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

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Basic information

Entry
Database: PDB / ID: 5frm
TitleCrystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ384 (compound 4a)
Components
  • 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*CP*GP*CP*A)-3'
  • 5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP *AP*CP*A)-3'
  • PFV INTEGRASE
KeywordsRECOMBINATION / VIRAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / TRANSFERASE / VIRAL NUCLEOPROTEIN / VIRION / DNA- BINDING / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / INHIBITOR / DNA-BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / 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 ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / 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 / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / 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 ...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 / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / Special / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Aspartic peptidase domain 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
Chem-WA5 / DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHUMAN SPUMARETROVIRUS
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsMaskell, D.P. / Pye, V.E. / Cherepanov, P.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: HIV-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases.
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.J.
History
DepositionDec 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_seq_map_depositor_info
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*CP*GP*CP*A)-3'
D: 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)101,81622
Polymers99,9444
Non-polymers1,87318
Water2,432135
1
A: PFV INTEGRASE
B: PFV INTEGRASE
C: 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*CP*GP*CP*A)-3'
D: 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: 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*CP*GP*CP*A)-3'
D: 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)203,63244
Polymers199,8878
Non-polymers3,74536
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area32830 Å2
ΔGint-346.8 kcal/mol
Surface area55960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.737, 159.737, 123.528
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 / PRO-POL POLYPROTEIN PR125POL / P87PRO-RT-RNASEH / P65PRO-RT / P42IN / PFV INTEGRASE


Mass: 44456.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN SPUMARETROVIRUS / Strain: HSRV2 / Variant: POL / Plasmid: PSSH6P-PFV-INFL / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): PC2 / References: UniProt: P14350

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain 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 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, 153 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.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-WA5 / 4-azanylidene-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide


Mass: 346.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12F2N4O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSYNTHETIC CONSTRUCT

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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: 3.17 Å3/Da / Density % sol: 65 % / Description: PROTEIN AND DNA COMPONENTS USED FROM 4BDZ
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, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97957
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.58→48.9 Å / Num. obs: 50773 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Redundancy: 11.5 % / Biso Wilson estimate: 69.16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.4
Reflection shellResolution: 2.58→2.72 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BDZ

