6QVK

The cryo-EM structure of bacteriophage phi29 prohead

  • Classification: VIRUS
  • Organism(s): Salasvirus phi29
  • Mutation(s): No 

  • Deposited: 2019-03-03 Released: 2019-06-12 
  • Deposition Author(s): Xu, J., Gui, M., Xiang, Y.
  • Funding Organization(s): Ministry of Science and Technology (China), National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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

Structural assembly of the tailed bacteriophage φ29.

Xu, J.Wang, D.Gui, M.Xiang, Y.

(2019) Nat Commun 10: 2366-2366

  • DOI: https://doi.org/10.1038/s41467-019-10272-3
  • Primary Citation of Related Structures:  
    6QVK, 6QX7, 6QYD, 6QYJ, 6QYM, 6QYY, 6QYZ, 6QZ0, 6QZ9, 6QZF

  • PubMed Abstract: 

    The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile tail. Here, we report the near-atomic structures of the ϕ29 pre-genome packaging head (prohead), the mature virion and the genome-emptied virion. Structural comparisons suggest local rotation or oscillation of the head-tail connector upon DNA packaging and release. Termination of the DNA packaging occurs through pressure-dependent correlative positional and conformational changes in the connector. The funnel-shaped tail lower collar attaches the expanded narrow end of the connector and has a 180-Å long, 24-strand β barrel narrow stem tube that undergoes conformational changes upon genome release. The appendages form an interlocked assembly attaching the tail around the collar. The membrane active long loops at the distal end of the tail knob exit during the late stage of infection and form the cone-shaped tip of a largely hydrophobic helix barrel, prepared for membrane penetration.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein
A [auth 1A],
AA [auth 5D],
AB [auth 1L],
AC [auth 6I],
AD [auth 2O],
AE [auth 7L],
AF [auth 3W],
AG [auth 8T],
AH [auth 4b],
AI [auth 9E],
B [auth 1B],
BA [auth 5E],
BB [auth 2F],
BC [auth 6J],
BD [auth 3M],
BE [auth 7M],
BF [auth 3X],
BG [auth 8U],
BH [auth 4c],
C [auth 1C],
CA [auth 5F],
CB [auth 2G],
CC [auth 6K],
CD [auth 3N],
CE [auth 7N],
CF [auth 4S],
CG [auth 8V],
CH [auth 4d],
D [auth 1D],
DA [auth 6A],
DB [auth 2H],
DC [auth 6L],
DD [auth 3O],
DE [auth 7O],
DF [auth 4T],
DG [auth 8W],
DH [auth 5Y],
E [auth 1E],
EA [auth 6B],
EB [auth 2I],
EC [auth 7F],
ED [auth 3P],
EE [auth 8M],
EF [auth 4U],
EG [auth 8X],
EH [auth 5Z],
F [auth 1F],
FA [auth 6C],
FB [auth 2J],
FC [auth 7G],
FD [auth 3Q],
FE [auth 8N],
FF [auth 4V],
FG [auth 9D],
FH [auth 5a],
G [auth 2A],
GA [auth 6D],
GB [auth 3G],
GC [auth 7H],
GD [auth 3R],
GE [auth 8O],
GF [auth 4W],
GG [auth 1Y],
GH [auth 5b],
H [auth 2B],
HA [auth 6E],
HB [auth 3H],
HC [auth 7I],
