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- PDB-9efk: Cryo-EM structure of the portal-tail complex of LME-1 phage -

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Basic information

Entry
Database: PDB / ID: 9efk
TitleCryo-EM structure of the portal-tail complex of LME-1 phage
Components
  • orf12
  • orf17
  • orf18
  • orf22
KeywordsVIRAL PROTEIN / LME-1 / legionella pneumophila / phage / portal / tail / podovirus / podophage
Function / homologyHead-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / symbiont entry into host cell / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsDeme, J.C. / Lea, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To Be Published
Title: Phage resistance as an unexpected environmental determinant of the accidental virulence of Legionella pneumophila against the human host.
Authors: Nicholson, B. / Sante, J.F. / Chaney, E.H. / Deme, J.C. / Deecker, S.R. / Sztanko, K. / Davidson, A.R. / Lea, S.M. / Ensminger, A.W.
History
DepositionNov 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: orf12
M: orf18
N: orf18
O: orf18
P: orf18
Q: orf18
R: orf18
AE: orf22
AF: orf22
AG: orf22
AN: orf22
AO: orf22
AP: orf22
AW: orf22
AX: orf22
AY: orf22
BF: orf22
BG: orf22
BH: orf22
BO: orf22
BP: orf22
BQ: orf22
BX: orf22
BY: orf22
BZ: orf22
B: orf12
C: orf12
D: orf12
E: orf12
F: orf12
G: orf12
H: orf12
I: orf12
J: orf12
K: orf12
L: orf12
T: orf17
AC: orf17
AD: orf17
S: orf17
X: orf17
U: orf17
V: orf17
W: orf17
Y: orf17
Z: orf17
AA: orf17
AB: orf17


Theoretical massNumber of molelcules
Total (without water)2,804,71148
Polymers2,804,71148
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
orf12


Mass: 62743.062 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A140AYN0
#2: Protein
orf18


Mass: 89921.969 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A140AYN6
#3: Protein
orf22


Mass: 68819.797 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A140AYP0
#4: Protein
orf17


Mass: 22792.135 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A140AYN5
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: LME-1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: LME-1 (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 100 nm
Image recordingElectron dose: 52.9 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: dev_5430 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88530 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 51.88 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047132450
ELECTRON MICROSCOPYf_angle_d0.5187180510
ELECTRON MICROSCOPYf_chiral_restr0.047320358
ELECTRON MICROSCOPYf_plane_restr0.004223562
ELECTRON MICROSCOPYf_dihedral_angle_d12.696548114

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