4bdz


Resolution: 2.58→48.897 Å / SU ML: 0.29 / σ(F): 0.17 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 4876 5.1 %
Rwork0.1849 --
obs0.1858 50703 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.375 Å2
Refinement stepCycle: LAST / Resolution: 2.58→48.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 732 113 135 5338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055413
X-RAY DIFFRACTIONf_angle_d0.6437537
X-RAY DIFFRACTIONf_dihedral_angle_d15.7223086
X-RAY DIFFRACTIONf_chiral_restr0.043835
X-RAY DIFFRACTIONf_plane_restr0.005820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.60930.33331560.3013036X-RAY DIFFRACTION100
2.6093-2.640.30691560.28943044X-RAY DIFFRACTION100
2.64-2.67220.32811850.28872995X-RAY DIFFRACTION100
2.6722-2.7060.28931750.28933055X-RAY DIFFRACTION100
2.706-2.74160.33021710.27923009X-RAY DIFFRACTION100
2.7416-2.77920.29381560.27013057X-RAY DIFFRACTION100
2.7792-2.81890.29691600.24743039X-RAY DIFFRACTION100
2.8189-2.8610.31431940.24733039X-RAY DIFFRACTION100
2.861-2.90570.27831770.25743005X-RAY DIFFRACTION100
2.9057-2.95330.30861640.24553061X-RAY DIFFRACTION100
2.9533-3.00420.29111250.23493065X-RAY DIFFRACTION100
3.0042-3.05880.24661550.24823073X-RAY DIFFRACTION100
3.0588-3.11770.25921450.22973001X-RAY DIFFRACTION100
3.1177-3.18130.26971580.22263058X-RAY DIFFRACTION100
3.1813-3.25050.2361560.223050X-RAY DIFFRACTION100
3.2505-3.32610.24461230.2063078X-RAY DIFFRACTION100
3.3261-3.40920.2531970.19892985X-RAY DIFFRACTION100
3.4092-3.50140.24971640.20473060X-RAY DIFFRACTION100
3.5014-3.60440.221580.20383034X-RAY DIFFRACTION100
3.6044-3.72070.22361490.1843062X-RAY DIFFRACTION100
3.7207-3.85360.20071720.1843023X-RAY DIFFRACTION100
3.8536-4.00780.21691670.18083010X-RAY DIFFRACTION100
4.0078-4.19010.16691730.15483045X-RAY DIFFRACTION100
4.1901-4.41090.14651850.14643031X-RAY DIFFRACTION100
4.4109-4.68710.15261650.14353044X-RAY DIFFRACTION100
4.6871-5.04860.14931650.14633048X-RAY DIFFRACTION100
5.0486-5.5560.19071720.16233019X-RAY DIFFRACTION100
5.556-6.35850.19991530.17713033X-RAY DIFFRACTION100
6.3585-8.00540.1681410.16033071X-RAY DIFFRACTION100
8.0054-48.90540.15911590.17193032X-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)
11.82870.419-0.97331.91971.41492.06830.01050.1879-0.1325-0.289-0.18450.66830.0148-0.80900.7746-0.0993-0.08110.8822-0.07070.9334-70.29226.5289-57.5935
20.57210.17410.53880.31550.27641.5827-0.0199-0.1125-0.09630.0261-0.00630.0080.25780.002200.6384-0.02450.05870.64820.02690.6542-35.018636.6149-8.5544
30.7992-0.1763-0.27170.4264-0.08440.6718-0.2628-0.35520.1652-0.1453-0.01120.1555-0.5657-0.45310.00040.7456-0.00850.0630.7919-0.01150.8583-47.00850.7067-2.469
40.53830.09720.30130.1085-0.16960.553-0.0675-0.38460.0844-0.04350.06560.21630.58080.059700.7507-0.16490.0560.7330.02050.7609-52.581724.2462-29.9666
51.00030.4022-0.25820.234-0.35090.9355-0.1705-0.309-0.3529-0.0458-0.05660.03660.7064-0.37350.00010.8758-0.17950.08740.7580.03580.7653-55.695526.3073-24.0708
63.7265-0.46820.21671.3802-0.55163.02-0.088-0.3359-0.0093-0.0336-0.0198-0.10230.0350.419100.65740.01840.03960.84410.01180.6271-18.84940.952913.206
72.27160.45130.22652.1979-0.76392.1039-0.0978-0.8158-0.25110.46460.09740.02520.1984-0.110600.8617-0.03040.08531.02250.01290.703-31.763733.003318.5129
80.23380.28320.0730.26770.0693-0.0042-0.36-0.46830.01030.57230.46530.6180.8321-0.703-0.00011.7612-0.1570.03681.5930.1071.6994-31.273119.040126.9497
90.4326-0.30660.05080.37130.17520.328-0.1459-0.6695-0.90371.11620.1975-0.33771.103-1.1359-0.00060.9343-0.23660.05730.93170.1530.8869-50.973932.5975-13.2903
10-0.03490.5326-0.29240.4854-0.31870.41540.1553-0.02790.16060.1173-0.23030.231-0.4911-0.22450.00010.8416-0.01580.00970.683-0.01520.8612-41.89566.3557-14.1082
110.21550.13860.26310.5145-0.31430.5564-0.0058-0.32670.21540.2174-0.27510.18170.31-0.35040.00011.1159-0.02410.12250.7764-0.05970.9838-44.022480.2822-13.0934
121.37970.38370.23380.3297-0.26330.46030.21070.37460.024-0.0116-0.6108-0.0344-0.0492-0.29640.00010.7095-0.0534-0.00610.6635-0.02920.7589-40.577952.1534-19.6226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 8:98)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 99:280)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 281:316)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 317:345)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 346:375)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 116:212)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 213:277)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 278:299)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 1:4)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 5:19)
11X-RAY DIFFRACTION11(CHAIN D AND RESID 1:7)
12X-RAY DIFFRACTION12(CHAIN D AND RESID 8:17)

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