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- EMDB-27719: Open state of T4 bacteriophage gp41 hexamer bound with single str... -

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Basic information

Entry
Database: EMDB / ID: EMD-27719
TitleOpen state of T4 bacteriophage gp41 hexamer bound with single strand DNA
Map data
Sample
  • Complex: Complex of T4 bacteriophage helicase gp41 with ssDNA/RNA hybrid
    • Protein or peptide: DnaB-like replicative helicase
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Keywordsphage / complex / helicase / REPLICATION-DNA-RNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / primosome complex / DNA replication, synthesis of primer / single-stranded DNA helicase activity / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / hydrolase activity / DNA binding / ATP binding
Similarity search - Function
Bacteriophage T4 DnaB-like replicative helicase / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DnaB-like replicative helicase
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFeng X / Li H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM013306 United States
CitationJournal: 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
DepositionJul 27, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27719.png

Downloads & links

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Map

FileDownload / File: emd_27719.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.08384404 - 0.14007996
Average (Standard dev.)-0.0000073141846 (±0.004531045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27719_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27719_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of T4 bacteriophage helicase gp41 with ssDNA/RNA hybrid

EntireName: Complex of T4 bacteriophage helicase gp41 with ssDNA/RNA hybrid
Components
  • Complex: Complex of T4 bacteriophage helicase gp41 with ssDNA/RNA hybrid
    • Protein or peptide: DnaB-like replicative helicase
    • DNA: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of T4 bacteriophage helicase gp41 with ssDNA/RNA hybrid

SupramoleculeName: Complex of T4 bacteriophage helicase gp41 with ssDNA/RNA hybrid
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia phage T4 (virus)

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Macromolecule #1: DnaB-like replicative helicase

MacromoleculeName: 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
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 48.797695 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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 QKWVEIE

UniProtKB: DnaB-like replicative helicase

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Macromolecule #2: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')

MacromoleculeName: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 2.996971 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 5 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMNaClsodium chloride
10.0 mMMgCl2Magnesium chloride
2.0 mMDTTDTT

Details: 20 mM HEPES pH 7.8, 100 mM NaCl, 10 mM MgCl2 and 2 mM DTT
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

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

6qem

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 690193
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 800000 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8due:
Open state of T4 bacteriophage gp41 hexamer bound with single strand DNA

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