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- EMDB-25365: In situ cryo-EM structure of bacteriophage Sf6 gp3:gp7:gp5 comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-25365
TitleIn situ cryo-EM structure of bacteriophage Sf6 gp3:gp7:gp5 complex in conformation 2 at 3.71A resolution
Map data
Sample
  • Virus: Shigella virus Sf6
    • Protein or peptide: Gene 7 protein
    • Protein or peptide: Gene 3 protein
    • Protein or peptide: Gene 5 protein
Keywordsbacteriophage / Sf6 portal / gp7 / coat protein / symmetry mismatch / STRUCTURAL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, short tail mechanism / metal ion binding
Similarity search - Function
Tail accessory factor GP4 / Phage P22-like portal protein / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Major capsid protein Gp5 / P22 coat protein - gene protein 5
Similarity search - Domain/homology
Gene 7 protein / Gene 5 protein / Gene 3 protein
Similarity search - Component
Biological speciesShigella phage Sf6 (virus) / Shigella virus Sf6
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsLi F / Cingolani G
Funding support United States, 1 items
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
DepositionNov 2, 2021-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25365.png

Downloads & links

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Map

FileDownload / File: emd_25365.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.12 Å/pix.
x 512 pix.
= 574.464 Å		1.12 Å/pix.
x 512 pix.
= 574.464 Å		1.12 Å/pix.
x 512 pix.
= 574.464 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.6
Minimum - Maximum-6.585805 - 13.410356500000001
Average (Standard dev.)-0.000000000000525 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 574.464 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Shigella virus Sf6

EntireName: Shigella virus Sf6
Components
  • Virus: Shigella virus Sf6
    • Protein or peptide: Gene 7 protein
    • Protein or peptide: Gene 3 protein
    • Protein or peptide: Gene 5 protein

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Supramolecule #1: Shigella virus Sf6

SupramoleculeName: Shigella virus Sf6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10761 / Sci species name: Shigella virus Sf6 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: Gene 7 protein

MacromoleculeName: Gene 7 protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf6 (virus)
Molecular weightTheoretical: 17.753889 KDa
SequenceString:
MATVLTKGEI VLFALRKFAI ASNASLTDVE PQSIEDGVND LEDMMSEWMI NPGDIGYAFA TGDEQPLPDD ESGLPRKYKH AVGYQLLLR MLSDYSLEPT PQVLSNAQRS YDALMTDTLV VPSMRRRGDF PVGQGNKYDV FTSDRYYPGD LPLIDGDIPN A

UniProtKB: Gene 7 protein

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Macromolecule #2: Gene 3 protein

MacromoleculeName: Gene 3 protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf6 (virus)
Molecular weightTheoretical: 79.558227 KDa
SequenceString: MAETLEKKHE RIMLRFDRAY SPQKEVREKC IEATRFARVP GGQWEGATAA GTKLDEQFEK YPKFEINKVA TELNRIIAEY RNNRITVKF RPGDREASEE LANKLNGLFR ADYEETDGGE ACDNAFDDAA TGGFGCFRLT SMLVNEYDPM DDRQRIAIEP I YDPSRSVW ...String:
MAETLEKKHE RIMLRFDRAY SPQKEVREKC IEATRFARVP GGQWEGATAA GTKLDEQFEK YPKFEINKVA TELNRIIAEY RNNRITVKF RPGDREASEE LANKLNGLFR ADYEETDGGE ACDNAFDDAA TGGFGCFRLT SMLVNEYDPM DDRQRIAIEP I YDPSRSVW FDPDAKKYDK SDALWAFCMY SLSPEKYEAE YGKKPPTSLD VTSMTSWEYN WFGADVIYIA KYYEVRKESV DV ISYRHPI TGEIATYDSD QVEDIEDELA IAGFHEVARR SVKRRRVYVS VVDGDGFLEK PRRIPGEHIP LIPVYGKRWF IDD IERVEG HIAKAMDPQR LYNLQVSMLA DTAAQDPGQI PIVGMEQIRG LEKHWEARNK KRPAFLPLRE VRDKSGNIIA GATP AGYTQ PAVMNQALAA LLQQTSADIQ EVTGGSQAMQ QMPSNIAQET VNNLMNRADM ASFIYLDNMA KSLKRAGEVW LSMAR EVYG SEREVRIVNE DGSDDIAVLS AQVVDRQTGA VVALNDLSVG RYDVTVDVGP SYTARRDATV SVLTNVLSSM LPTDPM RPA IQGIILDNID GEGLDDFKEY NRNQLLISGI AKPRNEKEQQ IVQQAQMAAQ SQPNPEMVLA QAQMVAAQAE AQKATNE TA QTQIKAFTAQ QDAMESQANT VYKLAQARNI DDKAVMEAIR LLKDVAESQQ QQFQSPPQSP ADLMPS

UniProtKB: Gene 3 protein

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Macromolecule #3: Gene 5 protein

MacromoleculeName: Gene 5 protein / type: protein_or_peptide / ID: 3 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf6 (virus)
Molecular weightTheoretical: 45.722031 KDa
SequenceString: MPNNLDSNVS QIVLKKFLPG FMSDLVLAKT VDRQLLAGEI NSSTGDSVSF KRPHQFSSLR TPTGDISGQN KNNLISGKAT GRVGNYITV AVEYQQLEEA IKLNQLEEIL APVRQRIVTD LETELAHFMM NNGALSLGSP NTPITKWSDV AQTASFLKDL G VNEGENYA ...String:
MPNNLDSNVS QIVLKKFLPG FMSDLVLAKT VDRQLLAGEI NSSTGDSVSF KRPHQFSSLR TPTGDISGQN KNNLISGKAT GRVGNYITV AVEYQQLEEA IKLNQLEEIL APVRQRIVTD LETELAHFMM NNGALSLGSP NTPITKWSDV AQTASFLKDL G VNEGENYA VMDPWSAQRL ADAQTGLHAS DQLVRTAWEN AQIPTNFGGI RALMSNGLAS RTQGAFGGTL TVKTQPTVTY NA VKDSYQF TVTLTGATAS VTGFLKAGDQ VKFTNTYWLQ QQTKQALYNG ATPISFTATV TADANSDSGG DVTVTLSGVP IYD TTNPQY NSVSRQVEAG DAVSVVGTAS QTMKPNLFYN KFFCGLGSIP LPKLHSIDSA VATYEGFSIR VHKYADGDAN VQKM RFDLL PAYVCFNPHM GGQFFGNP

UniProtKB: Gene 5 protein

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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

BufferpH: 7.5 / Component - Name: PBS
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 7977 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 67439
Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 39000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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