[English] 日本語
Yorodumi
- PDB-6l3g: Structural Basis for DNA Unwinding at Forked dsDNA by two coordin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l3g
TitleStructural Basis for DNA Unwinding at Forked dsDNA by two coordinating Pif1 helicases
Components
  • ATP-dependent DNA helicase
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*TP*TP*TP*T)-3')
KeywordsHYDROLASE/DNA / ATP dependent DNA helicase / Pif1 / dsDNA unwinding / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


DNA helicase activity / telomere maintenance / DNA repair
Similarity search - Function
DNA helicase Pif1-like / PIF1-like helicase / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / DNA / DNA (> 10) / ATP-dependent DNA helicase
Similarity search - Component
Biological speciesBacteroides sp. AF32-8BH (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSu, N. / Bharath, S.R. / Song, H.
Funding support China, United States, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670820 China
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35GM122601 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases.
Authors: Su, N. / Byrd, A.K. / Bharath, S.R. / Yang, O. / Jia, Y. / Tang, X. / Ha, T. / Raney, K.D. / Song, H.
History
DepositionOct 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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.value / _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
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*TP*TP*TP*T)-3')
A: ATP-dependent DNA helicase
B: ATP-dependent DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6749
Polymers108,5653
Non-polymers1,1096
Water905
1
D: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*TP*TP*TP*T)-3')
A: ATP-dependent DNA helicase
B: ATP-dependent DNA helicase
hetero molecules

D: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*TP*TP*TP*T)-3')
A: ATP-dependent DNA helicase
B: ATP-dependent DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,34718
Polymers217,1296
Non-polymers2,21812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+2/31
Buried area11760 Å2
ΔGint-88 kcal/mol
Surface area78950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.265, 131.265, 117.183
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

-
Components

-
DNA chain / Protein , 2 types, 3 molecules DAB

#1: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*TP*TP*TP*T)-3')


Mass: 9130.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein ATP-dependent DNA helicase / Pif1


Mass: 49716.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides sp. AF32-8BH (bacteria) / Gene: DWZ47_17845 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A373G551

-
Non-polymers , 4 types, 11 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 80 mM Sodium chloride, 40 mM Sodium cacodylate pH 6.0, 35% MPD, 12 mM Spermine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→43.7 Å / Num. obs: 17102 / % possible obs: 97.9 % / Redundancy: 6.2 % / CC1/2: 0.982 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.1
Reflection shellResolution: 3.3→3.56 Å / Num. unique obs: 3547 / CC1/2: 0.69

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XFITdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FHD

5fhd


Resolution: 3.3→33.566 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.62
RfactorNum. reflection% reflection
Rfree0.3031 835 4.89 %
Rwork0.2442 --
obs0.2472 17075 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.3 Å2 / Biso min: 34.85 Å2
Refinement stepCycle: final / Resolution: 3.3→33.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6614 425 66 5 7110
Biso mean--74.93 57.62 -
Num. residues----847
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3002-3.50680.37551250.33122753100
3.5068-3.77720.33771490.298272699
3.7772-4.15670.33931290.273272399
4.1567-4.75670.2851450.2283268897
4.7567-5.98740.31151570.2416265296
5.9874-33.560.26071300.1996269895

+
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://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