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- PDB-7sg7: In situ cryo-EM structure of bacteriophage Sf6 gp8:gp14N complex ... -

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Basic information

Entry
Database: PDB / ID: 7sg7
TitleIn situ cryo-EM structure of bacteriophage Sf6 gp8:gp14N complex at 2.8 A resolution
Components
  • Gene 14 protein
  • Gene 8 protein
KeywordsSTRUCTURAL PROTEIN / in situ / phage / gp8 / gp14
Function / homology
Function and homology information


virus tail / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
: / Tailspike protein, C-terminal / Bacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Gene 14 protein / Gene 8 protein
Similarity search - Component
Biological speciesShigella phage Sf6 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsLi, F. / Cingolani, G. / Hou, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140733 United States
CitationJournal: Sci Adv / Year: 2022
Title: High-resolution cryo-EM structure of the virus Sf6 genome delivery tail machine.
Authors: Fenglin Li / Chun-Feng David Hou / Ruoyu Yang / Richard Whitehead / Carolyn M Teschke / Gino Cingolani /
Abstract: Sf6 is a bacterial virus that infects the human pathogen Here, we describe the cryo-electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom ...Sf6 is a bacterial virus that infects the human pathogen Here, we describe the cryo-electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom resolution. We built de novo structures of all tail components and resolved four symmetry-mismatched interfaces. Unexpectedly, we found that the tail exists in two conformations, rotated by ~6° with respect to the capsid. The two tail conformers are identical in structure but differ solely in how the portal and head-to-tail adaptor carboxyl termini bond with the capsid at the fivefold vertex, similar to a diamond held over a five-pronged ring in two nonidentical states. Thus, in the mature Sf6 tail, the portal structure does not morph locally to accommodate the symmetry mismatch but exists in two energetic minima rotated by a discrete angle. We propose that the design principles of the Sf6 tail are conserved across P22-like Podoviridae.
History
DepositionOct 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gene 14 protein
B: Gene 14 protein
C: Gene 14 protein
T: Gene 8 protein
D: Gene 14 protein
I: Gene 14 protein
N: Gene 14 protein
S: Gene 8 protein
E: Gene 14 protein
J: Gene 14 protein
O: Gene 14 protein
U: Gene 8 protein
F: Gene 14 protein
K: Gene 14 protein
P: Gene 14 protein
V: Gene 8 protein
G: Gene 14 protein
L: Gene 14 protein
Q: Gene 14 protein
W: Gene 8 protein
H: Gene 14 protein
M: Gene 14 protein
R: Gene 14 protein
X: Gene 8 protein


Theoretical massNumber of molelcules
Total (without water)1,521,35424
Polymers1,521,35424
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area90440 Å2
ΔGint-523 kcal/mol
Surface area200400 Å2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "G" and resid 7 through 123)
d_2ens_1chain "B"
d_3ens_1(chain "C" and resid 7 through 123)
d_4ens_1(chain "D" and resid 7 through 123)
d_5ens_1(chain "E" and resid 7 through 123)
d_6ens_1(chain "F" and resid 7 through 123)
d_7ens_1(chain "A" and resid 7 through 123)
d_8ens_1(chain "H" and resid 7 through 123)
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "L"
d_13ens_1chain "M"
d_14ens_1(chain "N" and resid 7 through 123)
d_15ens_1(chain "O" and resid 7 through 123)
d_16ens_1(chain "P" and resid 7 through 123)
d_17ens_1(chain "Q" and resid 7 through 123)
d_18ens_1(chain "R" and resid 7 through 123)
d_1ens_2chain "T"
d_2ens_2chain "V"
d_3ens_2chain "U"
d_4ens_2chain "S"
d_5ens_2chain "X"
d_6ens_2chain "W"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNALAQ4 - 120
d_21ens_1ASNALAB1 - 117
d_31ens_1ASNALAC4 - 120
d_41ens_1ASNALAE4 - 120
d_51ens_1ASNALAI4 - 120
d_61ens_1ASNALAM4 - 120
d_71ens_1ASNALAA4 - 120
d_81ens_1ASNALAU4 - 120
d_91ens_1ASNALAF1 - 117
d_101ens_1ASNALAJ1 - 117
d_111ens_1ASNALAN1 - 117
d_121ens_1ASNALAR1 - 117
d_131ens_1ASNALAV1 - 117
d_141ens_1ASNALAG4 - 120
d_151ens_1ASNALAK4 - 120
d_161ens_1ASNALAO4 - 120
d_171ens_1ASNALAS4 - 120
d_181ens_1ASNALAW4 - 120
d_11ens_2PROGLUD1 - 471
d_21ens_2PROGLUP1 - 471
d_31ens_2PROGLUL1 - 471
d_41ens_2PROGLUH1 - 471
d_51ens_2PROGLUX1 - 471
d_61ens_2PROGLUT1 - 471

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein
Gene 14 protein


Mass: 67118.141 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf6 (virus) / References: UniProt: Q716G1
#2: Protein
Gene 8 protein


Mass: 52204.586 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf6 (virus) / References: UniProt: Q716G7

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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: Shigella virus Sf6 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Shigella virus Sf6
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / 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: OTHER
Electron lensMode: OTHER / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7977

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2RELION3.1.2image acquisition
4RELION3.1.2CTF correction
13RELION3.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 67439
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 91.24 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00339690
ELECTRON MICROSCOPYf_angle_d0.55453922
ELECTRON MICROSCOPYf_dihedral_angle_d4.5475436
ELECTRON MICROSCOPYf_chiral_restr0.0495868
ELECTRON MICROSCOPYf_plane_restr0.0047104
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2QELECTRON MICROSCOPYNCS constraints0.000701469147965
ens_1d_3QELECTRON MICROSCOPYNCS constraints0.000707696826634
ens_1d_4QELECTRON MICROSCOPYNCS constraints0.105194075138
ens_1d_5QELECTRON MICROSCOPYNCS constraints0.105209021229
ens_1d_6QELECTRON MICROSCOPYNCS constraints0.000705476283784
ens_1d_7QELECTRON MICROSCOPYNCS constraints0.000716290739605
ens_1d_8QELECTRON MICROSCOPYNCS constraints0.000719477535176
ens_1d_9QELECTRON MICROSCOPYNCS constraints0.000713206914845
ens_1d_10QELECTRON MICROSCOPYNCS constraints0.000718963364227
ens_1d_11QELECTRON MICROSCOPYNCS constraints0.00070830442899
ens_1d_12QELECTRON MICROSCOPYNCS constraints0.000712623821252
ens_1d_13QELECTRON MICROSCOPYNCS constraints0.00070111259956
ens_1d_14QELECTRON MICROSCOPYNCS constraints0.000706535250569
ens_1d_15QELECTRON MICROSCOPYNCS constraints0.000707417726613
ens_1d_16QELECTRON MICROSCOPYNCS constraints0.000717446956799
ens_1d_17QELECTRON MICROSCOPYNCS constraints0.000706442908308
ens_1d_18QELECTRON MICROSCOPYNCS constraints0.000712127082589
ens_2d_2DELECTRON MICROSCOPYNCS constraints0.000712167285879
ens_2d_3DELECTRON MICROSCOPYNCS constraints0.000700469214083
ens_2d_4DELECTRON MICROSCOPYNCS constraints0.000707026308809
ens_2d_5DELECTRON MICROSCOPYNCS constraints0.000702954341294
ens_2d_6DELECTRON MICROSCOPYNCS constraints0.000708501698763

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