+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27737 | |||||||||
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Title | T4 Bacteriophage primosome with single strand DNA, state 1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | phage / complex / helicase / REPLICATION-DNA-RNA complex | |||||||||
Function / homology | Function and homology information bidirectional double-stranded viral DNA replication / DNA primase activity / primosome complex / DNA replication, synthesis of primer / viral DNA genome replication / single-stranded DNA helicase activity / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / hydrolase activity ...bidirectional double-stranded viral DNA replication / DNA primase activity / primosome complex / DNA replication, synthesis of primer / viral DNA genome replication / single-stranded DNA helicase activity / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / hydrolase activity / DNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia phage T4 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Feng X / Li H | |||||||||
Funding support | United States, 2 items
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Citation | Journal: bioRxiv / Year: 2023 Title: Structural basis of the T4 bacteriophage primosome assembly and primer synthesis. Authors: Xiang Feng / Michelle M Spiering / Ruda de Luna Almeida Santos / Stephen J Benkovic / Huilin Li / Abstract: The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome complex to couple DNA unwinding with RNA primer synthesis for DNA replication. How a primosome is assembled and how the ...The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome complex to couple DNA unwinding with RNA primer synthesis for DNA replication. How a primosome is assembled and how the length of the RNA primer is defined in the T4 bacteriophage, or in any model system, are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates at resolutions up to 2.7 Å. We show that the gp41 helicase is an open spiral in the absence of ssDNA, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the open spiral to a closed ring that activates the helicase. We found that the activation of the gp41 helicase exposes a cryptic hydrophobic primase-binding surface allowing for the recruitment of the gp61 primase. The primase binds the gp41 helicase in a bipartite mode in which the N-terminal Zn-binding domain (ZBD) and the C-terminal RNA polymerase domain (RPD) each contain a helicase-interacting motif (HIM1 and HIM2, respectively) that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Based on two observed primosome conformations - one in a DNA-scanning mode and the other in a post RNA primer-synthesis mode - we suggest that the linker loop between the gp61 ZBD and RPD contributes to the T4 pentaribonucleotide primer. Our study reveals T4 primosome assembly process and sheds light on RNA primer synthesis mechanism. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27737.map.gz | 116.8 MB | EMDB map data format | |
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Header (meta data) | emd-27737-v30.xml emd-27737.xml | 22.9 KB 22.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27737_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_27737.png | 92.8 KB | ||
Others | emd_27737_half_map_1.map.gz emd_27737_half_map_2.map.gz | 98.3 MB 98.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27737 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27737 | HTTPS FTP |
-Validation report
Summary document | emd_27737_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_27737_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_27737_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_27737_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27737 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27737 | HTTPS FTP |
-Related structure data
Related structure data | 8dvfMC 8dtpC 8dueC 8duoC 8dviC 8dw6C 8dwjC 8g0zC 8gaoC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27737.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_27737_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27737_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of T4 bacteriophage primosome including helicase gp41, pr...
Entire | Name: Complex of T4 bacteriophage primosome including helicase gp41, primase gp61 and ssDNA/RNA hybrid |
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Components |
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-Supramolecule #1: Complex of T4 bacteriophage primosome including helicase gp41, pr...
Supramolecule | Name: Complex of T4 bacteriophage primosome including helicase gp41, primase gp61 and ssDNA/RNA hybrid type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Escherichia phage T4 (virus) |
-Macromolecule #1: DnaB-like replicative helicase
Macromolecule | Name: DnaB-like replicative helicase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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Source (natural) | Organism: Escherichia phage T4 (virus) |
Molecular weight | Theoretical: 53.662848 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVEIILSHLI FDQAYFSKVW PYMDSEYFES GPAKNTFKLI KSHVNEYHSV PSINALNVAL ENSSFTETEY SGVKTLISKL ADSPEDHSW LVKETEKYVQ QRAMFNATSK IIEIQTNAEL PPEKRNKKMP DVGAIPDIMR QALSISFDSY VGHDWMDDYE A RWLSYMNK ...String: MVEIILSHLI FDQAYFSKVW PYMDSEYFES GPAKNTFKLI KSHVNEYHSV PSINALNVAL ENSSFTETEY SGVKTLISKL ADSPEDHSW LVKETEKYVQ QRAMFNATSK IIEIQTNAEL PPEKRNKKMP DVGAIPDIMR QALSISFDSY VGHDWMDDYE A RWLSYMNK ARKVPFKLRI LNKITKGGAE TGTLNVLMAG VNVGKSLGLC SLAADYLQLG HNVLYISMEM AEEVCAKRID AN MLDVSLD DIDDGHISYA EYKGKMEKWR EKSTLGRLIV KQYPTGGADA NTFRSLLNEL KLKKNFVPTI IIVDYLGICK SCR IRVYSE NSYTTVKAIA EELRALAVET ETVLWTAAQV GKQAWDSSDV NMSDIAESAG LPATADFMLA VIETEELAAA EQQL IKQIK SRYGDKNKWN KFLMGVQKGN QKWVEIEQDS TPTEVNEVAG SQQIQAEQNR YQRNESTRAQ LDALANELKF UniProtKB: DnaB-like replicative helicase |
-Macromolecule #3: DNA primase
Macromolecule | Name: DNA primase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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Source (natural) | Organism: Escherichia phage T4 (virus) |
Molecular weight | Theoretical: 39.842043 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSSIPWIDNE FAYRALAHLP KFTQVNNSST FKLRFRCPVC GDSKTDQNKA RGWYYGDNNE GNIHCYNCNY HAPIGIYLKE FEPDLYREY IFEIRKEKGK SRPIEKPKEL PKQPEKKIIK SLPSCVRLDK LAEDHPIIKY VKARCIPKDK WKYLWFTTEW P KLVNSIAP ...String: MSSIPWIDNE FAYRALAHLP KFTQVNNSST FKLRFRCPVC GDSKTDQNKA RGWYYGDNNE GNIHCYNCNY HAPIGIYLKE FEPDLYREY IFEIRKEKGK SRPIEKPKEL PKQPEKKIIK SLPSCVRLDK LAEDHPIIKY VKARCIPKDK WKYLWFTTEW P KLVNSIAP GTYKKEISEP RLVIPIYNAN GKAESFQGRA LKKDAPQKYI TIEAYPEATK IYGVERVKDG DVYVLEGPID SL FIENGIA ITGGQLDLEV VPFKDRRVWV LDNEPRHPDT IKRMTKLVDA GERVMFWDKS PWKSKDVNDM IRKEGATPEQ IME YMKNNI AQGLMAKMRL SKYAKI UniProtKB: DNA primase |
-Macromolecule #2: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
Macromolecule | Name: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') / type: dna / ID: 2 Details: The observed DNA sequence is an average of different nucleotides because the protein lacks sequence specificity. Thus, each base was modeled as a T residue. Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia phage T4 (virus) |
Molecular weight | Theoretical: 3.605356 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT) |
-Macromolecule #4: DNA (5'-D(P*GP*GP*CP*TP*G)-3')
Macromolecule | Name: DNA (5'-D(P*GP*GP*CP*TP*G)-3') / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia phage T4 (virus) |
Molecular weight | Theoretical: 1.536035 KDa |
Sequence | String: (DG)(DG)(DC)(DT)(DG) |
-Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 5 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ChemComp-AGS: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 5 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 Component:
Details: 20 mM HEPES pH 7.8, 100 mM NaCl, 10 mM MgCl2 and 2 mM DTT | |||||||||||||||
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: OTHER | ||||||||
Output model | PDB-8dvf: |