[English] 日本語
Yorodumi
- PDB-6hpu: Crystal structure of human Pif1 helicase in complex with ADP-AlF4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hpu
TitleCrystal structure of human Pif1 helicase in complex with ADP-AlF4
ComponentsATP-dependent DNA helicase PIF1
KeywordsHYDROLASE / Pif1 / 5'-3' DNA helicase / Duplex Unwinding / Telomere Maintenance / DNA Repair
Function / homology
Function and homology information


5'-3' DNA/RNA helicase activity / telomerase inhibitor activity / G-quadruplex DNA binding / mitochondrial genome maintenance / : / regulation of telomere maintenance / DNA duplex unwinding / single-stranded DNA helicase activity / telomeric DNA binding / negative regulation of telomere maintenance via telomerase ...5'-3' DNA/RNA helicase activity / telomerase inhibitor activity / G-quadruplex DNA binding / mitochondrial genome maintenance / : / regulation of telomere maintenance / DNA duplex unwinding / single-stranded DNA helicase activity / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / telomere maintenance via telomerase / replication fork / 5'-3' DNA helicase activity / DNA recombination / DNA replication / DNA helicase / chromosome, telomeric region / DNA repair / magnesium ion binding / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding
Similarity search - Function
Helicase / : / : / DNA helicase Pif1, 2B domain / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / ATP-dependent DNA helicase PIF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.96 Å
AuthorsLevdikov, V.M. / Dehghani-Tafti, S. / Bax, B.D. / Sanders, C.M. / Antson, A.A.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural and functional analysis of the nucleotide and DNA binding activities of the human PIF1 helicase.
Authors: Dehghani-Tafti, S. / Levdikov, V. / Antson, A.A. / Bax, B. / Sanders, C.M.
History
DepositionSep 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,0768
Polymers90,9672
Non-polymers1,1096
Water00
1
A: ATP-dependent DNA helicase PIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0384
Polymers45,4841
Non-polymers5543
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent DNA helicase PIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0384
Polymers45,4841
Non-polymers5543
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.850, 209.850, 78.885
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

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


Mass: 45483.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SRM - cloning artefact / Source: (gene. exp.) Homo sapiens (human) / Gene: PIF1, C15orf20 / Plasmid: pET / Details (production host): pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H611, DNA helicase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical ChemComp-MG / MAGNESIUM ION


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.51 Å3/Da / Density % sol: 77.68 %
Crystal growTemperature: 274 K / Method: vapor diffusion, sitting drop / Details: MES, Ca-acetate, PEG 20K, PEG550 MME / PH range: 6-8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 3.96→104.93 Å / Num. obs: 17663 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 151.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.1
Reflection shellResolution: 3.96→4.06 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1273 / CC1/2: 0.892 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HPH

6hph


Resolution: 3.96→91.03 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 37.623 / SU ML: 0.487 / Cross valid method: THROUGHOUT / ESU R Free: 0.638 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25252 794 4.6 %RANDOM
Rwork0.17527 ---
obs0.17851 16607 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 151.675 Å2
Baniso -1Baniso -2Baniso -3
1--5.5 Å2-2.75 Å2-0 Å2
2---5.5 Å20 Å2
3---17.84 Å2
Refinement stepCycle: 1 / Resolution: 3.96→91.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6359 0 66 0 6425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0146610
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176048
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.6668972
X-RAY DIFFRACTIONr_angle_other_deg0.8271.6314195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0225854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46920.085353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.319151147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5781572
X-RAY DIFFRACTIONr_chiral_restr0.0660.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027511
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021159
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it13.90515.5393356
X-RAY DIFFRACTIONr_mcbond_other13.90415.5383355
X-RAY DIFFRACTIONr_mcangle_it21.39423.2434197
X-RAY DIFFRACTIONr_mcangle_other21.39323.2454198
X-RAY DIFFRACTIONr_scbond_it13.5916.1273252
X-RAY DIFFRACTIONr_scbond_other13.57816.1333249
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other21.07523.894759
X-RAY DIFFRACTIONr_long_range_B_refined31.39726391
X-RAY DIFFRACTIONr_long_range_B_other31.39426389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.96→4.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 85 -
Rwork0.333 1134 -
obs--96.06 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more