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- PDB-9mof: Structure of the bacteriophage T4 portal-neck-tail connector complex -

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Basic information

Entry
Database: PDB / ID: 9mof
TitleStructure of the bacteriophage T4 portal-neck-tail connector complex
Components
  • Hoc, highly immunogenic outer capsid protein
  • Soc, small outer capsid protein
  • gp13, neck protein
  • gp14, neck protein
  • gp15, tail terminator protein
  • gp18, tail sheath protein
  • gp19, tail tube protein
  • gp20, portal protein
  • gp23, major capsid protein
  • gp3, tube terminator protein
  • gpwac, fibritin
KeywordsVIRAL PROTEIN / bacteriophage T4 / portal vertex / phage neck / tail terminator protein / tube terminator protein / asymmetric phage reconstruction / DNA retention / neck stopper protein / head completion proteins
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral capsid, decoration / T=13 icosahedral viral capsid / viral genome packaging / viral release from host cell / virion component / viral capsid / structural molecule activity
Similarity search - Function
Bacteriophage T4, Gp14, neck protein / Virus neck protein / Portal protein Gp20 / Bacteriophage T4-like portal protein (Gp20) / Highly immunogenic outer capsid protein / Small outer capsid protein / Myoviridae tail sheath stabiliser / Small outer capsid protein superfamily / Myoviridae tail sheath stabiliser superfamily / T4-like virus Myoviridae tail sheath stabiliser ...Bacteriophage T4, Gp14, neck protein / Virus neck protein / Portal protein Gp20 / Bacteriophage T4-like portal protein (Gp20) / Highly immunogenic outer capsid protein / Small outer capsid protein / Myoviridae tail sheath stabiliser / Small outer capsid protein superfamily / Myoviridae tail sheath stabiliser superfamily / T4-like virus Myoviridae tail sheath stabiliser / Small outer capsid protein / Major capsid protein, Myoviridae / Major capsid protein Gp23 / : / Tail sheath protein Gp18-like domain I / Capsid protein, T4-like bacteriophage-like / : / 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 / PKD domain / : / 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 / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Fibritin C-terminal / Fibritin C-terminal region / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tail completion and sheath stabilizer protein / Tail tube protein / Small outer capsid protein / Tail sheath protein / Highly immunogenic outer capsid protein / Portal protein / Tail sheath stabilizer and completion protein / Major capsid protein / Fibritin / Neck protein gp13 / Neck protein gp14
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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

