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- PDB-5o6d: Structure of ScPif1 in complex with polydT and ATPgS -

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Basic information

Entry
Database: PDB / ID: 5o6d
TitleStructure of ScPif1 in complex with polydT and ATPgS
Components
  • ATP-dependent DNA helicase PIF1
  • DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
KeywordsHYDROLASE / Helicase SF1 ssDNA ATP analog
Function / homology
Function and homology information


telomerase inhibitor activity / G-quadruplex DNA unwinding / G-quadruplex DNA binding / telomere maintenance via recombination / mitochondrial genome maintenance / replication fork reversal / 5'-3' DNA helicase activity / double-strand break repair via break-induced replication / DNA duplex unwinding / DNA unwinding involved in DNA replication ...telomerase inhibitor activity / G-quadruplex DNA unwinding / G-quadruplex DNA binding / telomere maintenance via recombination / mitochondrial genome maintenance / replication fork reversal / 5'-3' DNA helicase activity / double-strand break repair via break-induced replication / DNA duplex unwinding / DNA unwinding involved in DNA replication / nuclear replication fork / negative regulation of telomere maintenance via telomerase / chromosome organization / DNA helicase activity / telomere maintenance / replication fork / mitochondrial membrane / single-stranded DNA binding / DNA helicase / DNA recombination / mitochondrial inner membrane / DNA replication / nucleolus / ATP hydrolysis activity / mitochondrion / ATP binding
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / ATP-dependent DNA helicase PIF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.283 Å
AuthorsLu, K.Y. / Chen, W.F. / Rety, S. / Liu, N.N. / Xu, X.G.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase.
Authors: Lu, K.Y. / Chen, W.F. / Rety, S. / Liu, N.N. / Wu, W.Q. / Dai, Y.X. / Li, D. / Ma, H.Y. / Dou, S.X. / Xi, X.G.
History
DepositionJun 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev ...audit_author / database_PDB_rev / database_PDB_rev_record / pdbx_seq_map_depositor_info
Item: _audit_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id

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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
B: ATP-dependent DNA helicase PIF1
C: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
D: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9478
Polymers126,8524
Non-polymers1,0954
Water0
1
A: ATP-dependent DNA helicase PIF1
C: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9744
Polymers63,4262
Non-polymers5482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-32 kcal/mol
Surface area25710 Å2
MethodPISA
2
B: ATP-dependent DNA helicase PIF1
D: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9744
Polymers63,4262
Non-polymers5482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-33 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.406, 90.783, 186.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATP-dependent DNA helicase PIF1 / DNA repair and recombination helicase PIF1 / Petite integration frequency protein 1 / Telomere ...DNA repair and recombination helicase PIF1 / Petite integration frequency protein 1 / Telomere stability protein 1


Mass: 61645.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: PIF1, TST1, YML061C, YM9958.01C / Plasmid: PET15b-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): C2566H / References: UniProt: P07271, DNA helicase
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')


Mass: 1780.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.44 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5 / Details: 100mM NaAc-HAc pH5.5 240mM NaF 14%-16% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 3.28→65 Å / Num. obs: 17964 / % possible obs: 89.7 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 82.89 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.62
Reflection shellResolution: 3.28→3.4 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 1952 / CC1/2: 0.88 / % possible all: 99.54

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O6B

5o6b


Resolution: 3.283→65 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.57
RfactorNum. reflection% reflectionSelection details
Rfree0.3219 950 5.31 %5%
Rwork0.2515 ---
obs0.2553 17899 89.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.283→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8372 222 64 0 8658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038817
X-RAY DIFFRACTIONf_angle_d0.69711894
X-RAY DIFFRACTIONf_dihedral_angle_d6.5975412
X-RAY DIFFRACTIONf_chiral_restr0.0421328
X-RAY DIFFRACTIONf_plane_restr0.0041482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2834-3.45650.3595980.32221855X-RAY DIFFRACTION99
3.4565-3.67310.3931020.2911927X-RAY DIFFRACTION99
3.6731-3.95660.35891340.25452294X-RAY DIFFRACTION99
3.9566-4.35470.26221510.23992682X-RAY DIFFRACTION100
4.3547-4.98470.28811610.21962646X-RAY DIFFRACTION99
4.9847-6.27960.3681540.25472718X-RAY DIFFRACTION100
6.2796-69.10740.3131500.25032827X-RAY DIFFRACTION99
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)
12.33360.6005-0.5494.8746-0.3274.00280.0186-0.2565-0.1114-0.65940.1531.25460.4863-0.4241-0.10810.43-0.0488-0.14340.37580.11620.6431-64.6165105.9204208.1373
20.51380.43580.41451.4666-0.94562.0203-0.37270.932-0.1232-1.7912-0.014-0.4023-0.02760.4853-0.66191.9767-0.03670.06210.873-0.17450.4851-46.558591.2422189.6878
36.9017-0.1199-0.47121.3517-1.90894.2924-1.0429-0.0968-1.8471-1.09640.59-0.71011.6322-0.21730.12021.1294-0.29660.21690.567-0.19240.8997-44.365884.0135214.3421
43.08330.81710.76385.19520.39332.3614-0.3109-0.1781-0.20560.0871-0.1784-1.5022-0.03370.93840.48190.63780.0857-0.06760.86390.11340.8791-25.4691102.0378217.7194
52.07060.26751.82183.3247-0.37253.63680.13010.1433-0.3296-1.07250.12120.01380.4090.1946-0.29270.73150.01190.09840.4509-0.03170.4486-48.018991.9434206.9162
60.84140.6441-0.75352.84370.83051.56170.7277-0.08870.3533-1.7356-0.40431.4522-0.2234-0.2311-0.46331.8927-0.1821-0.32380.62120.16150.9075-64.4589100.299189.5201
71.2397-0.21420.22133.288-1.05073.2076-0.02830.01670.0582-0.4664-0.031-0.7351-0.09240.33270.05210.1864-0.0830.13030.3992-0.11510.447-51.501952.0412201.84
81.9255-1.0994-1.71373.95341.06482.52420.00310.05090.92120.5063-0.1358-0.8731-0.62840.4430.12690.3881-0.0717-0.15990.39390.12270.4894-69.494666.9987213.2879
92.4131-0.2387-0.89885.5731-1.12882.69390.0488-0.51240.51160.67210.19511.2374-0.2057-0.2614-0.20390.5026-0.01450.05170.8745-0.06540.365-85.680553.3887220.9836
101.86331.5263-1.03943.06030.02792.9837-0.0735-0.13180.0252-0.30780.14710.0690.096-0.0663-0.19790.20940.0166-0.1450.31040.05520.2867-65.729156.436203.009
112.00611.2542-0.16129.29373.33471.23380.2278-1.1671-1.23320.7579-0.54980.92971.8607-0.93790.17261.1869-0.1736-0.0510.68830.03080.6963-55.782989.0488209.5163
127.1133-0.82651.08536.4261-0.41724.21970.9105-0.59270.7213-0.1745-0.8578-0.8505-1.38460.9609-0.34580.7952-0.15460.11930.3295-0.19310.6272-55.549664.9792208.9874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 237 through 415 )
2X-RAY DIFFRACTION2chain 'A' and (resid 416 through 488 )
3X-RAY DIFFRACTION3chain 'A' and (resid 489 through 526 )
4X-RAY DIFFRACTION4chain 'A' and (resid 527 through 662 )
5X-RAY DIFFRACTION5chain 'A' and (resid 663 through 733 )
6X-RAY DIFFRACTION6chain 'A' and (resid 734 through 778 )
7X-RAY DIFFRACTION7chain 'B' and (resid 237 through 478 )
8X-RAY DIFFRACTION8chain 'B' and (resid 479 through 535 )
9X-RAY DIFFRACTION9chain 'B' and (resid 536 through 619 )
10X-RAY DIFFRACTION10chain 'B' and (resid 620 through 778 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 8 )
12X-RAY DIFFRACTION12chain 'D' and (resid 3 through 8 )

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