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- PDB-9fi9: Human PIF + Z48847594 (OCCUPANCY 0.7) -

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Basic information

Entry
Database: PDB / ID: 9fi9
TitleHuman PIF + Z48847594 (OCCUPANCY 0.7)
ComponentsATP-dependent DNA helicase PIF1
KeywordsDNA BINDING PROTEIN / HELICASE / INHIBITOR / COMPLEX / AMPPNP
Function / homology
Function and homology information


protein-DNA-RNA complex disassembly / 5'-3' DNA/RNA helicase activity / telomerase inhibitor activity / G-quadruplex DNA binding / mitochondrial genome maintenance / single-stranded DNA helicase activity / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / mitochondrial nucleoid / Telomere Extension By Telomerase ...protein-DNA-RNA complex disassembly / 5'-3' DNA/RNA helicase activity / telomerase inhibitor activity / G-quadruplex DNA binding / mitochondrial genome maintenance / single-stranded DNA helicase activity / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / mitochondrial nucleoid / Telomere Extension By Telomerase / telomere maintenance via telomerase / 5'-3' DNA helicase activity / DNA recombination / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromosome, telomeric region / DNA repair / magnesium ion binding / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / nucleus
Similarity search - Function
: / : / DNA helicase Pif1, 2B domain / : / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / N-[4-(2-amino-1,3-thiazol-4-yl)phenyl]acetamide / ATP-dependent DNA helicase PIF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.727 Å
AuthorsBax, B.D. / Sanders, C.M. / Antson, A.A. / Brandao-Neto, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light SourceLB19204 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structure-based discovery of first inhibitors targeting the helicase activity of human PIF1.
Authors: Wever, M.J.A. / Scommegna, F.R. / Egea-Rodriguez, S. / Dehghani-Tafti, S. / Brandao-Neto, J. / Poisson, J.F. / Helfrich, I. / Antson, A.A. / Rodeschini, V. / Bax, B. / Roche, D. / Sanders, C.M.
History
DepositionMay 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase PIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2865
Polymers45,5001
Non-polymers7874
Water11,061614
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-21 kcal/mol
Surface area18500 Å2
Unit cell
Length a, b, c (Å)73.6, 143.714, 77.238
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-901-

HOH

21A-1249-

HOH

31A-1487-

HOH

41A-1493-

HOH

51A-1500-

HOH

61A-1504-

HOH

71A-1505-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ATP-dependent DNA helicase PIF1 / DNA repair and recombination helicase PIF1 / PIF1/RRM3 DNA helicase-like protein


Mass: 45499.582 Da / Num. of mol.: 1 / Mutation: 426 oxidised cysteine
Source method: isolated from a genetically manipulated source
Details: The electron density map suggested CYS 426 was oxidised
Source: (gene. exp.) Homo sapiens (human) / Gene: PIF1, C15orf20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H611, DNA helicase

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Non-polymers , 5 types, 618 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-O0J / N-[4-(2-amino-1,3-thiazol-4-yl)phenyl]acetamide


Mass: 233.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11N3OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: XCHEM 0.045ULS COMPOUND (0.5M) IN DMSO ECHO DISPENSED INTO CRYSTAL DROP DROP = 0.3ULS PROTEIN + 0.3ULS WELL +0.001ULS SEEDS. PROTEIN = 25ULS 30MGS/ML HUMAN PIF1 (206-620) IN 10MM TRIS PH 7. ...Details: XCHEM 0.045ULS COMPOUND (0.5M) IN DMSO ECHO DISPENSED INTO CRYSTAL DROP DROP = 0.3ULS PROTEIN + 0.3ULS WELL +0.001ULS SEEDS. PROTEIN = 25ULS 30MGS/ML HUMAN PIF1 (206-620) IN 10MM TRIS PH 7.5, 175MM NACL, 2%GLYCEROL, 5MM DTT, 0.1MM PMSF + 21ULS 10MM TRIS, 2.7ULS 0.2M MGCL2, 5ULS 100MM AMPPNP + 27ULS H2O. WELL = 4% GLYCEROL, 27% PEG 2KMME, 0.1M NAACETATE, 0.1M TRIS PH8.5. SET UP ON DOUGLAS INSTRUMENTS ROBOT - TRAY ON ICE - SET-UP ROOM TEMPERATURE - CRYSTALLISED 4 DEGREES C.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.727→27.849 Å / Num. obs: 43220 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 19.5
Reflection shellResolution: 1.727→1.772 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3023 / CC1/2: 0.866

