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- PDB-5mmb: Crystal structure of the Prototype Foamy Virus (PFV) intasome in ... -

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Basic information

Entry
Database: PDB / ID: 5mmb
TitleCrystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ434 (compound 6p)
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')
  • PFV INTEGRASE
KeywordsVIRAL PROTEIN / HIV / PFV / prototype foamy virus / integrase / strand transfer / INSTI / tetramer / intasome / integration / inhibitor / drug
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / virion component / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / virion component / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase 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 / DNA-directed DNA polymerase activity / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #110 / 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 ...Arc Repressor Mutant, subunit A - #110 / 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 / Arc Repressor Mutant, subunit A / 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 / Helix non-globular / Ribonuclease H-like superfamily/Ribonuclease H / Special / 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. / Nucleotidyltransferase; domain 5 / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HEXANE-1,6-DIOL / Chem-OUY / DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman spumaretrovirus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsMaskell, D.P. / Pye, V.E. / Cherepanov, P.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors.
Authors: Zhao, X.Z. / Smith, S.J. / Maskell, D.P. / Metifiot, M. / Pye, V.E. / Fesen, K. / Marchand, C. / Pommier, Y. / Cherepanov, P. / Hughes, S.H. / Burke, T.R.
History
DepositionDec 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 30, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Jan 17, 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: PFV INTEGRASE
B: PFV 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)102,37828
Polymers99,9444
Non-polymers2,43424
Water1,856103
1
A: PFV INTEGRASE
B: PFV 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: PFV INTEGRASE
B: PFV 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)204,75656
Polymers199,8878
Non-polymers4,86948
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area35240 Å2
ΔGint-452 kcal/mol
Surface area56120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.490, 160.490, 123.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PFV INTEGRASE / Pr125Pol


Mass: 44456.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: G217S, S218G = natural variance / 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, 127 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-OUY / methyl 3-[5-azanyl-6-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]-8-oxidanyl-7-oxidanylidene-1,8-naphthyridin-3-yl]propanoate


Mass: 432.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18F2N4O5
#9: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 3.99 Å3/Da / Density % sol: 69.17 %
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
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→71.77 Å / Num. obs: 40992 / % possible obs: 98.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.9
Reflection shellResolution: 2.77→2.84 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.075 / Mean I/σ(I) obs: 2 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BE2

4be2


Resolution: 2.77→57.765 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.06
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 2057 5.02 %Random selectino
Rwork0.1838 ---
obs0.1848 40989 98.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 76 Å2
Refinement stepCycle: LAST / Resolution: 2.77→57.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 732 146 103 5361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045481
X-RAY DIFFRACTIONf_angle_d0.5877584
X-RAY DIFFRACTIONf_dihedral_angle_d15.0283132
X-RAY DIFFRACTIONf_chiral_restr0.041840
X-RAY DIFFRACTIONf_plane_restr0.004827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7701-2.83460.35921360.30692500X-RAY DIFFRACTION97
2.8346-2.90540.35221530.28572531X-RAY DIFFRACTION98
2.9054-2.9840.28191290.25492563X-RAY DIFFRACTION98
2.984-3.07180.31541220.24842604X-RAY DIFFRACTION99
3.0718-3.17090.26651270.2382569X-RAY DIFFRACTION99
3.1709-3.28430.24641290.24182585X-RAY DIFFRACTION99
3.2843-3.41570.25331420.22212574X-RAY DIFFRACTION99
3.4157-3.57120.23011410.19662582X-RAY DIFFRACTION99
3.5712-3.75940.24511230.18772598X-RAY DIFFRACTION98
3.7594-3.99490.20661400.1842591X-RAY DIFFRACTION99
3.9949-4.30330.17331570.1582587X-RAY DIFFRACTION99
4.3033-4.73610.17391490.14152615X-RAY DIFFRACTION99
4.7361-5.4210.16851500.15222591X-RAY DIFFRACTION98
5.421-6.82820.15921240.1692670X-RAY DIFFRACTION98
6.8282-57.77790.17151350.17052772X-RAY DIFFRACTION97
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)
11.98660.2563-1.01241.85211.26761.84940.02990.1303-0.1445-0.1949-0.31970.6230.1239-0.8061-00.6966-0.1046-0.0740.831-0.09250.887-70.822726.7775-57.6662
20.59520.05480.44940.50040.17351.8871-0.0148-0.1827-0.04670.07810.0016-0.02080.2949-0.0393-00.5735-0.03410.05580.58960.02720.5969-35.629437.1037-8.7362
30.4848-0.126-0.23580.349-0.18770.3815-0.2728-0.4351-0.0605-0.2620.1060.1582-0.8237-0.638-0.00010.6943-0.01140.06820.7218-0.06430.826-46.806351.773-1.7936
40.6454-0.1905-0.35720.6034-0.06391.6223-0.1947-0.2034-0.29780.19160.03170.26080.6825-0.1506-00.7555-0.1910.06650.70220.04740.7402-54.651725.9729-26.8942
52.78820.74860.31410.8737-1.06752.844-0.1095-0.307-0.04830.07160.0484-0.17870.22990.3433-00.5857-0.00730.030.7818-0.01970.5908-20.418639.755512.9699
60.56620.12270.30330.80730.11820.1815-0.3204-0.6350.18520.1448-0.3207-0.15360.35110.981500.80290.0370.0941.27660.03460.6981-14.199647.716816.4916
71.50930.07820.94131.1613-0.85441.7077-0.1212-0.7901-0.36550.6040.16490.23570.3503-0.327500.8461-0.05560.11410.99870.03880.7034-33.587432.762518.0628
80.0740.10170.05350.14290.07750.0397-0.30610.4065-0.7067-0.461-0.4480.53090.6913-0.7394-0.00021.54980.01980.10071.47830.34491.8712-29.683117.83528.5551
90.10810.12270.27010.87091.48242.62690.0421-0.14240.09710.0365-0.11790.3348-0.4193-0.2647-00.5818-0.03710.03650.5872-0.00210.7531-44.161360.1701-14.0064
101.0590.5648-0.32230.7978-0.94131.42940.26970.10690.14470.1983-0.46960.3002-0.2913-0.2683-0.00010.6661-0.06660.02720.6281-0.05370.7244-42.357564.4125-17.0449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 9:98)
2X-RAY DIFFRACTION2(chain A and resid 99:280)
3X-RAY DIFFRACTION3(chain A and resid 281:315)
4X-RAY DIFFRACTION4(chain A and resid 316:375)
5X-RAY DIFFRACTION5(chain B and resid 116:196)
6X-RAY DIFFRACTION6(chain B and resid 197:215)
7X-RAY DIFFRACTION7(chain B and resid 216:280)
8X-RAY DIFFRACTION8(chain B and resid 281:297)
9X-RAY DIFFRACTION9(chain C and resid 1:19)
10X-RAY DIFFRACTION10(chain D and resid 1:17)

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