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Yorodumi- EMDB-0380: Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0380 | |||||||||
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Title | Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS1) | |||||||||
Map data | Structure of gp5 DNA polymerase binding to A and F subunits of gp4 primase-helicase hexamer complexed with trx, RNA/DNA hybrid, and incoming dTTP (LagS1) | |||||||||
Sample |
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Function / homology | Function and homology information DNA synthesis involved in DNA replication / DNA exonuclease activity / DNA primase activity / primosome complex / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA helicase activity / DNA-templated DNA replication ...DNA synthesis involved in DNA replication / DNA exonuclease activity / DNA primase activity / primosome complex / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA helicase activity / DNA-templated DNA replication / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / single-stranded DNA binding / 5'-3' DNA helicase activity / DNA helicase / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Enterobacteria phage T7 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Gao Y / Fox T / Val N / Yang W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0380.map.gz | 228.9 MB | EMDB map data format | |
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Header (meta data) | emd-0380-v30.xml emd-0380.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0380_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_0380.png | 107.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0380 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0380 | HTTPS FTP |
-Validation report
Summary document | emd_0380_validation.pdf.gz | 487.9 KB | Display | EMDB validaton report |
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Full document | emd_0380_full_validation.pdf.gz | 487.5 KB | Display | |
Data in XML | emd_0380_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_0380_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0380 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0380 | HTTPS FTP |
-Related structure data
Related structure data | 6n9vMC 0357C 0359C 0362C 0363C 0364C 0365C 0379C 0381C 0382C 0386C 0387C 0388C 0389C 0390C 0391C 0392C 0393C 0394C 0395C 6n7iC 6n7nC 6n7sC 6n7tC 6n7vC 6n7wC 6n9uC 6n9wC 6n9xC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0380.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of gp5 DNA polymerase binding to A and F subunits of gp4 primase-helicase hexamer complexed with trx, RNA/DNA hybrid, and incoming dTTP (LagS1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : gp5 DNA polymerase and two gp4 primase subunits complexed with tr...
Entire | Name: gp5 DNA polymerase and two gp4 primase subunits complexed with trx, RNA/DNA hybrid, and incoming dTTP (from gp4-gp5 lagging-strand complex LagS1) |
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Components |
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-Supramolecule #1: gp5 DNA polymerase and two gp4 primase subunits complexed with tr...
Supramolecule | Name: gp5 DNA polymerase and two gp4 primase subunits complexed with trx, RNA/DNA hybrid, and incoming dTTP (from gp4-gp5 lagging-strand complex LagS1) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Enterobacteria phage T7 (virus) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: DNA primase/helicase
Macromolecule | Name: DNA primase/helicase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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Source (natural) | Organism: Enterobacteria phage T7 (virus) |
Molecular weight | Theoretical: 62.73443 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDNSHDSDSV FLYHIPCDNC GSSDGNSLFS DGHTFCYVCE KWTAGNEDTK ERASKRKPSG GKPMTYNVWN FGESNGRYSA LTARGISKE TCQKAGYWIA KVDGVMYQVA DYRDQNGNIV SQKVRDKDKN FKTTGSHKSD ALFGKHLWNG GKKIVVTEGE I DMLTVMEL ...String: MDNSHDSDSV FLYHIPCDNC GSSDGNSLFS DGHTFCYVCE KWTAGNEDTK ERASKRKPSG GKPMTYNVWN FGESNGRYSA LTARGISKE TCQKAGYWIA KVDGVMYQVA DYRDQNGNIV SQKVRDKDKN FKTTGSHKSD ALFGKHLWNG GKKIVVTEGE I DMLTVMEL QDCKYPVVSL GHGASAAKKT CAANYEYFDQ FEQIILMFDM DEAGRKAVEE AAQVLPAGKV RVAVLPCKDA NE CHLNGHD REIMEQVWNA GPWIPDGVVS ALSLRERIRE HLSSEESVGL LFSGCTGIND KTLGARGGEV IMVTSGSGMG KST FVRQQA LQWGTAMGKK VGLAMLQESV EETAEDLIGL HNRVRLRQSD SLKREIIENG KFDQWFDELF GNDTFHLYDS FAEA ETDRL LAKLAYMRSG LGCDVIILDH ISIVVSASGE SDERKMIDNL MTKLKGFAKS TGVVLVVICH LKNPDKGKAH EEGRP VSIT DLRGSGALRQ LSDTIIALER NQQGDMPNLV LVRILKCRFT GDTGIAGYME YNKETGWLEP SSYSGEEESH SESTDW SND TDF |
-Macromolecule #2: DNA-directed DNA polymerase
Macromolecule | Name: DNA-directed DNA polymerase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase |
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Source (natural) | Organism: Enterobacteria phage T7 (virus) |
Molecular weight | Theoretical: 79.703578 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIVSAIAANA LLESVTKFHC GVIYDYSTAE YVSYRPSDFG AYLDALEAEV ARGGLIVFHN GHKYDVPALT KLAKLQLNRE FHLPRENCI DTLVLSRLIH SNLKDTDMGL LRSGKLPGKR FGSHALEAWG YRLGEMKGEY KDDFKRMLEE QGEEYVDGME W WNFNEEMM ...String: MIVSAIAANA LLESVTKFHC GVIYDYSTAE YVSYRPSDFG AYLDALEAEV ARGGLIVFHN GHKYDVPALT KLAKLQLNRE FHLPRENCI DTLVLSRLIH SNLKDTDMGL LRSGKLPGKR FGSHALEAWG YRLGEMKGEY KDDFKRMLEE QGEEYVDGME W WNFNEEMM DYNVQDVVVT KALLEKLLSD KHYFPPEIDF TDVGYTTFWS ESLEAVDIEH RAAWLLAKQE RNGFPFDTKA IE ELYVELA ARRSELLRKL TETFGSWYQP KGGTEMFCHP RTGKPLPKYP RIKTPKVGGI FKKPKNKAQR EGREPCELDT REY VAGAPY TPVEHVVFNP SSRDHIQKKL QEAGWVPTKY TDKGAPVVDD EVLEGVRVDD PEKQAAIDLI KEYLMIQKRI GQSA EGDKA WLRYVAEDGK IHGSVNPNGA VTGRATHAFP NLAQIPGVRS PYGEQCRAAF GAEHHLDGIT GKPWVQAGID ASGLE LRCL AHFMARFDNG EYAHEILNGD IHTKNQIAAE LPTRDNAKTF IYGFLYGAGD EKIGQIVGAG KERGKELKKK FLENTP AIA ALRESIQQTL VESSQWVAGE QQVKWKRRWI KGLDGRKVHV RSPHAALNTL LQSAGALICK LWIIKTEEML VEKGLKH GW DGDFAYMAWV HDEIQVGCRT EEIAQVVIET AQEAMRWVGD HWNFRCLLDT EGKMGPNWAI CH |
-Macromolecule #3: Primer
Macromolecule | Name: Primer / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Enterobacteria phage T7 (virus) |
Molecular weight | Theoretical: 1.842206 KDa |
Sequence | String: ACCAG(DOC) |
-Macromolecule #4: Template
Macromolecule | Name: Template / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Enterobacteria phage T7 (virus) |
Molecular weight | Theoretical: 13.402571 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DA)(DG)(DC)(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)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT) |
-Macromolecule #5: THYMIDINE-5'-TRIPHOSPHATE
Macromolecule | Name: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 6 / Formula: TTP |
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Molecular weight | Theoretical: 482.168 Da |
Chemical component information | ChemComp-TTP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 7 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Details: unspecified | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |