9MKB | pdb_00009mkb

Structure of the bacteriophage T4 portal-neck-tail complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

In situ structures of the portal-neck-tail complex of bacteriophage T4 inform a viral genome positioning mechanism.

Fokine, A.Zhu, J.Klose, T.Vago, F.Arnaud, C.A.Wang, Z.Khare, B.Rossmann, M.G.Chen, Z.Sun, L.Fang, Q.Kuhn, R.J.Rao, V.B.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-69106-8
  • Primary Citation Related Structures: 
    9MKB

  • PubMed Abstract: 

    The post-genome packaging mechanisms that govern the assembly of an infectious virion are poorly understood in bacteriophages and other viruses. Here, our near-atomic resolution cryo-EM structural analyses uncovered an assembly- and conformation-driven genome positioning mechanism in the tailed bacteriophage T4. We show that following headful packaging, which generates a pressurized head, a global conformational change occurs in the portal structure, probably triggering packaging termination and ejection of the packaging motor. Our high-resolution structures of the neck of the virion further show that the neck undergoes conformational changes upon docking of a pre-assembled tail onto the sealed neck, which then opens a genome-gate. Driven by the pressure of the packaged DNA, the genome travels through open neck channels, binds and compresses the resident tape-measure protein, and halts at the bottom of the second topmost disk of the tail tube. Pressure-suspended within the virion's innermost tunnel and secured by a baseplate plug, the genome remains poised to flow through the tunnel into a host cell upon receiving the host receptor recognition signal.


  • Organizational Affiliation
    • Department of Biological Sciences, Purdue University, West Lafayette, IN, USA. afokine@purdue.edu.

Macromolecule Content 

  • Total Structure Weight: 24,141.06 kDa 
  • Atom Count: 1,533,268 
  • Modeled Residue Count: 198,093 
  • Deposited Residue Count: 220,229 
  • Unique protein chains: 31

