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

  • 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major head protein
B [auth A1], CB [auth A3], GC [auth A4], GE [auth A6], UF [auth A7], IH [auth A8], ZK [auth AD], UL [auth AE], ON [auth AG], DQ [auth AJ], VQ [auth AK], OR [auth AL], MU [auth AP], FV [auth AQ], OW [auth AR], AY [auth AS], C [auth B1], DB [auth B3], HC [auth B4], HE [auth B6], VF [auth B7], JH [auth B8], AL [auth BD], VL [auth BE], PN [auth BG], EQ [auth BJ], WQ [auth BK], PR [auth BL], NU [auth BP], GV [auth BQ], PW [auth BR], BY [auth BS], A [auth C1], BB [auth C3], FC [auth C4], FE [auth C6], TF [auth C7], HH [auth C8], BL [auth CD], WL [auth CE], NN [auth CG], FQ [auth CJ], XQ [auth CK], NR [auth CL], OU [auth CP], EV [auth CQ], NW [auth CR], CY [auth CS], D [auth D1], EB [auth D3], IC [auth D4], IE [auth D6], WF [auth D7], KH [auth D8], CL [auth DD], RL [auth DE], QN [auth DG], GQ [auth DJ], YQ [auth DK], QR [auth DL], PU [auth DP], HV [auth DQ], QW [auth DR], XL [auth FE], I [auth I1], JB [auth I3], NC [auth I4], NE [auth I6], BG [auth I7], PH [auth I8], VN [auth IG], VR [auth IL], MV [auth IQ], VW [auth IR], IY [auth IS], J [auth J1], KB [auth J3], OC [auth J4], OE [auth J6], CG [auth J7], QH [auth J8], WN [auth JG], WR [auth JL], NV [auth JQ], WW [auth JR], JY [auth JS], K [auth K1], LB [auth K3], PC [auth K4], PE [auth K6], DG [auth K7], RH [auth K8], IL [auth KD], BM [auth KE], XN [auth KG], MQ [auth KJ], ER [auth KK], XR [auth KL], VU [auth KP], OV [auth KQ], XW [auth KR], KY [auth KS], L [auth L1], MB [auth L3], QC [auth L4], QE [auth L6], EG [auth L7], SH [auth L8], JL [auth LD], CM [auth LE], YN [auth LG], NQ [auth LJ], FR [auth LK], YR [auth LL], WU [auth LP], PV [auth LQ], YW [auth LR], DM [auth ME], EM [auth NE], Q [auth Q1], RB [auth Q3], VC [auth Q4], VE [auth Q6], JG [auth Q7], XH [auth Q8], DO [auth QG], DS [auth QL], UV [auth QQ], DX [auth QR], R [auth R1], SB [auth R3], WC [auth R4], WE [auth R6], KG [auth R7], YH [auth R8], EO [auth RG], ES [auth RL], VV [auth RQ], EX [auth RR], S [auth S1], TB [auth S3], XC [auth S4], XE [auth S6], LG [auth S7], ZH [auth S8], JM [auth SE], FO [auth SG], FS [auth SL], WV [auth SQ], FX [auth SR], T [auth T1], UB [auth T3], YC [auth T4], YE [auth T6], MG [auth T7], AI [auth T8], KM [auth TE], GO [auth TG], GS [auth TL], XV [auth TQ], GX [auth TR], LM [auth UE], MM [auth VE], X [auth X1], CD [auth X4], Y [auth Y1], ZB [auth Y3], DD [auth Y4], DF [auth Y6], RG [auth Y7], FI [auth Y8], LO [auth YG], LS [auth YL], CW [auth YQ], LX [auth YR], Z [auth Z1], ED [auth Z4], EF [auth Z6], SG [auth Z7], GI [auth Z8], MO [auth ZG], MS [auth ZL], MX [auth ZR], AA [auth a1], FD [auth a4], FF [auth a6], TG [auth a7], HI [auth a8], RM [auth aE], NO [auth aG], NS [auth aL], NX [auth aR], CC [auth b3], GF [auth b6], UG [auth b7], II [auth b8], SM [auth bE], OO [auth bG], OS [auth bL], FW [auth bQ], OX [auth bR], TM [auth cE], GW [auth cQ], UM [auth dE], HW [auth dQ], IW [auth eQ], FA [auth f1], KD [auth f4], GA [auth g1], LD [auth g4], LF [auth g6], ZG [auth g7], NI [auth g8], TO [auth gG], TS [auth gL], TX [auth gR], HA [auth h1], MD [auth h4], MF [auth h6], AH [auth h7], OI [auth h8], UO [auth hG], UX [auth hR], IA [auth i1], ND [auth i4], NF [auth i6], BH [auth i7], PI [auth i8], VO [auth iG], VX [auth iR], OF [auth j6], CH [auth j7], QI [auth j8], WO [auth jG], WX [auth jR]
408Staphylococcus phage P68Mutation(s): 0 
UniProt
Find proteins for Q859I3 (Staphylococcus phage P68)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Arstotzka protein
DY [auth DS], E [auth E1], FB [auth E3], JC [auth E4], JE [auth E6], XF [auth E7], LH [auth E8], DL [auth ED], SL [auth EE], RN [auth EG], HQ [auth EJ], ZQ [auth EK], RR [auth EL], QU [auth EP], IV [auth EQ], RW [auth ER], EY [auth ES], F [auth F1], GB [auth F3], KC [auth F4], KE [auth F6], YF [auth F7], MH [auth F8], EL [auth FD], SN [auth FG], IQ [auth FJ], AR [auth FK], SR [auth FL], RU [auth FP], JV [auth FQ], SW [auth FR], FY [auth FS], G [auth G1], HB [auth G3], LC [auth G4], LE [auth G6], ZF [auth G7], NH [auth G8], FL [auth GD], TL [auth GE], TN [auth GG], JQ [auth GJ], BR [auth GK], TR [auth GL], SU [auth GP], KV [auth GQ], TW [auth GR], GY [auth GS], H [auth H1], IB [auth H3], MC [auth H4], ME [auth H6], AG [auth H7], OH [auth H8], GL [auth HD], YL [auth HE], UN [auth HG], KQ [auth HJ], CR [auth HK], UR [auth HL], TU [auth HP], LV [auth HQ], UW [auth HR], ZL [auth IE], AM [auth JE], LY [auth LS], M [auth M1], NB [auth M3], RC [auth M4], RE [auth M6], FG [auth M7], TH [auth M8], KL [auth MD], ZN [auth MG], OQ [auth MJ], GR [auth MK], ZR [auth ML], XU [auth MP], QV [auth MQ], ZW [auth MR], MY [auth MS], N [auth N1], OB [auth N3], SC [auth N4], SE [auth N6], GG [auth N7], UH [auth N8], LL [auth ND], AO [auth NG], PQ [auth NJ], HR [auth NK], AS [auth NL], YU [auth NP], RV [auth NQ], AX [auth NR], O [auth O1], PB [auth O3], TC [auth O4], TE [auth O6], HG [auth O7], VH [auth O8], FM [auth OE], BO [auth OG], BS [auth OL], SV [auth OQ], BX [auth OR], P [auth P1], QB [auth P3], UC [auth P4], UE [auth P6], IG [auth P7], WH [auth P8], GM [auth PE], CO [auth PG], CS [auth PL], TV [auth PQ], CX [auth PR], HM [auth QE], IM [auth RE], U [auth U1], VB [auth U3], ZC [auth U4], ZE [auth U6], NG [auth U7], BI [auth U8], HO [auth UG], HS [auth UL], YV [auth UQ], HX [auth UR], V [auth V1], WB [auth V3], AD [auth V4], AF [auth V6], OG [auth V7], CI [auth V8], IO [auth VG], IS [auth VL], ZV [auth VQ], IX [auth VR], W [auth W1], XB [auth W3], BD [auth W4], BF [auth W6], PG [auth W7], DI [auth W8], NM [auth WE], JO [auth WG], JS [auth WL], AW [auth WQ], JX [auth WR], YB [auth X3], CF [auth X6], QG [auth X7], EI [auth X8], OM [auth XE], KO [auth XG], KS [auth XL], BW [auth XQ], KX [auth XR], PM [auth YE], AC [auth Z3], QM [auth ZE], DW [auth ZQ], BC [auth a3], EW [auth aQ], BA [auth b1], GD [auth b4], CA [auth c1], DC [auth c3], HD [auth c4], HF [auth c6], VG [auth c7], JI [auth c8], PO [auth cG], PS [auth cL], PX [auth cR], DA [auth d1], EC [auth d3], ID [auth d4], IF [auth d6], WG [auth d7], KI [auth d8], QO [auth dG], QS [auth dL], QX [auth dR], EA [auth e1], JD [auth e4], JF [auth e6], XG [auth e7], LI [auth e8], VM [auth eE], RO [auth eG], RS [auth eL], RX [auth eR], KF [auth f6], YG [auth f7], MI [auth f8], WM [auth fE], SO [auth fG], SS [auth fL], JW [auth fQ], SX [auth fR], XM [auth gE], KW [auth gQ], YM [auth hE], US [auth hL], LW [auth hQ], VS [auth iL], MW [auth iQ], JA [auth j1], OD [auth j4], KA [auth k1], PD [auth k4], PF [auth k6], DH [auth k7], RI [auth k8], XO [auth kG], XX [auth kR], LA [auth l1], QD [auth l4], QF [auth l6], EH [auth l7], SI [auth l8], YO [auth lG], YX [auth lR], MA [auth m1], RF [auth m6], FH [auth m7], TI [auth m8], ZO [auth mG], ZX [auth mR], SF [auth n6], GH [auth n7], UI [auth n8], AP [auth nG]
60Staphylococcus phage P68Mutation(s): 0 
UniProt
Find proteins for Q859I2 (Staphylococcus phage P68)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Portal protein327Staphylococcus phage P68Mutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Lower collar protein251Staphylococcus phage P68Mutation(s): 0 
UniProt
Find proteins for Q859I5 (Staphylococcus phage P68)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Minor structural protein647Staphylococcus phage P68Mutation(s): 0 
UniProt
Find proteins for Q859I6 (Staphylococcus phage P68)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Tail fibre protein133Staphylococcus phage P68Mutation(s): 0 
UniProt
Find proteins for Q859I1 (Staphylococcus phage P68)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Head fiber protein55Staphylococcus phage P68Mutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Inner core protein17Staphylococcus phage P68Mutation(s): 0 
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Experimental Data & Validation

Experimental Data

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

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