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- EMDB-0387: Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0387 | |||||||||
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Title | Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A)/Trx interacting with primase domains of two gp4 subunits (E and F), with gp4 helicase bound to a DNA fork and dTTP (LagL1) | |||||||||
![]() | T7 DNA polymerase/Trx interacting with two primase domains (E and F) of T7 helicase (gp4) in complex with a fork DNA substrate and dTTP (from gp4-gp5 lagging-strand complex LagL1) | |||||||||
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Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
![]() | Gao Y / Fox T / Val N / Yang W | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18 KB 18 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 104.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.3 KB | Display | ![]() |
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Full document | ![]() | 77.4 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0357C ![]() 0359C ![]() 0362C ![]() 0363C ![]() 0364C ![]() 0365C ![]() 0379C ![]() 0380C ![]() 0381C ![]() 0382C ![]() 0386C ![]() 0388C ![]() 0389C ![]() 0390C ![]() 0391C ![]() 0392C ![]() 0393C ![]() 0394C ![]() 0395C ![]() 6n7iC ![]() 6n7nC ![]() 6n7sC ![]() 6n7tC ![]() 6n7vC ![]() 6n7wC ![]() 6n9uC ![]() 6n9vC ![]() 6n9wC ![]() 6n9xC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | T7 DNA polymerase/Trx interacting with two primase domains (E and F) of T7 helicase (gp4) in complex with a fork DNA substrate and dTTP (from gp4-gp5 lagging-strand complex LagL1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.72 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : T7 DNA polymerase/Trx interacting with two primase domains (E and...
Entire | Name: T7 DNA polymerase/Trx interacting with two primase domains (E and F) of T7 helicase (gp4) in complex with a fork DNA substrate and dTTP (from gp4-gp5 lagging-strand complex LagL1) |
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Components |
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-Supramolecule #1: T7 DNA polymerase/Trx interacting with two primase domains (E and...
Supramolecule | Name: T7 DNA polymerase/Trx interacting with two primase domains (E and F) of T7 helicase (gp4) in complex with a fork DNA substrate and dTTP (from gp4-gp5 lagging-strand complex LagL1) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: gene product 4 helicase-primase
Macromolecule | Name: gene product 4 helicase-primase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: 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
Macromolecule | Name: gene product 5 DNA polymerase / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: 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
Macromolecule | Name: Thioredoxin / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: MSDKIIHLTD DSFDTDVLKA DGAILVDFWA EWCGPCKMIA PILDEIADEY QGKLTVAKLN IDQNPGTAP KYGIRGIPTL LLFKNGEVAA TKVGALSKGQ LKEFLDANLA |
-Macromolecule #4: Template
Macromolecule | Name: Template / type: dna / ID: 4 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Sequence | 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) ...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) |
-Macromolecule #5: Primer
Macromolecule | Name: Primer / type: dna / ID: 5 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: (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) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |