[English] 日本語
Yorodumi
- PDB-6hmf: D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hmf
TitleD-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease) H451 proof-reading deficient variant
ComponentsDNA polymerase II small subunit
KeywordsREPLICATION / DNA Polymerase D PolD
Function / homology
Function and homology information


exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
DNA polymerase II small subunit, archaeal / DNA polymerase delta/II small subunit family / DNA polymerase alpha/epsilon subunit B / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / : / DNA polymerase II small subunit
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRaia, P. / Delarue, M. / Sauguet, L.
Funding support France, 1items
OrganizationGrant numberCountry
France
CitationJournal: PLoS Biol / Year: 2019
Title: Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases.
Authors: Pierre Raia / Marta Carroni / Etienne Henry / Gérard Pehau-Arnaudet / Sébastien Brûlé / Pierre Béguin / Ghislaine Henneke / Erik Lindahl / Marc Delarue / Ludovic Sauguet /
Abstract: PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal ...PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP). We now report the DNA-bound cryo-electron microscopy (cryo-EM) structure of the heterodimeric DP1-DP2 PolD complex from Pyrococcus abyssi, revealing a unique DNA-binding site. Comparison of PolD and RNAPs extends their structural similarities and brings to light the minimal catalytic core shared by all cellular transcriptases. Finally, elucidating the structure of the PolD DP1-DP2 interface, which is conserved in all eukaryotic replicative DNAPs, clarifies their evolutionary relationships with PolD and sheds light on the domain acquisition and exchange mechanism that occurred during the evolution of the eukaryotic replisome.
History
DepositionSep 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase II small subunit
B: DNA polymerase II small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,77011
Polymers107,0952
Non-polymers6759
Water1,13563
1
A: DNA polymerase II small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8655
Polymers53,5471
Non-polymers3174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase II small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9056
Polymers53,5471
Non-polymers3575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.750, 91.240, 143.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase II small subunit / / Pol II / Exodeoxyribonuclease small subunit


Mass: 53547.434 Da / Num. of mol.: 2 / Mutation: H451A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: polB, PYRAB01210, PAB2266 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9V2F3, DNA-directed DNA polymerase, exodeoxyribonuclease I

-
Non-polymers , 6 types, 72 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.7
Details: cacodylate, sodium chloride, PEG 8000, calcium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0427 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0427 Å / Relative weight: 1
ReflectionResolution: 2.6→48 Å / Num. obs: 35506 / % possible obs: 100 % / Redundancy: 8.5 % / Biso Wilson estimate: 91.79 Å2 / Rsym value: 0.038 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4266 / CC1/2: 0.617 / Rpim(I) all: 0.647 / Rsym value: 0.647 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IHE

5ihe


Resolution: 2.6→47.19 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.893 / SU R Cruickshank DPI: 0.597 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.568 / SU Rfree Blow DPI: 0.289 / SU Rfree Cruickshank DPI: 0.297
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1653 4.66 %RANDOM
Rwork0.227 ---
obs0.229 35447 100 %-
Displacement parametersBiso mean: 84.38 Å2
Baniso -1Baniso -2Baniso -3
1-8.4719 Å20 Å20 Å2
2---22.4061 Å20 Å2
3---13.9342 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.6→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7036 0 23 63 7122
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097230HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.19826HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2466SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes177HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1024HARMONIC5
X-RAY DIFFRACTIONt_it7230HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion17.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion918SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8029SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2873 144 5.02 %
Rwork0.2556 2727 -
all0.2572 2871 -
obs--99.9 %
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)
11.04280.43710.19571.8959-1.01861.9998-0.24170.1148-0.0701-0.07520.1154-0.0635-0.00530.0640.1263-0.12410.06260.0328-0.0384-0.0066-0.24167.765972.059545.76
21.8337-0.27730.34711.24720.20481.9437-0.0207-0.2525-0.30920.0132-0.114-0.11310.19940.10670.1348-0.14430.05370.0548-0.19340.1062-0.118243.799643.059774.1577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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