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

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Basic information

Entry
Database: PDB / ID: 5mma
TitleCrystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ379 (compound 5'g)
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 / 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 / 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
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-VHT / DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman spumaretrovirus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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: 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)102,51729
Polymers99,9444
Non-polymers2,57425
Water4,125229
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)205,03558
Polymers199,8878
Non-polymers5,14750
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area35350 Å2
ΔGint-310 kcal/mol
Surface area56160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.570, 159.570, 124.140
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 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 , 8 types, 254 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.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-VHT / methyl 2-[[3-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridin-4-yl]amino]ethanoate


Mass: 418.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16F2N4O5
#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: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.95 Å3/Da / Density % sol: 68.89 %
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: 0.97957 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: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.55→71.36 Å / Num. obs: 52567 / % possible obs: 99.8 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 26.6
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 11 % / Rmerge(I) obs: 1.49 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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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: 2.55→71.36 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.61
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 2601 4.95 %random selection
Rwork0.1788 ---
obs0.1801 52565 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 71.7 Å2
Refinement stepCycle: LAST / Resolution: 2.55→71.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 732 159 229 5494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055522
X-RAY DIFFRACTIONf_angle_d0.5637635
X-RAY DIFFRACTIONf_dihedral_angle_d14.6493162
X-RAY DIFFRACTIONf_chiral_restr0.04844
X-RAY DIFFRACTIONf_plane_restr0.004829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.59650.4221370.37222563X-RAY DIFFRACTION99
2.5965-2.64640.28381480.29172557X-RAY DIFFRACTION99
2.6464-2.70040.25731510.25242582X-RAY DIFFRACTION99
2.7004-2.75920.26911280.24712588X-RAY DIFFRACTION100
2.7592-2.82330.30721350.23732577X-RAY DIFFRACTION100
2.8233-2.8940.27091320.21532609X-RAY DIFFRACTION100
2.894-2.97220.21481280.20962603X-RAY DIFFRACTION100
2.9722-3.05970.22141480.20242590X-RAY DIFFRACTION100
3.0597-3.15840.2481370.20342593X-RAY DIFFRACTION100
3.1584-3.27130.23461470.21322610X-RAY DIFFRACTION100
3.2713-3.40230.24611490.20112594X-RAY DIFFRACTION100
3.4023-3.55710.24111420.18982630X-RAY DIFFRACTION100
3.5571-3.74470.22331250.17732638X-RAY DIFFRACTION100
3.7447-3.97920.20551570.17022614X-RAY DIFFRACTION100
3.9792-4.28650.18081280.14942646X-RAY DIFFRACTION100
4.2865-4.71770.14841250.13752684X-RAY DIFFRACTION100
4.7177-5.40020.18271310.14952683X-RAY DIFFRACTION100
5.4002-6.80290.17581230.16762729X-RAY DIFFRACTION100
6.8029-71.38980.18191300.17282874X-RAY DIFFRACTION100
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)
10.35580.3120.06420.5110.38640.36930.0621-0.0911-0.24450.0055-0.17960.24520.1851-0.281500.5041-0.0814-0.05150.6063-0.08680.6612-70.20726.4589-57.7623
20.3183-0.10780.30450.1430.02191.2493-0.0161-0.14850.0032-0.00030.00670.02860.2001-0.0435-00.4359-0.03470.04370.45680.02960.4614-35.063736.4599-8.5636
30.4196-0.2652-0.27540.17010.24940.1767-0.1772-0.18820.1544-0.09990.01190.1554-0.2188-0.4510.00020.52850.00960.07070.6104-0.00430.6487-46.664450.9806-2.0719
40.2816-0.1419-0.04320.05570.06110.4493-0.16730.008-0.0134-0.03060.12340.11170.4677-0.2818-0.00080.5636-0.19190.07830.53620.04760.5557-54.15925.3669-27.0508
50.3169-0.02620.36410.1962-0.08580.464-0.1148-0.34340.0180.06690.10770.05670.04140.2702-00.4950.01490.03810.655-0.00540.4634-20.094739.357213.0552
60.210.1830.1540.48180.28390.1868-0.2186-0.69110.5082-0.1404-0.0655-0.2023-0.10290.3516-0.00780.5451-0.01430.03941.07940.01180.5302-13.851447.351516.5422
70.21920.23730.03150.2581-0.12110.2673-0.1449-0.4007-0.21210.2410.09610.29180.2715-0.3654-00.6347-0.03260.09040.82120.03670.516-33.312432.366118.1259
80.04880.02220.03870.01470.0190.0133-0.464-0.12420.0083-0.0555-0.33470.38910.6127-0.0212-0.00041.33580.06810.01791.14670.1351.2238-29.287417.130128.4608
90.02520.2924-0.18320.307-0.30860.88140.0409-0.1767-0.07610.0754-0.10330.1215-0.208-0.148400.5836-0.03530.04250.5027-0.01780.6564-43.712759.4001-14.0359
100.15990.2098-0.38380.2739-0.38860.33290.18530.0766-0.0135-0.0389-0.30210.0048-0.1587-0.20890.00010.5813-0.0155-0.00260.4346-0.06720.5598-41.576962.1875-17.3089
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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