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- PDB-9moh: Structure of the middle part of the bacteriophage T4 tail -

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Basic information

Entry
Database: PDB / ID: 9moh
TitleStructure of the middle part of the bacteriophage T4 tail
Components
  • gp18, tail sheath protein
  • gp19, tail tube protein
KeywordsVIRAL PROTEIN / bacteriophage T4 / contractile phage tail / sheath protein / tail tube protein / VIRUS
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / structural molecule activity
Similarity search - Function
: / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain ...: / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Tail tube protein / Tail sheath protein
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFokine, A. / Zhu, J. / Klose, T. / Vago, F. / Arnaud, C. / Wang, Z. / Khare, B. / Rossmann, M.G. / Chen, Z. / Sun, L. ...Fokine, A. / Zhu, J. / Klose, T. / Vago, F. / Arnaud, C. / Wang, Z. / Khare, B. / Rossmann, M.G. / Chen, Z. / Sun, L. / Fang, Q. / Kuhn, R. / Rao, V.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
CitationJournal: To Be Published
Title: In situ Atomic Structure of Phage T4 Head-Tail Connector Complex Shows Molecular Gates Open for Genome Ejection and DNA Pushed into the Tail Tube
Authors: Fokine, A. / Zhu, J. / Klose, T. / Vago, F. / Arnaud, C. / Wang, Z. / Khare, B. / Rossmann, M.G. / Chen, Z. / Sun, L. / Fang, Q. / Kuhn, R. / Rao, V.B.
History
DepositionDec 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K0: gp18, tail sheath protein
K1: gp18, tail sheath protein
K2: gp18, tail sheath protein
K3: gp18, tail sheath protein
K4: gp18, tail sheath protein
K5: gp18, tail sheath protein
K6: gp18, tail sheath protein
K7: gp18, tail sheath protein
K8: gp18, tail sheath protein
K9: gp18, tail sheath protein
L0: gp18, tail sheath protein
L1: gp18, tail sheath protein
L2: gp18, tail sheath protein
L3: gp18, tail sheath protein
L4: gp18, tail sheath protein
L5: gp18, tail sheath protein
L6: gp18, tail sheath protein
L7: gp18, tail sheath protein
L8: gp18, tail sheath protein
L9: gp18, tail sheath protein
LQ: gp18, tail sheath protein
LR: gp18, tail sheath protein
LS: gp18, tail sheath protein
LU: gp18, tail sheath protein
LV: gp18, tail sheath protein
LW: gp18, tail sheath protein
LX: gp18, tail sheath protein
LY: gp18, tail sheath protein
LZ: gp18, tail sheath protein
La: gp18, tail sheath protein
Lb: gp18, tail sheath protein
Lc: gp18, tail sheath protein
Ld: gp18, tail sheath protein
Le: gp18, tail sheath protein
Lv: gp18, tail sheath protein
Lw: gp18, tail sheath protein
Lx: gp18, tail sheath protein
Lz: gp18, tail sheath protein
M0: gp18, tail sheath protein
M1: gp18, tail sheath protein
M2: gp18, tail sheath protein
M3: gp18, tail sheath protein
M4: gp18, tail sheath protein
M5: gp18, tail sheath protein
M6: gp18, tail sheath protein
M7: gp18, tail sheath protein
M8: gp18, tail sheath protein
M9: gp18, tail sheath protein
MQ: gp18, tail sheath protein
MR: gp18, tail sheath protein
MS: gp18, tail sheath protein
MU: gp18, tail sheath protein
MV: gp18, tail sheath protein
MW: gp18, tail sheath protein
MX: gp18, tail sheath protein
MY: gp18, tail sheath protein
MZ: gp18, tail sheath protein
Ma: gp18, tail sheath protein
Mb: gp18, tail sheath protein
Mc: gp18, tail sheath protein
Md: gp18, tail sheath protein
Me: gp18, tail sheath protein
Mv: gp18, tail sheath protein
Mw: gp18, tail sheath protein
Mx: gp18, tail sheath protein
Mz: gp18, tail sheath protein
NV: gp18, tail sheath protein
NW: gp18, tail sheath protein
NX: gp18, tail sheath protein
NZ: gp18, tail sheath protein
Na: gp18, tail sheath protein
Nb: gp18, tail sheath protein
Nc: gp18, tail sheath protein
