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- PDB-5no1: Crystal structure of the Prototype Foamy Virus (PFV) intasome in ... -

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Basic information

Entry
Database: PDB / ID: 5no1
TitleCrystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ407 (compound 5g)
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 / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / virion component / 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 / establishment of integrated proviral latency / RNA-directed DNA polymerase / virion component / 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 / SH3 type barrels. / Integrase, catalytic core / Integrase catalytic domain profile. / 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-XZ4 / DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman spumaretrovirus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPye, 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
DepositionApr 10, 2017Deposition 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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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

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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)102,16525
Polymers99,9444
Non-polymers2,22121
Water1,964109
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)204,33050
Polymers199,8878
Non-polymers4,44242
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area33300 Å2
ΔGint-440 kcal/mol
Surface area55530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.570, 158.570, 123.060
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, 130 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-XZ4 / methyl 2-[[3-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]-7-methoxy-1-oxidanyl-2-oxidanylidene-1,8-naphthyridin-4-yl]amino]ethanoate


Mass: 448.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18F2N4O6
#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.: 8 / 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: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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, sitting 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: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→79.29 Å / Num. obs: 48670 / % possible obs: 99.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 19.5
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4760 / % possible all: 99.9

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Processing

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

4be2


Resolution: 2.6→56.063 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.98
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2438 5.01 %Random selection
Rwork0.1765 ---
obs0.1779 48668 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→56.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 732 132 109 5353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095472
X-RAY DIFFRACTIONf_angle_d0.7627577
X-RAY DIFFRACTIONf_dihedral_angle_d14.9483136
X-RAY DIFFRACTIONf_chiral_restr0.045839
X-RAY DIFFRACTIONf_plane_restr0.005827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.65310.34651350.30742644X-RAY DIFFRACTION100
2.6531-2.71080.31921520.28682672X-RAY DIFFRACTION100
2.7108-2.77380.31921410.27272670X-RAY DIFFRACTION100
2.7738-2.84320.30391530.24852683X-RAY DIFFRACTION100
2.8432-2.92010.30731500.23622660X-RAY DIFFRACTION100
2.9201-3.0060.30441170.21942723X-RAY DIFFRACTION100
3.006-3.1030.24621320.21882687X-RAY DIFFRACTION100
3.103-3.21390.24531380.22122702X-RAY DIFFRACTION100
3.2139-3.34260.23561350.18712716X-RAY DIFFRACTION100
3.3426-3.49470.24371550.18482676X-RAY DIFFRACTION100
3.4947-3.67890.20631370.17542718X-RAY DIFFRACTION100
3.6789-3.90930.21711500.18062713X-RAY DIFFRACTION100
3.9093-4.21110.17461570.15252718X-RAY DIFFRACTION100
4.2111-4.63470.16341570.13492728X-RAY DIFFRACTION100
4.6347-5.30490.14691540.14542754X-RAY DIFFRACTION100
5.3049-6.68190.20061300.17092819X-RAY DIFFRACTION100
6.6819-56.0760.18651450.16972947X-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)
11.88550.514-0.62371.60511.3491.7192-0.03290.0329-0.0185-0.1846-0.2410.5529-0.1011-0.53480.00020.7983-0.0843-0.05750.8604-0.09780.9422-69.807526.3281-57.3086
20.58040.09050.35270.59730.17932.1102-0.0096-0.1909-0.11170.06820.00230.00320.2887-0.038200.6539-0.01990.06220.68260.04310.7082-34.965736.3624-8.515
31.08360.0618-0.64050.39310.22930.5189-0.3251-0.3961-0.0003-0.21620.17060.1441-0.6381-0.40910.00010.7967-0.00110.04670.7631-0.03960.8861-46.419150.8133-2.019
41.1152-0.1013-0.25160.3930.20881.9316-0.1843-0.152-0.18950.02260.07640.1950.6187-0.06150.00020.8388-0.19830.07390.79540.05940.7959-53.701525.3647-26.7599
52.80110.40440.32580.648-0.89152.8228-0.1456-0.3572-0.06470.08570.0988-0.03540.17950.246400.66570.01090.03070.87120.01760.6976-20.051639.208712.9639
60.58730.2180.17060.78580.09260.076-0.192-0.95550.25810.0202-0.4172-0.21810.11780.28510.00040.8744-0.0120.05471.31160.01880.8109-13.824147.154216.4039
71.4425-0.49990.51031.0775-0.81461.2668-0.1917-0.6939-0.37250.45050.29840.24190.196-0.414900.8996-0.03880.11411.08620.07370.823-33.014132.235717.9878
80.03310.04320.08310.03470.07220.05740.08070.1962-0.2119-1.0297-0.8746-0.2650.456-0.3212-0.0011.6325-0.0310.02631.32580.10891.869-29.199417.168828.4172
90.17930.33370.37370.75771.11142.4919-0.0116-0.20360.09470.0256-0.08090.2545-0.3845-0.1286-00.7031-0.03870.03820.72230.00110.8773-43.4759.1848-13.8944
100.85890.5548-0.14050.9304-0.9241.18720.30360.07280.18470.269-0.56630.1804-0.2013-0.27350.00080.8278-0.02890.03190.7523-0.06020.8511-41.729163.415-16.9216
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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