6Q3G

Structure of native bacteriophage P68


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure and genome ejection mechanism ofStaphylococcus aureusphage P68.

Hrebik, D.Stverakova, D.Skubnik, K.Fuzik, T.Pantucek, R.Plevka, P.

(2019) Sci Adv 5: eaaw7414-eaaw7414

  • DOI: https://doi.org/10.1126/sciadv.aaw7414
  • Primary Citation of Related Structures:  
    6IAB, 6IAC, 6IAT, 6IAW, 6IB1, 6Q3G

  • PubMed Abstract: 

    Phages infecting Staphylococcus aureus can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect Gram-positive bacteria. Here, we present the structures of native S. aureus phage P68, genome ejection intermediate, and empty particle. The P68 head contains 72 subunits of inner core protein, 15 of which bind to and alter the structure of adjacent major capsid proteins and thus specify attachment sites for head fibers. Unlike in the previously studied phages, the head fibers of P68 enable its virion to position itself at the cell surface for genome delivery. The unique interaction of one end of P68 DNA with one of the 12 portal protein subunits is disrupted before the genome ejection. The inner core proteins are released together with the DNA and enable the translocation of phage genome across the bacterial membrane into the cytoplasm.


  • Organizational Affiliation

    Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major head protein
A [auth C1],
AA [auth a1],
AH [auth h7],
AI [auth T8],
AL [auth BD],
AY [auth AS],
B [auth A1],
BB [auth C3],
BG [auth I7],
BH [auth i7],
BL [auth CD],
BM [auth KE],
BY [auth BS],
C [auth B1],
CB [auth A3],
CC [auth b3],
CD [auth X4],
CG [auth J7],
CH [auth j7],
CL [auth DD],
CM [auth LE],
CW [auth YQ],
CY [auth CS],
D [auth D1],
DB [auth B3],
DD [auth Y4],
DF [auth Y6],
DG [auth K7],
DM [auth ME],
DO [auth QG],
DQ [auth AJ],
DS [auth QL],
DX [auth QR],
EB [auth D3],
ED [auth Z4],
EF [auth Z6],
EG [auth L7],
EM [auth NE],
EO [auth RG],
EQ [auth BJ],
ER [auth KK],
ES [auth RL],
EV [auth CQ],
EX [auth RR],
FA [auth f1],
FC [auth C4],
FD [auth a4],
FE [auth C6],
FF [auth a6],
FI [auth Y8],
FO [auth SG],
FQ [auth CJ],
FR [auth LK],
FS [auth SL],
FV [auth AQ],
FW [auth bQ],
FX [auth SR],
GA [auth g1],
GC [auth A4],
GE [auth A6],
GF [auth b6],
GI [auth Z8],
GO [auth TG],
GQ [auth DJ],
GS [auth TL],
GV [auth BQ],
GW [auth cQ],
GX [auth TR],
HA [auth h1],
HC [auth B4],
HE [auth B6],
HH [auth C8],
HI [auth a8],
HV [auth DQ],
HW [auth dQ],
I [auth I1],
IA [auth i1],
IC [auth D4],
IE [auth D6],
IH [auth A8],
II [auth b8],
IL [auth KD],
IW [auth eQ],
IY [auth IS],
J [auth J1],
JB [auth I3],
JG [auth Q7],
JH [auth B8],
JL [auth LD],
JM [auth SE],
JY [auth JS],
K [auth K1],
KB [auth J3],
KD [auth f4],
KG [auth R7],
KH [auth D8],
KM [auth TE],
KY [auth KS],
L [auth L1],
LB [auth K3],
LD [auth g4],
LF [auth g6],
LG [auth S7],
LM [auth UE],
LO [auth YG],
LS [auth YL],
LX [auth YR],
MB [auth L3],
MD [auth h4],
MF [auth h6],
MG [auth T7],
MM [auth VE],
MO [auth ZG],
MQ [auth KJ],
MS [auth ZL],
MU [auth AP],
MV [auth IQ],
MX [auth ZR],
NC [auth I4],
ND [auth i4],
NE [auth I6],
NF [auth i6],
NI [auth g8],
NN [auth CG],
NO [auth aG],
NQ [auth LJ],
NR [auth CL],
NS [auth aL],
NU [auth BP],
NV [auth JQ],
NW [auth CR],
NX [auth aR],
OC [auth J4],
OE [auth J6],
OF [auth j6],