HD [auth 4M],
HE [auth 8P],
HF [auth 4X],
HG [auth 1Z],
HH [auth 5c],
I [auth 2C],
IA [auth 6F],
IB [auth 3I],
IC [auth 7J],
ID [auth 4N],
IE [auth 8Q],
IF [auth 5S],
IG [auth 1a],
IH [auth 5d],
J [auth 2D],
JA [auth 7A],
JB [auth 3J],
JC [auth 8G],
JD [auth 4O],
JE [auth 8R],
JF [auth 5T],
JG [auth 1b],
JH [auth 6Y],
K [auth 2E],
KA [auth 7B],
KB [auth 3K],
KC [auth 8H],
KD [auth 4P],
KE [auth 9C],
KF [auth 5U],
KG [auth 1c],
KH [auth 6Z],
L [auth 3A],
LA [auth 7C],
LB [auth 3L],
LC [auth 8I],
LD [auth 4Q],
LE [auth 1S],
LF [auth 5V],
LG [auth 1d],
LH [auth 6a],
M [auth 3B],
MA [auth 7D],
MB [auth 4G],
MC [auth 8J],
MD [auth 4R],
ME [auth 1T],
MF [auth 5W],
MG [auth 2U],
MH [auth 6b],
N [auth 3C],
NA [auth 7E],
NB [auth 4H],
NC [auth 8K],
ND [auth 5M],
NE [auth 1U],
NF [auth 5X],
NG [auth 2V],
NH [auth 6c],
O [auth 3D],
OA [auth 8A],
OB [auth 4I],
OC [auth 8L],
OD [auth 5N],
OE [auth 1V],
OF [auth 6S],
OG [auth 2W],
OH [auth 6d],
P [auth 3E],
PA [auth 8B],
PB [auth 4J],
PC [auth 9B],
PD [auth 5O],
PE [auth 1W],
PF [auth 6T],
PG [auth 2X],
PH [auth 7U],
Q [auth 3F],
QA [auth 8C],
QB [auth 4K],
QC [auth 1M],
QD [auth 5P],
QE [auth 1X],
QF [auth 6U],
QG [auth 2Y],
QH [auth 7V],
R [auth 4A],
RA [auth 8D],
RB [auth 4L],
RC [auth 1N],
RD [auth 5Q],
RE [auth 2P],
RF [auth 6V],
RG [auth 3Y],
RH [auth 7W],
S [auth 4B],
SA [auth 8E],
SB [auth 5G],
SC [auth 1O],
SD [auth 5R],
SE [auth 2Q],
SF [auth 6W],
SG [auth 3Z],
SH [auth 7X],
T [auth 4C],
TA [auth 8F],
TB [auth 5H],
TC [auth 1P],
TD [auth 6M],
TE [auth 2R],
TF [auth 6X],
TG [auth 3a],
TH [auth 7Y],
U [auth 4D],
UA [auth 9A],
UB [auth 5I],
UC [auth 1Q],
UD [auth 6N],
UE [auth 2S],
UF [auth 7P],
UG [auth 3b],
UH [auth 8Y],
V [auth 4E],
VA [auth 1G],
VB [auth 5J],
VC [auth 1R],
VD [auth 6O],
VE [auth 2T],
VF [auth 7Q],
VG [auth 3c],
VH [auth 8Z],
W [auth 4F],
WA [auth 1H],
WB [auth 5K],
WC [auth 2K],
WD [auth 6P],
WE [auth 3S],
WF [auth 7R],
WG [auth 3d],
WH [auth 8a],
X [auth 5A],
XA [auth 1I],
XB [auth 5L],
XC [auth 2L],
XD [auth 6Q],
XE [auth 3T],
XF [auth 7S],
XG [auth 4Y],
XH [auth 8b],
Y [auth 5B],
YA [auth 1J],
YB [auth 6G],
YC [auth 2M],
YD [auth 6R],
YE [auth 3U],
YF [auth 7T],
YG [auth 4Z],
YH [auth 8c],
Z [auth 5C],
ZA [auth 1K],
ZB [auth 6H],
ZC [auth 2N],
ZD [auth 7K],
ZE [auth 3V],
ZF [auth 8S],
ZG [auth 4a],
ZH [auth 8d]
448Salasvirus phi29Mutation(s): 0 
UniProt
Find proteins for P13849 (Bacillus phage phi29)
Explore P13849 
Go to UniProtKB:  P13849
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13849
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid fiber protein
AJ [auth 7d],
AK [auth 6j],
AL [auth 3o],
AM [auth 2o],
AN [auth 9K],
AO [auth 7v],
BI [auth 1e],