Nd: gp18, tail sheath protein
Ne: gp18, tail sheath protein
Nf: gp18, tail sheath protein
Ng: gp18, tail sheath protein
Nh: gp18, tail sheath protein
Ni: gp18, tail sheath protein
Nj: gp18, tail sheath protein
Nv: gp18, tail sheath protein
Nw: gp18, tail sheath protein
Nx: gp18, tail sheath protein
Nz: gp18, tail sheath protein
OC: gp19, tail tube protein
OD: gp19, tail tube protein
OE: gp19, tail tube protein
OF: gp19, tail tube protein
OG: gp19, tail tube protein
OH: gp19, tail tube protein
OI: gp19, tail tube protein
OJ: gp19, tail tube protein
OK: gp19, tail tube protein
OL: gp19, tail tube protein
OM: gp19, tail tube protein
ON: gp19, tail tube protein
OO: gp19, tail tube protein
Oh: gp19, tail tube protein
Oi: gp19, tail tube protein
Oj: gp19, tail tube protein
Ok: gp19, tail tube protein
Ol: gp19, tail tube protein
Om: gp19, tail tube protein
On: gp19, tail tube protein
Oo: gp19, tail tube protein
Op: gp19, tail tube protein
Oq: gp19, tail tube protein
Or: gp19, tail tube protein
Os: gp19, tail tube protein
Ot: gp19, tail tube protein
PC: gp19, tail tube protein
PD: gp19, tail tube protein
PE: gp19, tail tube protein
PF: gp19, tail tube protein
PG: gp19, tail tube protein
PH: gp19, tail tube protein
PI: gp19, tail tube protein
PJ: gp19, tail tube protein
PK: gp19, tail tube protein
PL: gp19, tail tube protein
PM: gp19, tail tube protein
PN: gp19, tail tube protein
PO: gp19, tail tube protein
Ph: gp19, tail tube protein
Pi: gp19, tail tube protein
Pj: gp19, tail tube protein
Pk: gp19, tail tube protein
Pl: gp19, tail tube protein
Pm: gp19, tail tube protein
Pn: gp19, tail tube protein
Po: gp19, tail tube protein
Pp: gp19, tail tube protein
Pq: gp19, tail tube protein
Pr: gp19, tail tube protein
Ps: gp19, tail tube protein
Pt: gp19, tail tube protein
RC: gp19, tail tube protein
RD: gp19, tail tube protein
RE: gp19, tail tube protein
RF: gp19, tail tube protein
RG: gp19, tail tube protein
RH: gp19, tail tube protein
RI: gp19, tail tube protein
RJ: gp19, tail tube protein
RK: gp19, tail tube protein
RL: gp19, tail tube protein
RM: gp19, tail tube protein
RN: gp19, tail tube protein
RO: gp19, tail tube protein
RR: gp19, tail tube protein
RS: gp19, tail tube protein
RT: gp19, tail tube protein
Rk: gp19, tail tube protein
Rl: gp19, tail tube protein
Rm: gp19, tail tube protein
Rn: gp19, tail tube protein
Ro: gp19, tail tube protein
Rp: gp19, tail tube protein
Rq: gp19, tail tube protein
Rr: gp19, tail tube protein
Rs: gp19, tail tube protein
Rt: gp19, tail tube protein


Theoretical massNumber of molelcules
Total (without water)7,434,694162
Polymers7,434,694162
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 ...
gp18, tail sheath protein


Mass: 71348.625 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SVW9
#2: Protein ...
gp19, tail tube protein


Mass: 18479.613 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SVI2
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: Escherichia phage T4 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage T4 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Escherichia coli / Strain: B
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Ted Pella lacey carbon 400 mesh grids (catalog No: 01824) were used.

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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: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113800 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 61.95 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0083531702
ELECTRON MICROSCOPYf_angle_d0.708723054
ELECTRON MICROSCOPYf_chiral_restr0.050982074
ELECTRON MICROSCOPYf_plane_restr0.004994416
ELECTRON MICROSCOPYf_dihedral_angle_d15.4952190824

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