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- PDB-6p3e: Mobile loops and electrostatic interactions maintain the flexible... -

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Basic information

Entry
Database: PDB / ID: 6p3e
TitleMobile loops and electrostatic interactions maintain the flexible lambda tail tube
ComponentsTail tube protein
KeywordsVIRAL PROTEIN / Tail tube / siphoviridae / helical
Function / homology
Function and homology information


virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / host cell cytoplasm
Similarity search - Function
Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Biological speciesEscherichia phage lambda (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsCampbell, P. / Duda, R.L. / Nassur, J. / Hendrix, R.W. / Conway, J.F. / Huet, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM047795 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10 OD019995 United States
CitationJournal: J Mol Biol / Year: 2020
Title: Mobile Loops and Electrostatic Interactions Maintain the Flexible Tail Tube of Bacteriophage Lambda.
Authors: Patricia L Campbell / Robert L Duda / Jamie Nassur / James F Conway / Alexis Huet /
Abstract: The long flexible tail tube of bacteriophage lambda connects its capsid to the tail tip. On infection, a DNA ejection signal is passed from the tip, along the tube to the capsid that triggers passage ...The long flexible tail tube of bacteriophage lambda connects its capsid to the tail tip. On infection, a DNA ejection signal is passed from the tip, along the tube to the capsid that triggers passage of the DNA down the tube and into the host bacterium. The tail tube is built from repeating units of the major tail protein, gpV, which has two distinctive domains. Its N-terminal domain has the same fold as proteins that form the rigid inner tubes of contractile tail phages, such as T4, and its C-terminal domain adopt an Ig-like fold of unknown function. We determined structures of the lambda tail tube in free tails and in virions before and after DNA ejection using cryoelectron microscopy. Modeling of the density maps reveals how electrostatic interactions and a mobile loop participate in assembly and also impart flexibility to the tube while maintaining its integrity. We also demonstrate how a common protein fold produces rigid tubes in some phages but flexible tubes in others.
History
DepositionMay 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Tail tube protein
B: Tail tube protein
C: Tail tube protein
D: Tail tube protein
E: Tail tube protein
F: Tail tube protein
G: Tail tube protein
H: Tail tube protein
I: Tail tube protein
J: Tail tube protein
K: Tail tube protein
L: Tail tube protein
M: Tail tube protein
N: Tail tube protein
O: Tail tube protein
P: Tail tube protein
Q: Tail tube protein
R: Tail tube protein


Theoretical massNumber of molelcules
Total (without water)464,97218
Polymers464,97218
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryHelical symmetry: (Circular symmetry: 6 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 5 / Rise per n subunits: 42.8 Å / Rotation per n subunits: 17.5 °)

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Components

#1: Protein
Tail tube protein / TTP / Gene product V / gpV / Major tail protein V


Mass: 25831.779 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: V, lambdap13 / Production host: Escherichia coli (E. coli) / References: UniProt: P03733

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: tail tube of the lambda phage / Type: COMPLEX / Details: plasmid expression of the tail genes / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 37 kDa/nm / Experimental value: NO
Source (natural)Organism: Escherichia phage lambda (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMTris1
2100 mMpotassium glutamate1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: purified tail
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1240

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Processing

EM software
IDNameVersionCategory
1EMAN2particle selection
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10MDFFmodel refinement
11RELION2initial Euler assignment
12RELION2final Euler assignment
14RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 17.5 ° / Axial rise/subunit: 42.8 Å / Axial symmetry: C6
Particle selectionNum. of particles selected: 7934
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5543 / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingB value: 200 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Pdb chain-ID: A / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-ID
12K4Q

2k4q

2K4Q1
22L04

2l04

2L042

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