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- PDB-8a1q: HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Co... -

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Basic information

Entry
Database: PDB / ID: 8a1q
TitleHIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor STP0404 (Pirmitegravir)
ComponentsIntegrase
KeywordsVIRAL PROTEIN / Integrase / HIV / ALLINI / STP0404 / Allosteric Inhibitor / Inhibitor / Retrovirus / INLAI / NCINI / MINI / LEDGIN / pirmitegravir
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-WBV / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 / 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 / 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)105,58823
Polymers103,6184
Non-polymers1,97019
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint12 kcal/mol
Surface area18300 Å2
Unit cell
Length a, b, c (Å)62.262, 69.258, 64.106
Angle α, β, γ (deg.)90.000, 102.380, 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

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


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-WBV / (2S)-tert-butoxy{4-(4-chlorophenyl)-2,3,6-trimethyl-1-[(1-methyl-1H-pyrazol-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-5-yl}acetic acid / Pirmitegravir


Mass: 495.013 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H31ClN4O3 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
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: Dec 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.06→69.26 Å / Num. obs: 33086 / % possible obs: 100 % / Redundancy: 45.99 % / Biso Wilson estimate: 57.5 Å2 / CC1/2: 1 / Rpim(I) all: 0.025 / Rrim(I) all: 0.17 / Net I/σ(I): 19.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.06-2.10.416470.6030.7264.606
2.1-2.130.516460.7521.2328.076
2.13-2.170.616060.8560.9436.294
2.17-2.220.816660.930.6944.701
2.22-2.27116520.9080.4583.137
2.27-2.321.216440.9230.4953.407
2.32-2.381.416470.960.3852.638
2.38-2.441.816350.9630.3042.056
2.44-2.512.316460.9810.2291.552
2.51-2.63.216500.9870.161.081
2.6-2.693.816590.880.1340.923
2.69-2.85.116440.9910.1010.968
2.8-2.927.516590.9960.0690.478
2.92-3.0811.816390.9980.0450.31
3.08-3.2716.916610.9980.0320.219
3.27-3.522716550.9990.0230.155
3.52-3.8843.316710.9990.0170.112
3.88-4.4463.9166310.0130.091
4.44-5.5982.4167110.0110.076
5.59-69.3106.9172510.010.068

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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, 2B4J

