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- PDB-7adu: Crystal structure of the Prototype Foamy Virus (PFV) intasome in ... -

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Basic information

Entry
Database: PDB / ID: 7adu
TitleCrystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ440 (compound 5j)
Components
  • DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
  • Integrase
KeywordsVIRAL PROTEIN / Integrase / Intasome / Protein DNA complex / INSTI / Drug / HIV / Retrovirus / Integration
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / virion component / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / telomerase activity / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / virion component / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / telomerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding
Similarity search - Function
Endonuclease III; domain 1 - #70 / Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain ...Endonuclease III; domain 1 - #70 / Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Endonuclease III; domain 1 / SH3 type barrels. - #140 / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-R7K / DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman spumaretrovirus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsPye, V.E. / Cherepanov, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteFC10061 United Kingdom
CitationJournal: Acs Infect Dis. / Year: 2021
Title: HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants.
Authors: Smith, S.J. / Zhao, X.Z. / Passos, D.O. / Pye, V.E. / Cherepanov, P. / Lyumkis, D. / Burke Jr., T.R. / Hughes, S.H.
History
DepositionSep 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: 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 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,23926
Polymers99,9444
Non-polymers2,29622
Water3,333185
1
A: Integrase
B: Integrase
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules

A: Integrase
B: Integrase
C: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,47952
Polymers199,8878
Non-polymers4,59244
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area33530 Å2
ΔGint-499 kcal/mol
Surface area56380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.469, 159.469, 123.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Integrase / Pr125Pol


Mass: 44456.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human spumaretrovirus / Gene: pol / Production host: Escherichia coli (E. coli)
References: UniProt: P14350, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, Transferases; ...References: UniProt: P14350, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')


Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')


Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 207 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-R7K / ~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-5-(hydroxymethyl)-1,4-bis(oxidanyl)-2-oxidanylidene-1,8-naphthyridine-3-carboxamide


Mass: 377.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13F2N3O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.93 Å3/Da / Density % sol: 68.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryocooled / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97957 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.62→97.64 Å / Num. obs: 48059 / % possible obs: 99.4 % / Redundancy: 14 % / Biso Wilson estimate: 52.93 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.064 / Net I/σ(I): 11.1
Reflection shellResolution: 2.62→2.66 Å / Redundancy: 14.5 % / Rmerge(I) obs: 2.2 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 33332 / CC1/2: 0.722 / Rpim(I) all: 0.857

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Processing

Software
NameVersionClassification
PHENIXdev_3900refinement
PHENIXdev_3900refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BDZ