BJ [auth 8e],
BK [auth 6k],
BL [auth 3p],
BM [auth 2p],
BN [auth 9L],
BO [auth 7w],
CI [auth 1f],
CJ [auth 8f],
CK [auth 6l],
CL [auth 4i],
CM [auth 2q],
CN [auth 9I],
CO [auth 7x],
DI [auth 1g],
DJ [auth 8g],
DK [auth 7e],
DL [auth 4j],
DM [auth 2r],
DN [auth 1u],
DO [auth 9M],
EI [auth 1h],
EJ [auth 8h],
EK [auth 7f],
EL [auth 5i],
EM [auth 2s],
EN [auth 1v],
EO [auth 9N],
FI [auth 2Z],
FJ [auth 8i],
FK [auth 7g],
FL [auth 5j],
FM [auth 3q],
FN [auth 1w],
FO [auth 9O],
GI [auth 2a],
GJ [auth 8j],
GK [auth 7h],
GL [auth 6m],
GM [auth 3r],
GN [auth 1x],
GO [auth 9P],
HI [auth 2b],
HJ [auth 9F],
HK [auth 7i],
HL [auth 6n],
HM [auth 3s],
HN [auth 2t],
HO [auth 9Q],
II [auth 2c],
IJ [auth 1i],
IK [auth 8k],
IL [auth 6o],
IM [auth 3t],
IN [auth 2u],
IO [auth 9R],
JI [auth 2d],
JJ [auth 1j],
JK [auth 8l],
JL [auth 6p],
JM [auth 4k],
JN [auth 2v],
JO [auth 9J],
KI [auth 3e],
KJ [auth 1k],
KK [auth 8m],
KL [auth 7j],
KM [auth 4l],
KN [auth 2w],
LI [auth 3f],
LJ [auth 1l],
LK [auth 8n],
LL [auth 7k],
LM [auth 5k],
LN [auth 2x],
MI [auth 3g],
MJ [auth 2e],
MK [auth 8o],
ML [auth 7l],
MM [auth 5l],
MN [auth 3u],
NI [auth 3h],
NJ [auth 2f],
NK [auth 8p],
NL [auth 7m],
NM [auth 6q],
NN [auth 3v],
OI [auth 4e],
OJ [auth 2g],
OK [auth 9G],
OL [auth 7n],
OM [auth 6r],
ON [auth 3w],
PI [auth 4f],
PJ [auth 2h],
PK [auth 1m],
PL [auth 8q],
PM [auth 6s],
PN [auth 3x],
QI [auth 5e],
QJ [auth 2i],
QK [auth 1n],
QL [auth 8r],
QM [auth 6t],
QN [auth 4m],
RI [auth 5f],
RJ [auth 3i],
RK [auth 1o],
RL [auth 8s],
RM [auth 7o],
RN [auth 4n],
SI [auth 6e],
SJ [auth 3j],
SK [auth 1p],
SL [auth 8t],
SM [auth 7p],
SN [auth 5m],
TI [auth 6f],
TJ [auth 3k],
TK [auth 2j],
TL [auth 8u],
TM [auth 7q],
TN [auth 5n],
UI [auth 6g],
UJ [auth 3l],
UK [auth 2k],
UL [auth 8v],
UM [auth 7r],
UN [auth 6u],
VI [auth 6h],
VJ [auth 4g],
VK [auth 2l],
VL [auth 9H],
VM [auth 7s],
VN [auth 6v],
WI [auth 7Z],
WJ [auth 4h],
WK [auth 2m],
WL [auth 1q],
WM [auth 8w],
WN [auth 6w],
XI [auth 7a],
XJ [auth 5g],
XK [auth 2n],
XL [auth 1r],
XM [auth 8x],
XN [auth 6x],
YI [auth 7b],
YJ [auth 5h],
YK [auth 3m],
YL [auth 1s],
YM [auth 8y],
YN [auth 7t],
ZI [auth 7c],
ZJ [auth 6i],
ZK [auth 3n],
ZL [auth 1t],
ZM [auth 8z],
ZN [auth 7u]
281Salasvirus phi29Mutation(s): 0 
UniProt
Find proteins for B3VMP4 (Bacillus phage phi29)
Explore B3VMP4 
Go to UniProtKB:  B3VMP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3VMP4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0501100
Ministry of Science and Technology (China)China2015CB910102
National Natural Science Foundation of ChinaChina31470721

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Author supporting evidence, Data collection, Database references