7VRT

The unexpanded head structure of phage T4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of a large prolate virus capsid in unexpanded and expanded states generate insights into the icosahedral virus assembly.

Fang, Q.Tang, W.C.Fokine, A.Mahalingam, M.Shao, Q.Rossmann, M.G.Rao, V.B.

(2022) Proc Natl Acad Sci U S A 119: e2203272119-e2203272119

  • DOI: https://doi.org/10.1073/pnas.2203272119
  • Primary Citation of Related Structures:  
    7VRT, 7VS5

  • PubMed Abstract: 

    Many icosahedral viruses assemble proteinaceous precursors called proheads or procapsids. Proheads are metastable structures that undergo a profound structural transition known as expansion that transforms an immature unexpanded head into a mature genome-packaging head. Bacteriophage T4 is a model virus, well studied genetically and biochemically, but its structure determination has been challenging because of its large size and unusually prolate-shaped, ∼1,200-Å-long and ∼860-Å-wide capsid. Here, we report the cryogenic electron microscopy (cryo-EM) structures of T4 capsid in both of its major conformational states: unexpanded at a resolution of 5.1 Å and expanded at a resolution of 3.4 Å. These are among the largest structures deposited in Protein Data Bank to date and provide insights into virus assembly, head length determination, and shell expansion. First, the structures illustrate major domain movements and ∼70% additional gain in inner capsid volume, an essential transformation to contain the entire viral genome. Second, intricate intracapsomer interactions involving a unique insertion domain dramatically change, allowing the capsid subunits to rotate and twist while the capsomers remain fastened at quasi-threefold axes. Third, high-affinity binding sites emerge for a capsid decoration protein that clamps adjacent capsomers, imparting extraordinary structural stability. Fourth, subtle conformational changes at capsomers' periphery modulate intercapsomer angles between capsomer planes that control capsid length. Finally, conformational changes were observed at the symmetry-mismatched portal vertex, which might be involved in triggering head expansion. These analyses illustrate how small changes in local capsid subunit interactions lead to profound shifts in viral capsid morphology, stability, and volume.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein
A [auth aa],
AA [auth ba],
AB [auth ca],
AC [auth da],
AD [auth eg],
AE [auth fg],
AF [auth gg],
B [auth ab],
BA [auth bb],
BB [auth cb],
BC [auth db],
BD [auth eh],
BE [auth fh],
BF [auth gh],
C [auth ac],
CA [auth bc],
CB [auth cc],
CC [auth dc],
CD [auth ei],
CE [auth fi],
CF [auth gi],
D [auth ad],
DA [auth bd],
DB [auth cd],
DC [auth dd],
DD [auth ej],
DE [auth fj],
DF [auth gj],
E [auth ae],
EA [auth be],
EB [auth ce],
EC [auth de],
ED [auth ek],
EE [auth fk],
EF [auth gk],
F [auth af],
FA [auth bf],
FB [auth cf],
FC [auth df],
FD [auth el],
FE [auth fl],
FF [auth gl],
G [auth ag],
GA [auth bg],
GB [auth cg],
GC [auth dg],
GD [auth em],
GE [auth fm],
GF [auth gm],
H [auth ah],
HA [auth bh],
HB [auth ch],
HC [auth dh],
HD [auth en],
HE [auth fn],
HF [auth gn],
I [auth ai],
IA [auth bi],
IB [auth ci],
IC [auth di],
ID [auth eo],
IE [auth fo],
IF [auth go],
J [auth aj],
JA [auth bj],
JB [auth cj],
JC [auth dj],
JD [auth ep],
JE [auth fp],
JF [auth gp],
K [auth ak],
KA [auth bk],
KB [auth ck],
KC [auth dk],
KD [auth eq],
KE [auth fq],
KF [auth gq],
L [auth al],
LA [auth bl],
LB [auth cl],
LC [auth dl],
LD [auth er],
LE [auth fr],
LF [auth gr],
M [auth am],
MA [auth bm],
MB [auth cm],
MC [auth dm],
MD [auth es],
ME [auth fs],
MF [auth gs],
N [auth an],
NA [auth bn],
NB [auth cn],
NC [auth dn],
ND [auth et],
NE [auth ft],
NF [auth gt],
O [auth ao],
OA [auth bo],
OB [auth co],
OC [auth do],
OD [auth eu],
OE [auth fu],
OF [auth gu],
P [auth ap],
PA [auth bp],
PB [auth cp],
PC [auth dp],
PD [auth ev],
PE [auth fv],
PF [auth gv],
Q [auth aq],
QA [auth bq],
QB [auth cq],
QC [auth dq],
QD [auth ew],
QE [auth fw],
QF [auth gw],
R [auth ar],
RA [auth br],
RB [auth cr],
RC [auth dr],
RD [auth ex],
RE [auth fx],
RF [auth gx],
S [auth as],
SA [auth bs],
SB [auth cs],
SC [auth dy],
SD [auth ey],
SE [auth fy],
SF [auth gy],
T [auth at],
TA [auth bt],
TB [auth ct],
TC [auth dz],
TD [auth ez],
TE [auth fz],
TF [auth gz],
U [auth au],
UA [auth bu],
UB [auth cu],
UC [auth ea],
UD [auth fa],
UE [auth ga],
UF [auth ha],
V [auth av],
VA [auth bv],
VB [auth cv],
VC [auth eb],
VD [auth fb],
VE [auth gb],
VF [auth hb],
W [auth aw],
WA [auth bw],
WB [auth cw],
WC [auth ec],
WD [auth fc],
WE [auth gc],
WF [auth hc],
X [auth ax],
XA [auth bx],
XB [auth cx],
XC [auth ed],
XD [auth fd],
XE [auth gd],
XF [auth hd],
Y [auth ay],
YA [auth by],
YB [auth cy],
YC [auth ee],
YD [auth fe],
YE [auth ge],
Z [auth az],
ZA [auth bz],
ZB [auth cz],
ZC [auth ef],
ZD [auth ff],
ZE [auth gf]
521Tequatrovirus T4Mutation(s): 0 
UniProt
Find proteins for P04535 (Enterobacteria phage T4)
Explore P04535 
Go to UniProtKB:  P04535
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04535
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid vertex protein427Tequatrovirus T4Mutation(s): 0 
UniProt
Find proteins for P19896 (Enterobacteria phage T4)
Explore P19896 
Go to UniProtKB:  P19896
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19896
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI081726
National Science Foundation (NSF, United States)United StatesMCB-0923873

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Data collection