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Assembly

Deposited unit
0: gp14, neck protein
1: gp18, tail sheath protein
2: gp18, tail sheath protein
3: gp18, tail sheath protein
4: gp18, tail sheath protein
5: gp18, tail sheath protein
6: gp19, tail tube protein
7: gp19, tail tube protein
8: gp19, tail tube protein
9: gp19, tail tube protein
A: gpwac, fibritin
A0: gp20, portal protein
A1: gp20, portal protein
A2: gp20, portal protein
A3: gp20, portal protein
A4: gp23, major capsid protein
A5: gp23, major capsid protein
A6: gp13, neck protein
A7: gp23, major capsid protein
A8: gp23, major capsid protein
A9: gp23, major capsid protein
AA: gp19, tail tube protein
AB: gp15, tail terminator protein
AC: gp3, tube terminator protein
AD: gp18, tail sheath protein
AE: gp19, tail tube protein
AF: gp19, tail tube protein
AG: gp19, tail tube protein
AH: gp19, tail tube protein
AI: gp19, tail tube protein
AJ: gp19, tail tube protein
AK: gp18, tail sheath protein
AL: gp18, tail sheath protein
AM: gp18, tail sheath protein
AN: gp18, tail sheath protein
AO: gp18, tail sheath protein
AP: gp18, tail sheath protein
AQ: Hoc, highly immunogenic outer capsid protein
AR: Hoc, highly immunogenic outer capsid protein
AS: Hoc, highly immunogenic outer capsid protein
AT: Hoc, highly immunogenic outer capsid protein
AU: Hoc, highly immunogenic outer capsid protein
AV: gp23, major capsid protein
AW: gp23, major capsid protein
AX: gp23, major capsid protein
AY: gp13, neck protein
AZ: gp23, major capsid protein
Aa: gp13, neck protein
Ab: gp13, neck protein
Ac: gp23, major capsid protein
Ad: gp23, major capsid protein
Ae: gp23, major capsid protein
Af: gp23, major capsid protein
Ag: gp23, major capsid protein
Ah: gp23, major capsid protein
Ai: gp23, major capsid protein
Aj: gp23, major capsid protein
Ak: gp23, major capsid protein
Al: gp13, neck protein
Am: gp23, major capsid protein
An: gp23, major capsid protein
Ao: gp23, major capsid protein
Ap: gp23, major capsid protein
Aq: gp13, neck protein
Ar: gp13, neck protein
As: gp13, neck protein
At: gp13, neck protein
Au: gp23, major capsid protein
Av: gp20, portal protein
Aw: gp23, major capsid protein
Ax: gp20, portal protein
Ay: gp23, major capsid protein
Az: gp23, major capsid protein
B: gpwac, fibritin
B1: gp18, tail sheath protein
B2: gp18, tail sheath protein
B3: gp18, tail sheath protein
B4: gp18, tail sheath protein
B5: gp18, tail sheath protein
B6: gp18, tail sheath protein
B7: gp18, tail sheath protein
BA: gp20, portal protein
BB: gp20, portal protein
BC: gp13, neck protein
BD: gp20, portal protein
BE: gp13, neck protein
BF: gp20, portal protein
BG: gp20, portal protein
BH: gp20, portal protein
BI: gp23, major capsid protein
BJ: gp23, major capsid protein
BK: gp23, major capsid protein
BL: gp13, neck protein
BM: gp23, major capsid protein
BN: Soc, small outer capsid protein
BO: Soc, small outer capsid protein
BP: Soc, small outer capsid protein
BQ: Soc, small outer capsid protein
BR: Soc, small outer capsid protein
BS: Soc, small outer capsid protein
BT: Soc, small outer capsid protein
BU: Soc, small outer capsid protein
BV: Soc, small outer capsid protein
BW: Soc, small outer capsid protein
BX: gp19, tail tube protein
BY: gp19, tail tube protein
BZ: gp19, tail tube protein
Ba: gp19, tail tube protein
Bb: gp19, tail tube protein
Bc: gp19, tail tube protein
Bd: gp19, tail tube protein
Be: gp19, tail tube protein
Bf: gp19, tail tube protein
Bg: gp19, tail tube protein
Bh: gp19, tail tube protein
Bi: gp19, tail tube protein
Bj: gp19, tail tube protein
Bk: gp19, tail tube protein
Bl: gp19, tail tube protein
Bm: gp19, tail tube protein
Bn: gp19, tail tube protein
Bo: gp19, tail tube protein
Bp: gp18, tail sheath protein
Bq: gp18, tail sheath protein
Br: gp18, tail sheath protein
Bs: gp18, tail sheath protein
Bt: gp18, tail sheath protein
Bu: gp18, tail sheath protein
Bv: gp18, tail sheath protein
Bw: gp18, tail sheath protein
Bx: gp18, tail sheath protein
By: gp18, tail sheath protein
Bz: gp18, tail sheath protein
C: gpwac, fibritin
D: gpwac, fibritin
E: gpwac, fibritin
F: gpwac, fibritin
G: gpwac, fibritin
H: gpwac, fibritin
I: gpwac, fibritin
J: gpwac, fibritin
K: gpwac, fibritin
L: gpwac, fibritin
M: gpwac, fibritin
N: gpwac, fibritin
O: gpwac, fibritin
P: gpwac, fibritin
Q: gpwac, fibritin
R: gpwac, fibritin
S: gpwac, fibritin
T: gpwac, fibritin
U: gpwac, fibritin
V: gpwac, fibritin
W: gpwac, fibritin
X: gpwac, fibritin
Y: gpwac, fibritin
Z: gpwac, fibritin
a: gpwac, fibritin
b: gpwac, fibritin
c: gpwac, fibritin
d: gpwac, fibritin
e: gpwac, fibritin
f: gpwac, fibritin
g: gpwac, fibritin
h: gpwac, fibritin
i: gpwac, fibritin
j: gpwac, fibritin
k: gp14, neck protein
l: gp14, neck protein
m: gp14, neck protein
n: gp14, neck protein
o: gp19, tail tube protein
p: gp14, neck protein
q: gp15, tail terminator protein
r: gp15, tail terminator protein
s: gp15, tail terminator protein
t: gp15, tail terminator protein
u: gp15, tail terminator protein
v: gp3, tube terminator protein
w: gp3, tube terminator protein
x: gp3, tube terminator protein
y: gp3, tube terminator protein
z: gp3, tube terminator protein


Theoretical massNumber of molelcules
Total (without water)8,175,301183
Polymers8,175,301183
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

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Protein , 11 types, 183 molecules 0klmnp12345ADAKALAMANAOAPB1B2B3B4B5B6B7BpBqBrBsBt...

#1: Protein
gp14, neck protein / Gene product 14 / gp14


Mass: 29597.836 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P11111
#2: Protein ...
gp18, tail sheath protein


Mass: 71348.625 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SVW9
#3: Protein ...
gp19, tail tube protein


Mass: 18479.613 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SVI2
#4: Protein ...
gpwac, fibritin / Collar protein / Whisker antigen control protein


Mass: 51909.164 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P10104
#5: Protein
gp20, portal protein / gp20


Mass: 61117.082 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SW10
#6: Protein ...
gp23, major capsid protein / Gene product 23 / Major head protein / gp23


Mass: 56074.242 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P04535
#7: Protein
gp13, neck protein / Gene product 13 / gp13


Mass: 34772.211 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: P11110
#8: Protein
gp15, tail terminator protein


Mass: 31587.486 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9XHN5
#9: Protein
gp3, tube terminator protein


Mass: 19723.143 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SU76
#10: Protein
Hoc, highly immunogenic outer capsid protein


Mass: 40416.547 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SW08
#11: Protein
Soc, small outer capsid protein / Soc


Mass: 9129.147 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T4 (virus) / References: UniProt: A0A7S9SVQ6

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Details

Has protein modificationY

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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 supportDetails: The grids were glow-discharged using a PELCO easyGlow system for 60s at 25mA.
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: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 53.53 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0022443809
ELECTRON MICROSCOPYf_angle_d0.5046602142
ELECTRON MICROSCOPYf_chiral_restr0.042966825
ELECTRON MICROSCOPYf_plane_restr0.003978948
ELECTRON MICROSCOPYf_dihedral_angle_d13.2494161673

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