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- EMDB-0362: Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase i... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0362 | |||||||||
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Title | Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (form II) | |||||||||
![]() | bacteriophage T7 gene product 4 (gp4) helicase primase DNA complex II | |||||||||
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![]() | helicase / ATPase / hexamer / DNA replication / HYDROLASE / TRANSFERASE-DNA complex | |||||||||
Function / homology | ![]() DNA primase activity / primosome complex / viral DNA genome replication / DNA helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / single-stranded DNA binding / 5'-3' DNA helicase activity / DNA helicase / ATP hydrolysis activity / zinc ion binding ...DNA primase activity / primosome complex / viral DNA genome replication / DNA helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / single-stranded DNA binding / 5'-3' DNA helicase activity / DNA helicase / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
![]() | Gao Y / Cui Y | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 5.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.7 KB 14.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 147.8 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n7sMC ![]() 0357C ![]() 0359C ![]() 0363C ![]() 0364C ![]() 0365C ![]() 0379C ![]() 0380C ![]() 0381C ![]() 0382C ![]() 0386C ![]() 0387C ![]() 0388C ![]() 0389C ![]() 0390C ![]() 0391C ![]() 0392C ![]() 0393C ![]() 0394C ![]() 0395C ![]() 6n7iC ![]() 6n7nC ![]() 6n7tC ![]() 6n7vC ![]() 6n7wC ![]() 6n9uC ![]() 6n9vC ![]() 6n9wC ![]() 6n9xC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | bacteriophage T7 gene product 4 (gp4) helicase primase DNA complex II | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 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 : Bacteriophage T7 gene product 4 (gp4) helicase primase DNA complex II
Entire | Name: Bacteriophage T7 gene product 4 (gp4) helicase primase DNA complex II |
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Components |
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-Supramolecule #1: Bacteriophage T7 gene product 4 (gp4) helicase primase DNA complex II
Supramolecule | Name: Bacteriophage T7 gene product 4 (gp4) helicase primase DNA complex II type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 62.73443 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 UniProtKB: DNA helicase/primase |
-Macromolecule #2: DNA (25-MER)
Macromolecule | Name: DNA (25-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 7.594877 KDa |
Sequence | String: (DT)(DG)(DG)(DT)(DC)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT) |
-Macromolecule #3: THYMIDINE-5'-TRIPHOSPHATE
Macromolecule | Name: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: TTP |
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Molecular weight | Theoretical: 482.168 Da |
Chemical component information | ![]() ChemComp-TTP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-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: SUPER-RESOLUTION / Average electron dose: 72.0 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 |