OI [auth h8],
ON [auth AG],
OO [auth bG],
OR [auth AL],
OS [auth bL],
OU [auth CP],
OV [auth KQ],
OW [auth AR],
OX [auth bR],
PC [auth K4],
PE [auth K6],
PH [auth I8],
PI [auth i8],
PN [auth BG],
PR [auth BL],
PU [auth DP],
PV [auth LQ],
PW [auth BR],
Q [auth Q1],
QC [auth L4],
QE [auth L6],
QH [auth J8],
QI [auth j8],
QN [auth DG],
QR [auth DL],
QW [auth DR],
R [auth R1],
RB [auth Q3],
RG [auth Y7],
RH [auth K8],
RL [auth DE],
RM [auth aE],
S [auth S1],
SB [auth R3],
SG [auth Z7],
SH [auth L8],
SM [auth bE],
T [auth T1],
TB [auth S3],
TF [auth C7],
TG [auth a7],
TM [auth cE],
TO [auth gG],
TS [auth gL],
TX [auth gR],
UB [auth T3],
UF [auth A7],
UG [auth b7],
UL [auth AE],
UM [auth dE],
UO [auth hG],
UV [auth QQ],
UX [auth hR],
VC [auth Q4],
VE [auth Q6],
VF [auth B7],
VL [auth BE],
VN [auth IG],
VO [auth iG],
VQ [auth AK],
VR [auth IL],
VU [auth KP],
VV [auth RQ],
VW [auth IR],
VX [auth iR],
WC [auth R4],
WE [auth R6],
WF [auth D7],
WL [auth CE],
WN [auth JG],
WO [auth jG],
WQ [auth BK],
WR [auth JL],
WU [auth LP],
WV [auth SQ],
WW [auth JR],
WX [auth jR],
X [auth X1],
XC [auth S4],
XE [auth S6],
XH [auth Q8],
XL [auth FE],
XN [auth KG],
XQ [auth CK],
XR [auth KL],
XV [auth TQ],
XW [auth KR],
Y [auth Y1],
YC [auth T4],
YE [auth T6],
YH [auth R8],
YN [auth LG],
YQ [auth DK],
YR [auth LL],
YW [auth LR],
Z [auth Z1],
ZB [auth Y3],
ZG [auth g7],
ZH [auth S8],
ZK [auth AD]
408Staphylococcus phage P68Mutation(s): 0 
UniProt
Find proteins for Q859I3 (Staphylococcus phage P68)
Explore Q859I3 
Go to UniProtKB:  Q859I3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ859I3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Arstotzka protein
AC [auth Z3],
AD [auth V4],
AF [auth V6],
AG [auth H7],
AM [auth JE],
AO [auth NG],
AP [auth nG],
AR [auth FK],
AS [auth NL],
AW [auth WQ],
AX [auth NR],
BA [auth b1],
BC [auth a3],
BD [auth W4],
BF [auth W6],
BI [auth U8],
BO [auth OG],
BR [auth GK],
BS [auth OL],
BW [auth XQ],
BX [auth OR],
CA [auth c1],
CF [auth X6],
CI [auth V8],
CO [auth PG],
CR [auth HK],
CS [auth PL],
CX [auth PR],
DA [auth d1],
DC [auth c3],
DH [auth k7],
DI [auth W8],
DL [auth ED],
DW [auth ZQ],
DY [auth DS],
E [auth E1],
EA [auth e1],
EC [auth d3],
EH [auth l7],
EI [auth X8],
EL [auth FD],
EW [auth aQ],
EY [auth ES],
F [auth F1],
FB [auth E3],
FG [auth M7],
FH [auth m7],
FL [auth GD],
FM [auth OE],
FY [auth FS],
G [auth G1],
GB [auth F3],
GD [auth b4],
GG [auth N7],
GH [auth n7],
GL [auth HD],
GM [auth PE],
GR [auth MK],
GY [auth GS],
H [auth H1],
HB [auth G3],
HD [auth c4],
HF [auth c6],
HG [auth O7],
HM [auth QE],
HO [auth UG],
HQ [auth EJ],
HR [auth NK],
HS [auth UL],
HX [auth UR],
IB [auth H3],
ID [auth d4],
IF [auth d6],
IG [auth P7],
IM [auth RE],
IO [auth VG],
IQ [auth FJ],
IS [auth VL],
IV [auth EQ],
IX [auth VR],
JA [auth j1],
JC [auth E4],
JD [auth e4],
JE [auth E6],
JF [auth e6],
JI [auth c8],
JO [auth WG],
JQ [auth GJ],
JS [auth WL],
JV [auth FQ],
JW [auth fQ],
JX [auth WR],
KA [auth k1],
KC [auth F4],
KE [auth F6],
KF [auth f6],
KI [auth d8],
KL [auth MD],
KO [auth XG],
KQ [auth HJ],
KS [auth XL],
KV [auth GQ],
KW [auth gQ],
KX [auth XR],
LA [auth l1],
LC [auth G4],
LE [auth G6],
LH [auth E8],
LI [auth e8],
LL [auth ND],
LV [auth HQ],
LW [auth hQ],
LY [auth LS],
M [auth M1],
MA [auth m1],
MC [auth H4],
ME [auth H6],
MH [auth F8],
MI [auth f8],
MW [auth iQ],
MY [auth MS],
N [auth N1],
NB [auth M3],
NG [auth U7],
NH [auth G8],
NM [auth WE],
O [auth O1],
OB [auth N3],
OD [auth j4],
OG [auth V7],
OH [auth H8],
OM [auth XE],
OQ [auth MJ],
P [auth P1],
PB [auth O3],
PD [auth k4],
PF [auth k6],
PG [auth W7],
PM [auth YE],
PO [auth cG],
PQ [auth NJ],
PS [auth cL],
PX [auth cR],
QB [auth P3],
QD [auth l4],
QF [auth l6],
QG [auth X7],
QM [auth ZE],
QO [auth dG],
QS [auth dL],
QU [auth EP],
QV [auth MQ],
QX [auth dR],
RC [auth M4],
RE [auth M6],
RF [auth m6],
RI [auth k8],
RN [auth EG],
RO [auth eG],
RR [auth EL],
RS [auth eL],
RU [auth FP],
RV [auth NQ],
RW [auth ER],
RX [auth eR],
SC [auth N4],
SE [auth N6],
SF [auth n6],
SI [auth l8],
SL [auth EE],
SN [auth FG],
SO [auth fG],
SR [auth FL],
SS [auth fL],
SU [auth GP],
SV [auth OQ],
SW [auth FR],
SX [auth fR],
TC [auth O4],
TE [auth O6],
TH [auth M8],
TI [auth m8],
TL [auth GE],
TN [auth GG],
TR [auth GL],
TU [auth HP],
TV [auth PQ],
TW [auth GR],
U [auth U1],
UC [auth P4],
UE [auth P6],
UH [auth N8],
UI [auth n8],
UN [auth HG],
UR [auth HL],
US [auth hL],
UW [auth HR],
V [auth V1],
VB [auth U3],
VG [auth c7],
VH [auth O8],
VM [auth eE],
VS [auth iL],
W [auth W1],
WB [auth V3],
WG [auth d7],
WH [auth P8],
WM [auth fE],
XB [auth W3],
XF [auth E7],
XG [auth e7],
XM [auth gE],
XO [auth kG],
XU [auth MP],
XX [auth kR],
YB [auth X3],
YF [auth F7],
YG [auth f7],
YL [auth HE],
YM [auth hE],
YO [auth lG],
YU [auth NP],
YV [auth UQ],
YX [auth lR],
ZC [auth U4],
ZE [auth U6],
ZF [auth G7],
ZL [auth IE],
ZN [auth MG],
ZO [auth mG],
ZQ [auth EK],
ZR [auth ML],
ZV [auth VQ],
ZW [auth MR],
ZX [auth mR]
60Staphylococcus phage P68Mutation(s): 0 
UniProt
Find proteins for Q859I2 (Staphylococcus phage P68)
Explore Q859I2 
Go to UniProtKB:  Q859I2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ859I2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein327Staphylococcus phage P68Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Lower collar protein251Staphylococcus phage P68Mutation(s): 0 
UniProt
Find proteins for Q859I5 (Staphylococcus phage P68)
Explore Q859I5 
Go to UniProtKB:  Q859I5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ859I5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Minor structural protein647Staphylococcus phage P68Mutation(s): 0 
UniProt
Find proteins for Q859I6 (Staphylococcus phage P68)
Explore Q859I6 
Go to UniProtKB:  Q859I6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ859I6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Tail fibre protein133Staphylococcus phage P68Mutation(s): 0 
UniProt
Find proteins for Q859I1 (Staphylococcus phage P68)
Explore Q859I1 
Go to UniProtKB:  Q859I1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ859I1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Head fiber protein55Staphylococcus phage P68Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Inner core protein17Staphylococcus phage P68Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIXdev:3042

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic15-21631Y
Czech Science FoundationCzech Republic18-17810S
European Molecular Biology OrganizationCzech Republic3041
Czech Republic16-29916A

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release