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- EMDB-7076: Mechanisms of Opening and Closing of the Bacterial Replicative He... -

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Entry
Database: EMDB / ID: EMD-7076
TitleMechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex
Map dataDnaB-LambdaP helicase-helicase loader complex from single particle cryoEM at 4.1A. The suggested viewing thresholds are 0.0276 (Chimera) or an isomesh level of 6 (PyMol).
Sample
  • Complex: DnaB helicase - Lambda P helicase loader DNA replication complex
    • Complex: E coli DnaB helicase
      • Protein or peptide: Replicative DNA helicase
    • Complex: Lambda P helicase loader
      • Protein or peptide: Replication protein P
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsHelicase Loader / Helicase / DNA replication / ATPase / DNA Replication Initiation / Bacteriophage Lambda / REPLICATION
Function / homology
Function and homology information


DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / bidirectional double-stranded viral DNA replication / DNA 5'-3' helicase / primosome complex / DNA replication, synthesis of primer ...DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / bidirectional double-stranded viral DNA replication / DNA 5'-3' helicase / primosome complex / DNA replication, synthesis of primer / replisome / DNA duplex unwinding / response to ionizing radiation / DNA unwinding involved in DNA replication / replication fork processing / DNA replication initiation / DNA helicase activity / isomerase activity / helicase activity / 5'-3' DNA helicase activity / DNA helicase / DNA replication / hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Replication P / Replication protein P / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. ...Replication P / Replication protein P / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replicative DNA helicase / Helicase loader / Replicative DNA helicase DnaB
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Enterobacteria phage lambda (virus) / Escherichia coli O111:NM (bacteria) / Escherichia phage lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsChase J / Catalano A
Funding support United States, 12 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM084162 United States
National Science Foundation (NSF, United States)MCB 1818255 United States
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)5G12MD007603-30 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM109824 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103314 United States
Other governmentPA200A150068 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM128303 United States
Other privateSF349247 (Simons Foundation) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateF00316 (Agouron Institute) United States
National Institutes of Health/Office of the DirectorOD019994 United States
Other privateSM-2015-289297 (Silicon Mechanics/Research Cluster Grant program) United States
CitationJournal: Elife / Year: 2018
Title: Mechanisms of opening and closing of the bacterial replicative helicase.
Authors: Jillian Chase / Andrew Catalano / Alex J Noble / Edward T Eng / Paul Db Olinares / Kelly Molloy / Danaya Pakotiprapha / Martin Samuels / Brian Chait / Amedee des Georges / David Jeruzalmi /
Abstract: Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and ...Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and closing of the helicase, which enable and restrict access to an internal chamber, are not known. Here, we investigate these mechanisms in the DnaB helicase•bacteriophage λ helicase loader (λP) complex. We show that five copies of λP bind at DnaB subunit interfaces and reconfigure the helicase into an open spiral conformation that is intermediate to previously observed closed ring and closed spiral forms; reconfiguration also produces openings large enough to admit ssDNA into the inner chamber. The helicase is also observed in a restrained inactive configuration that poises it to close on activating signal, and transition to the translocation state. Our findings provide insights into helicase opening, delivery to the origin and ssDNA entry, and closing in preparation for translocation.
History
DepositionOct 18, 2017-
Header (metadata) releaseMar 6, 2019-
Map releaseMar 6, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bbm
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7076.png

Downloads & links

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Map

FileDownload / File: emd_7076.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDnaB-LambdaP helicase-helicase loader complex from single particle cryoEM at 4.1A. The suggested viewing thresholds are 0.0276 (Chimera) or an isomesh level of 6 (PyMol).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0276 / Movie #1: 0.03
Minimum - Maximum-0.09008105 - 0.161977
Average (Standard dev.)0.000051110845 (±0.0061288467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.920273.920273.920
α/β/γ90.00090.00090.000
start NX/NY/NZ-163-114-126
NX/NY/NZ210124170
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0900.1620.000

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Supplemental data

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Sample components

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Entire : DnaB helicase - Lambda P helicase loader DNA replication complex

EntireName: DnaB helicase - Lambda P helicase loader DNA replication complex
Components
  • Complex: DnaB helicase - Lambda P helicase loader DNA replication complex
    • Complex: E coli DnaB helicase
      • Protein or peptide: Replicative DNA helicase
    • Complex: Lambda P helicase loader
      • Protein or peptide: Replication protein P
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: DnaB helicase - Lambda P helicase loader DNA replication complex

