6920.921820.9980.0180.08299.77
2.69-2.8628.421890.9990.0150.06799.73
2.86-3.0840.721920.9990.0120.05399.82
3.08-3.3962.522110.9990.10.04499.95
3.39-3.8898.7220710.0080.037100
3.88-4.89130.1222310.0070.031100
4.89-65.25142.4228010.0070.031100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T6E, 4O55

6t6e

4o55


Resolution: 1.8→52.71 Å / SU ML: 0.3133 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.0036
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2092 2174 4.99 %
Rwork0.1814 41428 -
obs0.1827 43602 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→52.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 121 180 3341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373248
X-RAY DIFFRACTIONf_angle_d0.62274368
X-RAY DIFFRACTIONf_chiral_restr0.0463474
X-RAY DIFFRACTIONf_plane_restr0.0043536
X-RAY DIFFRACTIONf_dihedral_angle_d14.30951189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.51141650.52232537X-RAY DIFFRACTION98.54
1.84-1.880.39421220.41922551X-RAY DIFFRACTION98.74
1.88-1.930.31041320.33362550X-RAY DIFFRACTION98.78
1.93-1.980.26941330.24042578X-RAY DIFFRACTION98.87
1.98-2.040.21321470.19792539X-RAY DIFFRACTION98.93
2.04-2.110.23281480.18762578X-RAY DIFFRACTION99.2
2.11-2.180.24661410.19332565X-RAY DIFFRACTION99.27
2.18-2.270.24561250.20642582X-RAY DIFFRACTION99.23
2.27-2.370.22521220.18842594X-RAY DIFFRACTION99.56
2.37-2.50.241240.17922615X-RAY DIFFRACTION99.6
2.5-2.650.18351270.1852608X-RAY DIFFRACTION99.74
2.65-2.860.2321520.18992578X-RAY DIFFRACTION99.74
2.86-3.140.23161340.18332622X-RAY DIFFRACTION99.82
3.14-3.60.15651290.16862619X-RAY DIFFRACTION100
3.6-4.530.19531240.14652644X-RAY DIFFRACTION100
4.54-52.710.19441490.17892668X-RAY DIFFRACTION99.51
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)
14.403575796221.7899242331-3.945358229950.977615664454-1.397482482183.67180547928-0.354126318491-0.860036168877-1.46773821397-0.0550573498636-0.39984618314-1.04572070110.434303090951.60805836765-0.1731149869070.4559504103666.23075023492E-5-0.09576603521050.9850812890720.05664821157420.452754880375-17.445620268113.52821890222.78314597245
20.01440454930990.0130828665980.02193435476350.01949661312270.03882633123650.044229346741-1.114752656830.0291657367473-0.05978335047920.343289097947-1.13810787503-0.137672600316-0.279617834959-0.0479989294392-0.00261233072471.20196286181-0.1429257551990.05411891387931.30743333529-0.1476627247161.22640258526-28.61698105935.917805477938.8448337909
31.496853124150.1479988190870.09628487213760.39881862668-0.7314157111811.25114509454-0.2354485418340.2322276087010.174208143416-0.2409963011910.008273922539470.165114001645-0.05707367822460.296892491693-0.0002222878030010.5550733455320.05384789075110.0178596659580.634803971346-0.001588978554290.463838151778-22.603125896815.0204883296-0.522098366897
40.700874824395-0.8458204293930.3243281699361.37407714687-0.8549634109311.55310339166-0.1096379200690.577147603570.338638409214-0.36138984236-0.0652600890133-0.136758551967-0.05542862297940.752902275699-0.000491921497970.464009299213-0.03817935289830.03521904139221.02716460180.007113064282820.440846029487-19.188355721816.53277295992.35891873429
52.492314922630.103089325756-0.3245061996281.50099011475-0.9770297289692.79544828872-0.04548827224260.46731522568-0.453100664201-0.140385253357-0.0440980426253-0.005537672205350.552783885627-0.249454998941-7.79380353884E-50.383148355752-0.02448076720260.03158768615250.382844717188-0.07910997557780.416089349139-1.989212820067.5570455426215.3942710073
63.743243150580.65785418290.8764071760883.74693634585-0.6392043058722.24772296651-0.07547043787090.00954348704918-0.5915015029050.113004289092-0.0294781320523-0.3426099723990.5713450376290.507282219696-0.001266652895590.4618283576970.07020262999380.0136819409910.3329837345160.04526834985610.4800324907688.202317064655.6159801615129.4170577831