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.727→27.849 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.982 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.111 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1943 2134 4.94 %
Rwork0.1545 41061 -
all0.156 --
obs-43195 99.617 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.497 Å2
Baniso -1Baniso -2Baniso -3
1--2.317 Å20 Å2-0 Å2
2--1.102 Å20 Å2
3---1.214 Å2
Refinement stepCycle: LAST / Resolution: 1.727→27.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 49 614 3848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123784
X-RAY DIFFRACTIONr_angle_refined_deg1.811.8365188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.885.86552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43610680
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.33210170
X-RAY DIFFRACTIONr_chiral_restr0.1190.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022944
X-RAY DIFFRACTIONr_nbd_refined0.230.21740
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22406
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.2512
X-RAY DIFFRACTIONr_metal_ion_refined0.2590.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.2133
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.299
X-RAY DIFFRACTIONr_mcbond_it2.1282.381894
X-RAY DIFFRACTIONr_mcangle_it3.0154.2642428
X-RAY DIFFRACTIONr_scbond_it3.3472.7891890
X-RAY DIFFRACTIONr_scangle_it5.0684.9472745
X-RAY DIFFRACTIONr_lrange_it11.2634.83220545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.727-1.7720.2711590.26428880.26531700.9380.94196.11990.254
1.772-1.820.31590.2428820.24330420.9380.95599.96710.225
1.82-1.8730.261480.21328690.21530170.9390.9631000.201
1.873-1.930.2591430.20927740.21129200.9540.96399.89730.191
1.93-1.9930.2391460.18626820.18828290.9440.97299.96470.165
1.993-2.0620.1821300.15826010.15927310.9720.9781000.135
2.062-2.140.2381240.16125020.16426260.9570.9791000.135
2.14-2.2270.1771200.14824280.14925480.9820.9811000.118
2.227-2.3250.1591210.14423410.14524630.9810.98499.95940.117
2.325-2.4380.241960.16322400.16623360.9610.9821000.131
2.438-2.5680.2161110.1621070.16322180.9730.9821000.125
2.568-2.7230.2051040.15220280.15521320.9740.9851000.124
2.723-2.9090.191050.14818720.1519780.9740.98599.94940.128
2.909-3.1390.1861040.14517740.14718780.9760.9861000.129
3.139-3.4340.184830.13416280.13617130.9770.98999.88320.127
3.434-3.8320.169770.13514940.13715760.9830.9999.68270.135
3.832-4.4110.159730.11113260.11413990.9840.9931000.116
4.411-5.3690.137670.12711360.12712030.9880.991000.137
5.369-7.4560.235480.189090.1829580.9670.98499.89560.184
7.456-27.8490.218160.1965800.1975960.9810.9831000.214
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)
10.5370.0308-0.0460.0919-0.10450.26470.0022-0.04240.0145-0.0094-0.00740.010.00330.01050.00530.04070.00330.01150.02940.00470.0351-6.2287-23.38371.617
20.08860.1641-0.0730.3216-0.12860.3269-0.0048-0.02020.0049-0.0378-0.02410.00890.0134-0.00760.02890.0452-0.004-0.00210.0319-0.01510.0557-23.2301-24.1131-20.756
30.2580.09690.44520.97680.330.8005-0.0764-0.02150.0646-0.0724-0.04580.0192-0.1292-0.04230.12210.06350.0198-0.00320.0092-0.00960.0574-16.6339-0.1-15.4893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp207 - 379
2X-RAY DIFFRACTION2ALLAp382 - 435
3X-RAY DIFFRACTION2ALLAp552 - 602
4X-RAY DIFFRACTION3ALLAp440 - 548

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