[English] 日本語
Yorodumi
- EMDB-0392: Structure of bacteriophage T7 leading-strand DNA polymerase (D5A/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0392
TitleStructure of bacteriophage T7 leading-strand DNA polymerase (D5A/E7A)/Trx and of gp4 (E343Q) bound to a DNA fork (Lead2)
Map dataT7 DNA polymerase/Trx interacting with C-terminal tail of helicase domains E of T7 helicase (gp4) in complex with a fork DNA substrate and dTTP (from gp4-gp5 leading-strand complex Lead2)
Sample
  • Complex: T7 DNA polymerase/Trx interacting with C-terminal tail of helicase domains E of T7 helicase (gp4) in complex with a fork DNA substrate and dTTP (from gp4-gp5 leading-strand complex Lead2)
    • Protein or peptide: gene product 4 helicase-primase
    • Protein or peptide: gene product 5 DNA polymerase
    • Protein or peptide: Thioredoxin 1
    • DNA: Primer
    • DNA: Template
Biological speciesEnterobacteria phage T7 (virus) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.3 Å
AuthorsGao Y / Fox T / Val N / Yang W
CitationJournal: Science / Year: 2019
Title: Structures and operating principles of the replisome.
Authors: Yang Gao / Yanxiang Cui / Tara Fox / Shiqiang Lin / Huaibin Wang / Natalia de Val / Z Hong Zhou / Wei Yang /
Abstract: Visualization in atomic detail of the replisome that performs concerted leading- and lagging-DNA strand synthesis at a replication fork has not been reported. Using bacteriophage T7 as a model ...Visualization in atomic detail of the replisome that performs concerted leading- and lagging-DNA strand synthesis at a replication fork has not been reported. Using bacteriophage T7 as a model system, we determined cryo-electron microscopy structures up to 3.2-angstroms resolution of helicase translocating along DNA and of helicase-polymerase-primase complexes engaging in synthesis of both DNA strands. Each domain of the spiral-shaped hexameric helicase translocates sequentially hand-over-hand along a single-stranded DNA coil, akin to the way AAA+ ATPases (adenosine triphosphatases) unfold peptides. Two lagging-strand polymerases are attached to the primase, ready for Okazaki fragment synthesis in tandem. A β hairpin from the leading-strand polymerase separates two parental DNA strands into a T-shaped fork, thus enabling the closely coupled helicase to advance perpendicular to the downstream DNA duplex. These structures reveal the molecular organization and operating principles of a replisome.
History
DepositionDec 5, 2018-
Header (metadata) releaseFeb 20, 2019-
Map releaseMar 6, 2019-
UpdateMar 6, 2019-
Current statusMar 6, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0392.png

Downloads & links

-
Map

FileDownload / File: emd_0392.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT7 DNA polymerase/Trx interacting with C-terminal tail of helicase domains E of T7 helicase (gp4) in complex with a fork DNA substrate and dTTP (from gp4-gp5 leading-strand complex Lead2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 240 pix.
= 412.8 Å		1.72 Å/pix.
x 240 pix.
= 412.8 Å		1.72 Å/pix.
x 240 pix.
= 412.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.07714784 - 0.1995317
Average (Standard dev.)0.00025801855 (±0.004878608)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 412.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z412.800412.800412.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0770.2000.000

-
Supplemental data

-
Sample components

-
Entire : T7 DNA polymerase/Trx interacting with C-terminal tail of helicas...

EntireName: T7 DNA polymerase/Trx interacting with C-terminal tail of helicase domains E of T7 helicase (gp4) in complex with a fork DNA substrate and dTTP (from gp4-gp5 leading-strand complex Lead2)
Components
  • Complex: T7 DNA polymerase/Trx interacting with C-terminal tail of helicase domains E of T7 helicase (gp4) in complex with a fork DNA substrate and dTTP (from gp4-gp5 leading-strand complex Lead2)
    • Protein or peptide: gene product 4 helicase-primase
    • Protein or peptide: gene product 5 DNA polymerase
    • Protein or peptide: Thioredoxin 1
    • DNA: Primer
    • DNA: Template

-
Supramolecule #1: T7 DNA polymerase/Trx interacting with C-terminal tail of helicas...

SupramoleculeName: T7 DNA polymerase/Trx interacting with C-terminal tail of helicase domains E of T7 helicase (gp4) in complex with a fork DNA substrate and dTTP (from gp4-gp5 leading-strand complex Lead2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Enterobacteria phage T7 (virus)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Macromolecule #1: gene product 4 helicase-primase