4bdz


Resolution: 2.62→71.32 Å / SU ML: 0.3322 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.2919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2315 2414 5.02 %
Rwork0.2021 45645 -
obs0.2036 48059 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.97 Å2
Refinement stepCycle: LAST / Resolution: 2.62→71.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 732 133 185 5430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235458
X-RAY DIFFRACTIONf_angle_d0.52157592
X-RAY DIFFRACTIONf_chiral_restr0.0379841
X-RAY DIFFRACTIONf_plane_restr0.0041826
X-RAY DIFFRACTIONf_dihedral_angle_d17.10852077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.670.4011440.3572557X-RAY DIFFRACTION96.36
2.67-2.730.30441470.34112618X-RAY DIFFRACTION98.71
2.73-2.790.38461340.31332644X-RAY DIFFRACTION98.79
2.79-2.860.34611510.29682605X-RAY DIFFRACTION99.21
2.86-2.940.33371420.28872664X-RAY DIFFRACTION99.19
2.94-3.030.30981200.26072658X-RAY DIFFRACTION99.5
3.03-3.130.30541360.26892682X-RAY DIFFRACTION99.47
3.13-3.240.28171330.24032664X-RAY DIFFRACTION99.64
3.24-3.370.27171370.19752680X-RAY DIFFRACTION99.61
3.37-3.520.24591530.19752648X-RAY DIFFRACTION99.57
3.52-3.710.22531370.18762697X-RAY DIFFRACTION99.79
3.71-3.940.21941460.18642683X-RAY DIFFRACTION99.4
3.94-4.240.17561550.16092680X-RAY DIFFRACTION99.51
4.24-4.670.16371550.14262710X-RAY DIFFRACTION99.31
4.67-5.340.18091540.1572736X-RAY DIFFRACTION99.72
5.35-6.730.20421260.18342787X-RAY DIFFRACTION100
6.73-71.320.21531440.19432932X-RAY DIFFRACTION99.77
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)
10.4384654473480.124654510982-0.07404773369940.491133130890.4730561880650.336537052936-0.0094183303608-0.0429182153654-0.0440778441318-0.0450404713005-0.2628006103890.1825095798520.00899976448454-0.31843902154-0.1211769823080.292479379557-0.0998963701903-0.07191918796550.410972014074-0.1153636786170.447045455674-70.19954544126.5046011573-57.570462712
20.4297156540620.03880310593020.396819409740.3489673265960.1709102508251.58403936923-0.0364120675573-0.162996497762-0.01723822571190.03353393846220.02057451932480.0001273386646130.239904467395-0.0334551102945-0.0003371776213180.28431605388-0.03084453534280.05374136880770.3012878004890.03373853113710.292526480752-35.175741260936.6124987347-8.6601981427
30.366594944845-0.222378550304-0.1856305468380.01058197335430.3355056227410.168401737278-0.350764307247-0.221671836012-0.0513978201489-0.3178323705150.1581078040670.134209109637-0.760465301634-0.303640500779-0.00207255461420.473843732276-0.01996115854920.04089146918480.533891479197-0.03549603747860.476109541742-46.755109649251.0720455624-1.95102010211
40.322601121572-0.124638415654-0.09332286294220.6874539589960.01587461029912.2494855341-0.141004919133-0.173263240465-0.1363216586290.1019851723930.1094063668030.1520861002580.961113255121-0.1496975408110.3292810394640.431537882301-0.2704874658860.08611120489140.3915087353960.04773489672150.394227771306-54.052055443225.5020427834-26.8458753871
50.577075093095-0.1102750243310.01094061062340.395533180465-0.1312584322960.768489081518-0.0635736307238-0.276344336594-0.06779045026960.111199537175-0.007414736055620.08279152574950.04169749635410.1773147625243.38365452075E-60.312334541463-0.001317062593850.01104885452410.5065902769210.02702543000920.332161396961-20.149862141939.369273099513.0309953342
60.1508438019090.3414098222560.0823015568051.330749982740.3704064760430.112831405968-0.285141777185-0.8959845918380.603792753453-0.162415640953-0.3146341017280.03266394149980.09137460297210.224387401575-0.2749002258610.3409194174750.01875478840080.1230291295421.02387359608-0.004024814098390.343651801256-13.938092890347.353950445716.4959922518
70.4195208586970.0911951890397-0.07192521467820.2292693028730.04019016251480.422921432485-0.0982525289185-0.610392203154-0.255469995410.4229405682650.1139550462630.2078070121380.244477171902-0.4113048442810.04282293277530.511060825768-0.03814993214220.1080597395410.6843030803170.07259182432090.384944359877-33.370240968132.392145400618.1270773026
80.03466883106960.002310895426290.0483310273478-0.0003673250559960.03648268728990.00676013570879-0.570795364398-0.02815642250070.231568082695-0.33510706988-0.7498344749460.2645806409730.621029491129-0.21710577762-0.0002110172739041.419584745190.07625290342120.01177481425091.08404022780.1098519298551.45999947648-29.291987178217.199121633128.4809084952
9-0.03127054970820.6528669856030.04683989184610.483695461129-0.09279099889150.763437174741-0.0417264090131-0.0892209017592-9.7056914792E-50.0646632817063-0.002836854007670.164505035705-0.222764898528-0.184093249982-0.0006733115260480.368201301603-0.04022931473150.01798520171980.343584048855-0.01293141903550.483170669029-43.774386132159.4970392056-13.913868777
100.3294567142850.293893832127-0.8483695387690.318547261792-0.537817347399-0.1013737796810.3153735870790.05263987625330.01563618779560.0662071415454-0.437551413871-0.0836643135125-0.173631438264-0.261801156094-0.01978507259830.457917101286-0.035563791509-0.03308780146160.322828833331-0.04516078439930.397638747971-41.981590418763.8015331702-16.9469379805
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 9:98)AA9 - 981 - 90
22(chain A and resid 99:280)AA99 - 28091 - 272
33(chain A and resid 281:315)AA281 - 315273 - 307
44(chain A and resid 316:375)AA316 - 375308 - 367
55(chain B and resid 116:196)BB116 - 1961 - 81
66(chain B and resid 197:215)BB197 - 21582 - 100
77(chain B and resid 216:280)BB216 - 280101 - 165
88(chain B and resid 281:297)BB281 - 297166 - 182
99(chain C and resid 1:19)CC1 - 19
1010(chain D and resid 1:17)DD1 - 17

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