70.650513910066-0.199438605589-0.4070002111280.779979619980.4325881370210.367775989215-0.1573569202280.802961493104-0.100346749975-0.23893369516-0.34396417405-0.5077332935980.04586312454810.745092804455-0.00103942526080.3842606252010.05652732297550.08568467471050.7881743534830.0008181392617310.59019466498816.874856803814.407244172510.7532365573
80.821060091358-0.486694458970.1660007366551.99284580816-0.2557107575010.0599031687021-0.07020941833090.6101048025920.353071058802-0.183529938126-0.332612650061-0.0477727339114-0.828890597157-0.854826429252-0.2577115212840.9372638213660.27803227375-0.3369213899621.32170635977-0.2165128881760.6075882136746.9568507836320.489707601948.9566484054
90.65685320935-0.343527924138-0.01009847656960.213999380910.2982170668530.903834488247-0.3424794980310.170513922645-0.02407082228090.701554923349-0.02498497311420.248586771892-0.1930542745030.3903327168061.79686090804E-50.8183979683470.194413383336-0.09918037491630.854503993302-0.04064824300870.61427275403211.807710970916.657263290252.8864769113
100.01576590201610.02327373727470.01720104092220.0321404772850.00711114138830.0132594445019-0.4652571118140.0103734758132.497678073220.237932490242-0.7806486652880.150735952412-1.59614260368-0.2296663594020.0009729260871941.041225400040.0538277292594-0.3008738471881.02794998174-0.01492784024111.0682279272713.318860236526.314258062155.1818582072
110.124666788542-0.1581050791590.1973994471950.187189525365-0.2265821140520.2525002198460.03700961638030.02585364381190.1880737554640.245294572055-0.45065994777-0.1709193429910.608955978013-0.855835180956-5.13607186337E-50.8157408042420.0234456481697-0.09462852625791.04481216177-0.0394846066590.5185310216997.3300890048615.562266498753.3707781568
128.21471798855.52979778775-7.442981015396.02456622389-4.346405856876.93911168103-0.3770200910310.348207803108-0.7230823395660.366467588106-0.122400112143-1.408085685290.1821333654170.403070737051-0.5713758264230.5595163454140.195908443419-0.2561951776651.65665597553-0.08591449821280.73719792557417.561754783214.624272265736.8227502681
130.237153126665-0.39734281259-0.1844338664360.6993847020370.6157480203160.835399537988-0.3504970629110.1540837214940.8574815076970.1791092896230.203153204391-0.391991533873-0.5762760972360.1974348271050.000188184439720.449770694482-0.06436994759820.0196743042250.4145603744490.06411114524880.527044446965.3026702784830.245511499224.2125140529
141.90689520029-1.31812618912-0.6155061858342.136175574280.2102208901563.206274820130.102767682139-0.1878985288470.2036253258790.244772080043-0.064106367922-0.178950250243-0.3935646991070.3454693341480.0001032669853150.396328619136-0.0729576618975-0.01211632456920.281755854179-0.001352653402390.4135063060334.3568282786524.995440324129.6111691622
152.12084756156-0.5938043577430.4985302026382.284019976770.7912652083643.642672570540.1430235302840.5192504452380.689181684514-0.278550194358-0.0545676199978-0.123727567596-0.6809128494390.09880084583450.0001449648105540.4394398349140.001478588611220.03343226961780.4143059977020.07624630881560.4229512258620.63954081755726.81738521313.4616897301
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 222:228)AA222 - 2281 - 7
22(chain A and resid 229:234)AA229 - 2348 - 13
33(chain A and resid 235:254)AA235 - 25414 - 33
44(chain A and resid 255:273)AA255 - 27334 - 52
55(chain B and resid 57:139)BG57 - 1391 - 83
66(chain B and resid 140:194)BG140 - 19484 - 126
77(chain B and resid 195:211)BG195 - 211127 - 143
88(chain C and resid 222:234)CJ222 - 2341 - 11
99(chain C and resid 235:250)CJ235 - 25012 - 27
1010(chain C and resid 251:256)CJ251 - 25628 - 33
1111(chain C and resid 257:268)CJ257 - 26834 - 45
1212(chain C and resid 269:273)CJ269 - 27346 - 50
1313(chain D and resid 56:68)DN56 - 681 - 13
1414(chain D and resid 69:139)DN69 - 13914 - 84
1515(chain D and resid 140:208)DN140 - 20885 - 141

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