MacromoleculeName: gene product 4 helicase-primase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T7 (virus)
SequenceString: MDNSHDSDSV FLYHIPCDNC GSSDGNSLFS DGHTFCYVCE KWTAGNEDTK ERASKRKPSG GKPMTYNVW NFGESNGRYS ALTARGISKE TCQKAGYWIA KVDGVMYQVA DYRDQNGNIV S QKVRDKDK NFKTTGSHKS DALFGKHLWN GGKKIVVTEG EIDMLTVMEL ...String:
MDNSHDSDSV FLYHIPCDNC GSSDGNSLFS DGHTFCYVCE KWTAGNEDTK ERASKRKPSG GKPMTYNVW NFGESNGRYS ALTARGISKE TCQKAGYWIA KVDGVMYQVA DYRDQNGNIV S QKVRDKDK NFKTTGSHKS DALFGKHLWN GGKKIVVTEG EIDMLTVMEL QDCKYPVVSL GH GASAAKK TCAANYEYFD QFEQIILMFD MDEAGRKAVE EAAQVLPAGK VRVAVLPCKD ANE CHLNGH DREIMEQVWN AGPWIPDGVV SALSLRERIR EHLSSEESVG LLFSGCTGIN DKTL GARGG EVIMVTSGSG MGKSTFVRQQ ALQWGTAMGK KVGLAMLQES VEETAEDLIG LHNRV RLRQ SDSLKREIIE NGKFDQWFDE LFGNDTFHLY DSFAEAETDR LLAKLAYMRS GLGCDV IIL DHISIVVSAS GESDERKMID NLMTKLKGFA KSTGVVLVVI CHLKNPDKGK AHEEGRP VS ITDLRGSGAL RQLSDTIIAL ERNQQGDMPN LVLVRILKCR FTGDTGIAGY MEYNKETG W LEPSSYSGEE ESHSESTDWS NDTDF

-
Macromolecule #2: gene product 5 DNA polymerase

MacromoleculeName: gene product 5 DNA polymerase / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T7 (virus)
SequenceString: MIVSAIAANA LLESVTKFHC GVIYDYSTAE YVSYRPSDFG AYLDALEAEV ARGGLIVFHN GHKYDVPAL TKLAKLQLNR EFHLPRENCI DTLVLSRLIH SNLKDTDMGL LRSGKLPGKR F GSHALEAW GYRLGEMKGE YKDDFKRMLE EQGEEYVDGM EWWNFNEEMM ...String:
MIVSAIAANA LLESVTKFHC GVIYDYSTAE YVSYRPSDFG AYLDALEAEV ARGGLIVFHN GHKYDVPAL TKLAKLQLNR EFHLPRENCI DTLVLSRLIH SNLKDTDMGL LRSGKLPGKR F GSHALEAW GYRLGEMKGE YKDDFKRMLE EQGEEYVDGM EWWNFNEEMM DYNVQDVVVT KA LLEKLLS DKHYFPPEID FTDVGYTTFW SESLEAVDIE HRAAWLLAKQ ERNGFPFDTK AIE ELYVEL AARRSELLRK LTETFGSWYQ PKGGTEMFCH PRTGKPLPKY PRIKTPKVGG IFKK PKNKA QREGREPCEL DTREYVAGAP YTPVEHVVFN PSSRDHIQKK LQEAGWVPTK YTDKG APVV DDEVLEGVRV DDPEKQAAID LIKEYLMIQK RIGQSAEGDK AWLRYVAEDG KIHGSV NPN GAVTGRATHA FPNLAQIPGV RSPYGEQCRA AFGAEHHLDG ITGKPWVQAG IDASGLE LR CLAHFMARFD NGEYAHEILN GDIHTKNQIA AELPTRDNAK TFIYGFLYGA GDEKIGQI V GAGKERGKEL KKKFLENTPA IAALRESIQQ TLVESSQWVA GEQQVKWKRR WIKGLDGRK VHVRSPHAAL NTLLQSAGAL ICKLWIIKTE EMLVEKGLKH GWDGDFAYMA WVHDEIQVGC RTEEIAQVV IETAQEAMRW VGDHWNFRCL LDTEGKMGPN WAICH

-
Macromolecule #3: Thioredoxin 1

MacromoleculeName: Thioredoxin 1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString:
MSDKIIHLTD DSFDTDVLKA DGAILVDFWA EWCGPCKMIA PILDEIADEY QGKLTVAKLN IDQNPGTAP KYGIRGIPTL LLFKNGEVAA TKVGALSKGQ LKEFLDANLA

-
Macromolecule #4: Primer

MacromoleculeName: Primer / type: dna / ID: 4 / Classification: DNA
Source (natural)Organism: Enterobacteria phage T7 (virus)
SequenceString:
(DG)(DG)(DT)(DA)(DC)(DA)(DA)(DC)(DT)(DT) (DG)(DA)(DC)(DG)(DA)(DC)(DA)(DT)(DA)(DG) (DC)(DG)(DT)(DG)(DOA)

-
Macromolecule #5: Template

MacromoleculeName: Template / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: Enterobacteria phage T7 (virus)
SequenceString: (DT)(DT)(DT)(DG)(DG)(DT)(DC)(DA)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DC) (DG)(DG)(DA)(DG)(DT)(DC)(DG)(DT)(DT)(DT) (DC)(DG)(DA)(DC)(DT)(DC)(DC) ...String:
(DT)(DT)(DT)(DG)(DG)(DT)(DC)(DA)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DC) (DG)(DG)(DA)(DG)(DT)(DC)(DG)(DT)(DT)(DT) (DC)(DG)(DA)(DC)(DT)(DC)(DC)(DG)(DT)(DT) (DA)(DT)(DC)(DA)(DC)(DG)(DC)(DT)(DA)(DT) (DG)(DT)(DC)(DG)(DT)(DC)(DA)(DA)(DG)(DT) (DT)(DG)(DT)(DA)(DC)(DC)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMpotassium chlorideKCl
3.0 mMDTT
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK I

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1t8e


Details: 1T8E, 1NUI
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 19847
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

1t8e

RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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