SupramoleculeName: DnaB helicase - Lambda P helicase loader DNA replication complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: pET24a containing full-length DnaB was co-expressed with pCDFDuet containing full-length LambdaP in BL21(DE3) cells. The resolution of the LambdaP portion of our EM map did not permit the ...Details: pET24a containing full-length DnaB was co-expressed with pCDFDuet containing full-length LambdaP in BL21(DE3) cells. The resolution of the LambdaP portion of our EM map did not permit the unambiguous assignment of the amino acid sequence to the structure. As such, the model for LambdaP was built as a poly alanine model. Additionally, only half of LambdaP was observed in our maps due to the intrinsic flexibility of the amino and carboxy terminal domains of LambdaP. Subsequent experiments determined that the observed portion of LambdaP in our maps corresponds to the C-terminal domain.
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #2: E coli DnaB helicase

SupramoleculeName: E coli DnaB helicase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: E coli DnaB helicase is observed as an open-spiral hexamer, in which one of the interfaces is breached. Five ADP molecules are observed at the five intact ATP binding sites. Additionally, ...Details: E coli DnaB helicase is observed as an open-spiral hexamer, in which one of the interfaces is breached. Five ADP molecules are observed at the five intact ATP binding sites. Additionally, clear density is observed for five of six linkers permitting unambiguous assignment of NTD to parent CTD domain.
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Lambda P helicase loader

SupramoleculeName: Lambda P helicase loader / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: Five lambda P molecules were observed bound to the five intact DnaB subunit interfaces. Unambiguous assignment of side chain density for lambda P was not possible due to the resolution of ...Details: Five lambda P molecules were observed bound to the five intact DnaB subunit interfaces. Unambiguous assignment of side chain density for lambda P was not possible due to the resolution of this region of the EM map. Instead, a polyalanine model was built for each lambda P molecule. Additionally, density for approximately half of the expected 233 residues of lambda P was observed owing to flexibility between domains. Subsequent experiments confirmed that the observed region of Lambda P is the C-terminal domain, which interacts with DnaB.
Source (natural)Organism: Enterobacteria phage lambda (virus)

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Macromolecule #1: Replicative DNA helicase

MacromoleculeName: Replicative DNA helicase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Escherichia coli O111:NM (bacteria)
Molecular weightTheoretical: 52.450945 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAGNKPFNKQ QAEPRERDPQ VAGLKVPPHS IEAEQSVLGG LMLDNERWDD VAERVVADDF YTRPHRHIFT EMARLQESGS PIDLITLAE SLERQGQLDS VGGFAYLAEL SKNTPSAANI SAYADIVRER AVVREMISVA NEIAEAGFDP QGRTSEDLLD L AESRVFKI ...String:
MAGNKPFNKQ QAEPRERDPQ VAGLKVPPHS IEAEQSVLGG LMLDNERWDD VAERVVADDF YTRPHRHIFT EMARLQESGS PIDLITLAE SLERQGQLDS VGGFAYLAEL SKNTPSAANI SAYADIVRER AVVREMISVA NEIAEAGFDP QGRTSEDLLD L AESRVFKI AESRANKDEG PKNIADVLDA TVARIEQLFQ QPHDGVTGVN TGYDDLNKKT AGLQPSDLII VAARPSMGKT TF AMNLVEN AAMLQDKPVL IFSLEMPSEQ IMMRSLASLS RVDQTKIRTG QLDDEDWARI SGTMGILLEK RNIYIDDSSG LTP TEVRSR ARRIAREHGG IGLIMIDYLQ LMRVPALSDN RTLEIAEISR SLKALAKELN VPVVALSQLN RSLEQRADKR PVNS DLRES GSIEQDADLI MFIYRDEVYH ENSDLKGIAE IIIGKQRNGP IGTVRLTFNG QWSRFDNYAG PQYDDE

UniProtKB: Replicative DNA helicase

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Macromolecule #2: Replication protein P

MacromoleculeName: Replication protein P / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage lambda (virus)
Molecular weightTheoretical: 23.141221 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKNIAAQMVN FDREQMRRIA NNMPEQYDEK PQVQQVAQII NGVFSQLLAT FPASLANRDQ NEVNEIRRQW VLAFRENGIT TMEQVNAGM RVARRQNRPF LPSPGQFV(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK) ...String:
MKNIAAQMVN FDREQMRRIA NNMPEQYDEK PQVQQVAQII NGVFSQLLAT FPASLANRDQ NEVNEIRRQW VLAFRENGIT TMEQVNAGM RVARRQNRPF LPSPGQFV(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)