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
gp14, neck protein256Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P11111 (Enterobacteria phage T4)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
gp18, tail sheath protein
AC [auth B5],
AE [auth Bx],
AF [auth L3],
AG [auth M4],
AH [auth Nd],
AO [auth b5],
AP [auth cO],
B [auth 1],
BC [auth B6],
BE [auth By],
BF [auth L4],
BG [auth M5],
BH [auth Ne],
BO [auth b6],
BP [auth cP],
C [auth 2],
CC [auth B7],
CE [auth Bz],
CF [auth L5],
CG [auth M6],
CH [auth Nf],
CO [auth b7],
D [auth 3],
DF [auth L6],
DG [auth M7],
DH [auth Ng],
DO [auth b8],
DP [auth dS],
E [auth 4],
EF [auth L7],
EG [auth M8],
EH [auth Nh],
EO [auth b9],
EP [auth dT],
F [auth 5],
FA [auth AK],
FF [auth L8],
FG [auth M9],
FH [auth Ni],
FO [auth bN],
FP [auth dU],
GA [auth AL],
GF [auth L9],
GG [auth MS],
GH [auth Nj],
GO [auth bO],
GP [auth dV],
HA [auth AM],
HF [auth LS],
HG [auth MU],
HH [auth Nx],
HO [auth bP],
HP [auth dW],
IA [auth AN],
IF [auth LU],
IG [auth MV],
IH [auth Nz],
IO [auth bQ],
IP [auth dZ],
JA [auth AO],
JF [auth LV],
JG [auth MW],
JO [auth bR],
KA [auth AP],
KF [auth LW],
KG [auth MX],
KO [auth bY],
LF [auth LX],
LG [auth MY],
ME [auth K0],
MF [auth LY],
MG [auth MZ],
MO [auth cA],
NE [auth K1],
NF [auth LZ],
NG [auth Ma],
NO [auth cB],
OE [auth K2],
OF [auth La],
OG [auth Mb],
OO [auth cC],
PE [auth K3],
PF [auth Lb],
PG [auth Mc],
PO [auth cD],
QE [auth K4],
QF [auth Lc],
QG [auth Md],
QO [auth cE],
RE [auth K5],
RF [auth Ld],
RG [auth Me],
RO [auth cF],
SD [auth Bp],
SE [auth K6],
SF [auth Le],
SG [auth Mx],
SO [auth cG],
TD [auth Bq],
TE [auth K7],
TF [auth Lx],
TG [auth Mz],
TO [auth cH],
UD [auth Br],
UE [auth K8],
UF [auth Lz],
UO [auth cI],
VD [auth Bs],
VE [auth K9],
VG [auth NX],
VO [auth cJ],
WB [auth B1],
WD [auth Bt],
WF [auth M0],
WG [auth NZ],
WO [auth cK],
XB [auth B2],
XD [auth Bu],
XE [auth L0],
XF [auth M1],
XG [auth Na],
XN [auth b0],
XO [auth cL],
Y [auth AD],
YB [auth B3],
YD [auth Bv],
YE [auth L1],
YF [auth M2],
YG [auth Nb],
YN [auth b3],
YO [auth cM],
ZB [auth B4],
ZD [auth Bw],
ZE [auth L2],
ZF [auth M3],
ZG [auth Nc],
ZN [auth b4],
ZO [auth cN]
659Escherichia phage T4Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
gp19, tail tube protein
AA [auth AF],
AD [auth BX],
AI [auth Oo],
AJ [auth Pr],
AK [auth Rt],
AR [auth ht],
BA [auth AG],
BD [auth BY],
BI [auth Op],
BJ [auth Ps],
BR [auth hu],
CA [auth AH],
CD [auth BZ],
CI [auth Oq],
CJ [auth Pt],
CR [auth hv],
DA [auth AI],
DD [auth Ba],
DI [auth Or],
DQ [auth h1],
DR [auth hw],
EA [auth AJ],
ED [auth Bb],
EI [auth Os],
EQ [auth h2],
ER [auth hx],
FD [auth Bc],
FI [auth Ot],
FJ [auth RE],
FQ [auth hI],
FR [auth hy],
FS [auth o],
G [auth 6],
GD [auth Bd],
GJ [auth RF],
GQ [auth hJ],
GR [auth hz],
H [auth 7],
HD [auth Be],
HI [auth PE],
HJ [auth RG],
HQ [auth hK],
I [auth 8],
ID [auth Bf],
II [auth PF],
IJ [auth RH],
IQ [auth hL],
J [auth 9],
JD [auth Bg],
JI [auth PG],
JJ [auth RI],
JQ [auth hM],
KD [auth Bh],
KH [auth OE],
KI [auth PH],
KJ [auth RJ],
KQ [auth hX],
LD [auth Bi],
LH [auth OF],
LI [auth PI],
LJ [auth RK],
LQ [auth he],
MD [auth Bj],
MH [auth OG],
MI [auth PJ],
MJ [auth RL],
MQ [auth hf],
ND [auth Bk],
NH [auth OH],
NI [auth PK],
NJ [auth RM],
NQ [auth hg],
OD [auth Bl],
OH [auth OI],
OI [auth PL],
OJ [auth RN],
OQ [auth hh],
PD [auth Bm],
PH [auth OJ],
PI [auth PM],
PJ [auth RO],
PQ [auth hi],
QD [auth Bn],
QH [auth OK],
QI [auth PN],
QJ [auth RT],
QQ [auth hj],
RD [auth Bo],
RH [auth OL],
RI [auth PO],
RJ [auth Rk],
RQ [auth hk],
SH [auth OM],
SI [auth Pj],
SJ [auth Rl],
SQ [auth hl],
TH [auth ON],
TI [auth Pk],
TJ [auth Rm],
TQ [auth hm],
UH [auth OO],
UI [auth Pl],
UJ [auth Rn],
UQ [auth hn],
V [auth AA],
VH [auth Oj],
VI [auth Pm],
VJ [auth Ro],
VQ [auth ho],
WH [auth Ok],
WI [auth Pn],
WJ [auth Rp],
WQ [auth hp],
XH [auth Ol],
XI [auth Po],
XJ [auth Rq],
XQ [auth hq],
YH [auth Om],
YI [auth Pp],
YJ [auth Rr],
YQ [auth hr],
Z [auth AE],
ZH [auth On],
ZI [auth Pq],
ZJ [auth Rs],
ZQ [auth hs]
163Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for A0A7S9SVI2 (Escherichia phage T4)
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
gpwac, fibritin487Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P10104 (Enterobacteria phage T4)
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
gp20, portal protein524Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for A0A7S9SW10 (Escherichia phage T4)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
gp23, major capsid protein521Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P04535 (Enterobacteria phage T4)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
gp13, neck protein309Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P11110 (Enterobacteria phage T4)
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
gp15, tail terminator protein272Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for A0A7S9XHN5 (Escherichia phage T4)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
gp3, tube terminator protein176Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for A0A7S9SU76 (Escherichia phage T4)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Hoc, highly immunogenic outer capsid proteinLA [auth AQ],
MA [auth AR],
NA [auth AS],
OA [auth AT],
PA [auth AU]
376Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for A0A7S9SW08 (Escherichia phage T4)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Soc, small outer capsid protein80Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for A0A7S9SVQ6 (Escherichia phage T4)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
gp12, short tail fiber protein527Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P10930 (Enterobacteria phage T4)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
gp9, baseplate wedge tail fiber connector288Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for A0A7S9SWG4 (Escherichia phage T4)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
gp11, baseplate wedge protein219Escherichia phage T4Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
gp10, baseplate wedge protein602Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P10928 (Enterobacteria phage T4)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
gp7, baseplate wedge protein1,032Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P19061 (Enterobacteria phage T4)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
gp8, baseplate wedge protein334Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for A0A7S9SVZ9 (Escherichia phage T4)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
gp6, baseplate wedge protein660Escherichia phage T4Mutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
gp5, baseplate central spike proteinAQ [auth gH],
YP [auth gE],
ZP [auth gG]
575Escherichia phage T4Mutation(s): 0 
EC: 3.2.1.17
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
gp5.4, tip of the central spikeBQ [auth gd]97Escherichia phage T4Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
gp27, baseplate hub proteinIR [auth iC],
JR [auth iD],
KR [auth iF]
391Escherichia phage T4Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
gp29, tape measure proteinMR [auth ja],
NR [auth jb],
OR [auth jc]
590Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P13337 (Enterobacteria phage T4)
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
gp53, baseplate wedge protein196Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for A0A7S9XI21 (Escherichia phage T4)
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
gp25, baseplate protein132Escherichia phage T4Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
gp48, baseplate protein364Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for A0A7S9SVT9 (Escherichia phage T4)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
gp54, baseplate protein320Escherichia phage T4Mutation(s): 0 
UniProt
Find proteins for P13341 (Enterobacteria phage T4)
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
unassigned peptide A25Escherichia phage T4Mutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
unassigned peptide BCT [auth sQ],
DT [auth sT],
ET [auth sU]
18Escherichia phage T4Mutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
unassigned peptide CGT [auth tS],
HT [auth tX],
IT [auth tY]
10Escherichia phage T4Mutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
unassigned peptide DKT [auth uR],
LT [auth uV],
MT [auth uW]
7Escherichia phage T4Mutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
unassigned peptide EOT [auth vZ],
PT [auth va],
QT [auth vb]
9Escherichia phage T4Mutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI081726

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-07-08
    Changes: Data collection, Database references