6t6e

2b4j


Resolution: 2.06→62.61 Å / SU ML: 0.3666 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.3354
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 1633 4.95 %
Rwork0.2194 31343 -
obs0.2203 32976 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.91 Å2
Refinement stepCycle: LAST / Resolution: 2.06→62.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 132 110 3470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00153442
X-RAY DIFFRACTIONf_angle_d0.45944627
X-RAY DIFFRACTIONf_chiral_restr0.0432495
X-RAY DIFFRACTIONf_plane_restr0.0028577
X-RAY DIFFRACTIONf_dihedral_angle_d10.51131254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.120.42621280.40082555X-RAY DIFFRACTION98.86
2.12-2.190.34651480.35232613X-RAY DIFFRACTION99.57
2.19-2.270.31981100.29652599X-RAY DIFFRACTION99.38
2.27-2.360.29151270.28452590X-RAY DIFFRACTION99.74
2.36-2.470.30851240.27322647X-RAY DIFFRACTION99.82
2.47-2.60.35011250.27712596X-RAY DIFFRACTION99.96
2.6-2.760.27091320.25492613X-RAY DIFFRACTION100
2.76-2.970.28061430.25182617X-RAY DIFFRACTION99.96
2.97-3.270.29711230.24872630X-RAY DIFFRACTION99.96
3.27-3.740.21411580.20922606X-RAY DIFFRACTION100
3.74-4.710.20841520.18442624X-RAY DIFFRACTION100
4.72-62.610.20231630.19222653X-RAY DIFFRACTION99.36
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)
11.02672107572-1.39131239956-0.8459716331892.153985581740.9963027696471.09310631736-0.5367659908650.266247760407-0.8731824406530.3159510488090.04653687306940.918577178782-0.193107693449-0.670956743252-0.1162156304380.665849822762-0.17497238272-0.3441666936391.24058657423-0.06209664853260.793180119821-22.192611754-0.3300199818885.22571049207
20.9509872931160.518639720147-0.3433301076790.410491908689-0.4768603753320.4978513129790.4005472829820.494170478895-0.201557773647-1.33989382042-0.5449244957850.404818436020.09819612175990.651185024775.25301201712E-50.984037453727-0.0588745638801-0.05780116086271.201200725660.001115972339190.868270352717-23.77476536332.496982594434.13867189807
30.4063962232570.305212604224-0.413659252720.985662648243-0.8978547411310.844074248440.03271652738490.4557044202080.488831734102-0.804918268238-0.09039709995770.623746753839-0.285843495845-1.07695749583-0.0005641247211231.06987244676-0.00238122680621-0.09007755984511.46879054931-0.001146159941051.06618536187-27.47768756861.993022432263.21575920375
43.481804769321.85248689684-1.739925980922.73203912272-0.5261610360080.9661553363510.0544070764741.102978438790.843539623974-1.790898242890.2924711993011.16741241758-0.854430177882-0.470740443517-0.002972768739081.00509361485-0.145042804159-0.1600753461341.31620172980.123736339770.57868373498-7.75271932697.474191533231.26120808177
53.29854550577-0.2792624485342.307191797532.531279608530.5394665284881.81199896458-0.2430661947470.0404111456678-1.12989303337-0.07983494642220.0983628114680.1224957499060.646063784351-0.172579477675-0.0007545018279690.563251795741-0.03752949828320.0637265189370.3252842942720.01367505084420.6638491841490.662396393096-7.6860622245519.2236203524
62.188414042590.351966234395-0.4839643762172.665845982020.2300382174821.72422590412-0.2038007563380.920697550316-0.79306699398-0.3418178874490.162263042725-0.1690543802830.255212968968-0.179509023433-9.86100859443E-50.534305343413-0.03859423439280.05247620052540.599190235982-0.14367918880.63757639149-5.5597504988-3.8912235832310.6311691081
70.009395759132610.08756220945920.07530664347340.2493938535690.3194329729810.3674796201880.228643112639-0.579465201199-0.8170641969280.4706586848210.0320162255268-0.6493136713420.604818317422-0.3468962830240.0006204834608211.24926877290.1867866983090.1850447837650.6825778269740.2483652930581.281480820223.097048882-17.719661810417.4451485536
84.88074961172-0.3250488776991.006406330521.199448176410.2145117553541.20790109938-0.00720044850544-0.450724534255-1.071521842720.0707210430693-0.0592079189546-0.5897282698960.4479863235781.1250209914-0.0001026399580080.5670342223840.06024169134650.03533863606570.5356749688250.05117139443930.75124720773412.5742725888-4.0186903984321.894298619
90.7223484554940.226664935152-0.07316388781090.262735344047-0.3142572158741.37651794817-0.418681951476-0.506679776357-0.1182852068280.7525450798270.650298418457-0.1955308999080.1743686220851.073619368920.0008416553751720.9742941815160.135288411814-0.1582750599351.45695066214-0.06167285887380.82002655556811.29700846587.4261585788248.3553011295
100.974094459499-0.535132921473-0.1563035799810.3235845252450.1978631408320.415032326527-0.4258361596831.03405857117-0.1313766888761.108514642290.82464340488-1.39112426823-0.01656723204891.71825244446-6.06696922449E-51.194343164910.0613359972741-0.2869477074841.75596061932-0.003152076907010.96711458259216.10555986647.8955027662253.3201514553
111.52625424368-0.8852837505820.09645634161160.8091396647310.05766577065940.0435455656859-0.764647434845-0.712425077378-2.120867760490.342950491373-0.5009878778670.9436577945841.26910382294-0.457093579745-0.06930364779581.37349347559-0.15784951693-0.08366286629431.306479470690.168386146250.9215752928377.192532058991.4623266491650.7102779151
120.5821003315570.1909786064610.004938378041650.547110864770.1162746818670.405555708705-0.540277139982-0.662227463551-0.2120233867940.8124880803190.853105867092-0.9119483737780.2671821819981.24527126909-0.0147119345220.847207055550.0839305409159-0.2273243477821.26290750949-0.1060888354130.93811627594119.06084651921.1308793324632.453653487
134.24763764422-0.688637369380.1705083208953.54509769437-0.1840211356474.28143948142-0.00540768192737-0.770362071430.3910290826260.216989270968-0.027425486382-0.250723386888-0.7415985314010.2937283608753.08519534529E-50.569775950241-0.06170188604840.01178694386320.515125105269-0.06302893822480.4880482130536.4169450578812.602798879626.343872711
140.3480834775570.0157246155559-0.2692482333710.1149447473640.07579140973380.240322730475-0.639241613023-0.2100833743741.28386571721-0.4848745600770.09190666162560.128383627402-1.080154449540.449629871325-0.0001358743802430.9835760364910.0612292175580.005416312725140.6734039602850.09897384812470.9215335572390.23008956626221.182488733313.8943698398
151.410692176190.6175233695171.630155363012.242335986980.914698764151.97449996424-0.421563383820.719156142720.4769698872-0.1708412110860.08657844581830.0714593348579-0.346500013187-0.3575113771430.0003247414032360.5541738633580.0585310362494-0.03658649212290.5737856098630.06133096656710.55099890066-5.4591564722811.265803684110.8056043752
160.5589035304040.7347656691390.1015612101921.120245989270.4464696842530.6005258830210.518044908810.4635507699451.2218166586-0.542266974123-0.250474821143-1.05019787069-0.1922092344860.5760578094490.0001868961962730.728340388718-0.02541229955030.1880383179510.8264341680380.04096615660520.82616869514817.10888583518.88375960467.86211624389
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 221:232)AA221 - 2321 - 12
22(chain A and resid 233:246)AA233 - 24613 - 26
33(chain A and resid 247:266)AA247 - 26627 - 46
44(chain A and resid 267:277)AA267 - 27747 - 57
55(chain B and resid 57:93)BB57 - 931 - 37
66(chain B and resid 94:140)BB94 - 14038 - 84
77(chain B and resid 141:159)BB141 - 15985 - 99
88(chain B and resid 160:211)BB160 - 211100 - 151
99(chain C and resid 222:245)CK222 - 2451 - 24
1010(chain C and resid 246:259)CK246 - 25925 - 38
1111(chain C and resid 260:266)CK260 - 26639 - 45
1212(chain C and resid 267:279)CK267 - 27946 - 58
1313(chain D and resid 57:139)DL57 - 1391 - 83
1414(chain D and resid 140:164)DL140 - 16484 - 100
1515(chain D and resid 165:189)DL165 - 189101 - 125
1616(chain D and resid 190:211)DL190 - 211126 - 147

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