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

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Basic information

Entry
Database: PDB / ID: 5fro
TitleCrystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ446 (compound 4f)
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
KeywordsTRANSFERASE / RECOMBINATION / VIRAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / VIRAL NUCLEOPROTEIN / VIRION / DNA- BINDING / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / INHIBITOR / DNA-BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / virion component / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / virion component / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / 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
Chem-XXJ / DNA / DNA (> 10) / Pro-Pol polyprotein
Similarity search - Component
Biological speciesHUMAN SPUMARETROVIRUS
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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_asym_id / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry / _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)101,53719
Polymers99,9444
Non-polymers1,59415
Water3,513195
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)203,07438
Polymers199,8878
Non-polymers3,18730
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area31760 Å2
ΔGint-345.7 kcal/mol
Surface area56060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.900, 159.900, 123.770
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


Mass: 44456.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: UNIPROT KB P14350 / 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 , 6 types, 210 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-XXJ / 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide


Mass: 514.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20F2N4O5S
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSYNTHETIC

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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: 1
DetectorType: DECTRIS PILATUS 6M / 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: 2.67→56.53 Å / Num. obs: 44515 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 14.4 % / Biso Wilson estimate: 61.13 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.4
Reflection shellResolution: 2.67→2.77 Å / Redundancy: 7 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2 / % possible all: 98

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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: 2.67→56.533 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 4274 5.1 %
Rwork0.181 --
obs0.1821 44474 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.031 Å2
Refinement stepCycle: LAST / Resolution: 2.67→56.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 732 95 195 5383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065410
X-RAY DIFFRACTIONf_angle_d0.6187500
X-RAY DIFFRACTIONf_dihedral_angle_d15.6643087
X-RAY DIFFRACTIONf_chiral_restr0.04836
X-RAY DIFFRACTIONf_plane_restr0.005822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.70030.2821490.30042706X-RAY DIFFRACTION98
2.7003-2.73210.33621560.29772686X-RAY DIFFRACTION98
2.7321-2.76540.34311450.28572707X-RAY DIFFRACTION98
2.7654-2.80040.32111370.27012708X-RAY DIFFRACTION98
2.8004-2.83730.30941510.26232660X-RAY DIFFRACTION98
2.8373-2.87610.27411640.2742683X-RAY DIFFRACTION97
2.8761-2.91720.30481590.26632706X-RAY DIFFRACTION98
2.9172-2.96080.33611380.25182697X-RAY DIFFRACTION98
2.9608-3.0070.25261050.23862733X-RAY DIFFRACTION97
3.007-3.05630.24541380.2422675X-RAY DIFFRACTION98
3.0563-3.1090.2711450.21572720X-RAY DIFFRACTION98
3.109-3.16560.2721200.21232708X-RAY DIFFRACTION97
3.1656-3.22640.22931350.21372646X-RAY DIFFRACTION97
3.2264-3.29230.19561170.20122731X-RAY DIFFRACTION97
3.2923-3.36390.26881520.19082688X-RAY DIFFRACTION98
3.3639-3.44210.2331680.19642652X-RAY DIFFRACTION97
3.4421-3.52820.23841390.19612677X-RAY DIFFRACTION97
3.5282-3.62360.20491470.17962692X-RAY DIFFRACTION97
3.6236-3.73020.18861310.17632703X-RAY DIFFRACTION97
3.7302-3.85050.1781370.17372668X-RAY DIFFRACTION97
3.8505-3.98810.19621470.16512679X-RAY DIFFRACTION97
3.9881-4.14780.16971630.15612655X-RAY DIFFRACTION97
4.1478-4.33650.1561750.14092622X-RAY DIFFRACTION97
4.3365-4.5650.14091260.13532660X-RAY DIFFRACTION96
4.565-4.85090.13341580.13712642X-RAY DIFFRACTION97
4.8509-5.22520.16561500.14032641X-RAY DIFFRACTION96
5.2252-5.75050.17781570.15452623X-RAY DIFFRACTION96
5.7505-6.58160.19991090.17582672X-RAY DIFFRACTION95
6.5816-8.28790.17031260.16592601X-RAY DIFFRACTION95
8.2879-56.54580.19591300.1792625X-RAY DIFFRACTION94
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)
10.3750.228-0.00390.52420.50220.5963-0.0586-0.0263-0.1201-0.1162-0.14730.2885-0.0323-0.286300.4351-0.0629-0.07480.5193-0.07810.5937-70.404926.585-57.6537
20.57790.17070.25810.370.00321.11680.0106-0.1668-0.0370.0493-0.0401-0.00090.17520.022900.4252-0.01280.03940.43790.02140.4401-35.199636.7831-8.6816
30.3238-0.108-0.20430.05660.09160.1519-0.2438-0.18650.0997-0.16140.03130.1896-0.4302-0.26170.00020.54430.01040.0450.5996-0.0210.6202-47.094350.8684-2.5025
40.0790.01810.01850.0712-0.10450.1681-0.16-0.3147-0.2688-0.01930.07380.09280.69190.09210.00040.5035-0.14850.05090.56670.04540.5912-52.80424.474-29.9594
50.2040.0684-0.22290.0498-0.06620.2244-0.2491-0.15410.0485-0.1380.10530.03640.4348-0.36290.00010.6167-0.13780.07420.50440.04850.5352-55.863626.554-24.066
60.5732-0.2238-0.0640.3766-0.02870.5504-0.1286-0.24350.06350.04290.0256-0.00310.02930.303400.4850.01560.03180.6720.01530.4675-18.962341.062913.2021
70.24040.0958-0.24490.337-0.22810.4048-0.1103-0.5446-0.06460.28980.1070.17670.0984-0.249900.5942-0.01640.07420.74550.02290.4578-31.976933.248418.5706
80.04810.04330.00760.03550.0037-0.0028-0.2346-0.09730.07350.1478-0.01690.51660.5213-0.57620.00011.3164-0.13560.09351.15530.19091.3536-31.959119.39926.9623
90.131-0.0973-0.02980.07350.02310.0052-0.0575-0.69760.21310.42030.07860.12020.522-0.4330.00290.6336-0.17280.03420.630.14920.5782-51.16332.818-13.3457
100.23330.2568-0.08240.2582-0.20730.4120.1564-0.05070.04350.0622-0.25860.1214-0.4172-0.220400.5806-0.00420.0380.4232-0.02270.5701-41.991966.5549-14.1435
110.05250.03920.00630.1385-0.15590.20230.1192-0.2133-0.18640.3622-0.46650.24850.30290.0797-0.01040.8148-0.0010.11190.4535-0.07450.5674-44.061580.5044-13.1225
120.17340.0426-0.04810.0649-0.07590.07070.03060.14520.00190.2319-0.4738-0.05420.0031-0.06190.00010.5411-0.04090.00580.4927-0.0340.6101-40.717252.3941-19.6795
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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