UniProtKB: Helicase loader

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

Concentration0.48 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMNa-HEPESSodium HEPES
450.0 mMNaClSodium Chloride
2.0 mMDTTDithiothreitol
0.5 mMMgCl2Magnesium Chloride
0.5 mMATPAdenosine triphosphate

Details: Concentrated BP sample (18mg/mL) was diluted with freshly prepared buffer to desired concentration (~1.5 micromolar) for grid preparation.
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
Details: The grid was coated with 50 nm of evaporated gold prior to use. All remaining carbon was removed by plasma cleaning for 5 minutes in a Gatan Solarus plasma cleaner.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3uL of sample was adhered to a fresh plasma cleaned grid and allowed to adsorb for 30 seconds, blotted for 3 seconds with a blot force of 4 and plunge frozen into liquid nitrogen-cooled ethane..
DetailsThe sample was monodisperse. Side views were more electron weak than top or bottom views creating challenges for particle picking. This issue was overcome with cryo-electron tomography techniques used for 1) initial model generation and 2) template generation for particle picking.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsSpherical aberration corrector: The Krios this data was collected on has a Cs of 2.7.
DetailsPreliminary grid screening was performed prior to Krios data collections. All microscope alignments were completed by the New York Structural Biology SEMC team.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 3 / Number real images: 2426 / Average exposure time: 10.0 sec. / Average electron dose: 8.0 e/Å2
Details: Single particle movies were recorded at a pixel size of 1.07 angstroms/pixel. Three 24-hour sessions produced 2,426 micrograph movies. In addition, five tilt series were collected from the ...Details: Single particle movies were recorded at a pixel size of 1.07 angstroms/pixel. Three 24-hour sessions produced 2,426 micrograph movies. In addition, five tilt series were collected from the same grids bi-directionally over a tilt range of -45 degrees to +45 degrees in 3 degree increments at a dose of 2.57 to 3.3 electrons per angstrom squared (total accumulated dose of 90 electrons per angstrom squared). Tilt series were collected at a pixel size of 1.76 angstroms and at defocus values of -2.8um, -6.1um and -9.3um.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -0.003 µm / Nominal defocus min: -0.001 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsImages collected were CTF corrected and selected based on CTF estimates of less than 10 angstrom at a confidence cutoff of 0.8 for subsequent processing.
Startup modelType of model: ORTHOGONAL TILT / Orthogonal tilt - Number images: 1000 / Orthogonal tilt - Tilt angle1: -45 degrees / Orthogonal tilt - Tilt angle2: 45 degrees
Details: Three tilt series were collected from same single-particle grids at a pixel size of 1.76 angstroms per pixel and defocus values of -2.8um, -6.1um and -9.3um. Tilt series were collected bi- ...Details: Three tilt series were collected from same single-particle grids at a pixel size of 1.76 angstroms per pixel and defocus values of -2.8um, -6.1um and -9.3um. Tilt series were collected bi-directionally over a tilt range of -45 degrees to +45 degrees in 3 degree increments, with a dose of 2.57 to 3.3 electrons per angstrom squared per tilt increment (subdivided over seven to nine frames.) A low resolution initial model was generated from ~1,000 particles picked from three tilt series. These tilt series were first aligned using a fiducial-less algorithm implemented in Appion-Portomo, then reconstructed using Tomo3D. 1,000 particles were picked from resulting tomograms (binned 4 x 4) to generate a ~40 angstrom initial model. Resolution was estimated by filtering procedures. The resulting volume served as an initial model and was projected to generate templates for template-based particle picking of single particle micrographs.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF
Software:
Namedetails
RELIONAuto refine and post processing was performed in Relion.
DynamoDynamo was used to generate sub-tomogram average, later used as initial model.

Details: Relion was used to independently refine half sets using 0.143 gold-standard to a resolution of 4.1A. A total of 90,883 particles went into this reconstruction.
Number images used: 90883
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

2r5u

residue_range: 1-173, source_name: PDB, initial_model_type: experimental model

3bh0

residue_range: 203-441, source_name: PDB, initial_model_type: experimental model
DetailsThe initial fitting was done with the 2R5U and 3BH0 models onto which the E. coli amino sequence had been built. The linker segments that connected these segments were built by hand. PHENIX real_space_refine was used to refine the complete model for the B6P5 entity.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6bbm:
Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex

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