6BBM

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanisms of opening and closing of the bacterial replicative helicase.

Chase, J.Catalano, A.Noble, A.J.Eng, E.T.Olinares, P.D.Molloy, K.Pakotiprapha, D.Samuels, M.Chait, B.des Georges, A.Jeruzalmi, D.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.41140

  • PubMed 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 closing of the helicase, which enable and restrict ...

    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 Escherichia coli 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.


    Organizational Affiliation

    Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States.,Department of Biochemistry, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States.,Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Biology, The Graduate Center of the City University of New York, New York, United States.,Department of Chemistry and Biochemistry, City College of New York, New York, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replicative DNA helicase
A, B, C, D, E, F
471Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dnaB (groP, grpA)
EC: 3.6.4.12
Find proteins for P0ACB0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACB0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Replication protein P
V, W, X, Y, Z
233Escherichia phage lambdaMutation(s): 0 
Gene Names: P
Find proteins for P03689 (Escherichia phage lambda)
Go to UniProtKB:  P03689
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, C, E, W
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
V, W, X, Y, Z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM084162
National Science Foundation (United States)United StatesMCB 1818255
National Institutes of Health/National Institute on Minority Health and Health DisparitiesUnited States5G12MD007603-30
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41 GM109824
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41 GM103314
Other governmentUnited StatesPA200A150068
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF32GM128303
Other privateUnited StatesSF349247 (Simons Foundation)
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103310
Other privateUnited StatesF00316 (Agouron Institute)
National Institutes of Health/Office of the DirectorUnited StatesOD019994
Other privateUnited StatesSM-2015-289297 (Silicon Mechanics/Research Cluster Grant program)

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-03-13
    Type: Data collection
  • Version 1.2: 2019-08-14
    Type: Data collection, Data processing, Experimental preparation