6Q3G

Structure of native bacteriophage P68


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 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:  

  • PubMed Abstract: 
  • Phages infecting <i>Staphylococcus aureus </i> 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. ...

    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

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major head protein
C1, A1, B1, D1, I1, J1, K1, L1, Q1, R1, S1, T1, X1, Y1, Z1, a1, f1, g1, h1, i1, C3, A3, B3, D3, I3, J3, K3, L3, Q3, R3, S3, T3, Y3, b3, C4, A4, B4, D4, I4, J4, K4, L4, Q4, R4, S4, T4, X4, Y4, Z4, a4, f4, g4, h4, i4, C6, A6, B6, D6, I6, J6, K6, L6, Q6, R6, S6, T6, Y6, Z6, a6, b6, g6, h6, i6, j6, C7, A7, B7, D7, I7, J7, K7, L7, Q7, R7, S7, T7, Y7, Z7, a7, b7, g7, h7, i7, j7, C8, A8, B8, D8, I8, J8, K8, L8, Q8, R8, S8, T8, Y8, Z8, a8, b8, g8, h8, i8, j8, AD, BD, CD, DD, KD, LD, DE, AE, BE, CE, FE, KE, LE, ME, NE, SE, TE, UE, VE, aE, bE, cE, dE, CG, AG, BG, DG, IG, JG, KG, LG, QG, RG, SG, TG, YG, ZG, aG, bG, gG, hG, iG, jG, AJ, BJ, CJ, DJ, KJ, LJ, AK, BK, CK, DK, KK, LK, CL, AL, BL, DL, IL, JL, KL, LL, QL, RL, SL, TL, YL, ZL, aL, bL, gL, AP, BP, CP, DP, KP, LP, CQ, AQ, BQ, DQ, IQ, JQ, KQ, LQ, QQ, RQ, SQ, TQ, YQ, bQ, cQ, dQ, eQ, CR, AR, BR, DR, IR, JR, KR, LR, QR, RR, SR, TR, YR, ZR, aR, bR, gR, hR, iR, jR, AS, BS, CS, IS, JS, KS
408Staphylococcus phage P68Mutation(s): 0 
Find proteins for Q859I3 (Staphylococcus phage P68)
Go to UniProtKB:  Q859I3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Arstotzka protein
E1, F1, G1, H1, M1, N1, O1, P1, U1, V1, W1, b1, c1, d1, e1, j1, k1, l1, m1, E3, F3, G3, H3, M3, N3, O3, P3, U3, V3, W3, X3, Z3, a3, c3, d3, E4, F4, G4, H4, M4, N4, O4, P4, U4, V4, W4, b4, c4, d4, e4, j4, k4, l4, E6, F6, G6, H6, M6, N6, O6, P6, U6, V6, W6, X6, c6, d6, e6, f6, k6, l6, m6, n6, E7, F7, G7, H7, M7, N7, O7, P7, U7, V7, W7, X7, c7, d7, e7, f7, k7, l7, m7, n7, E8, F8, G8, H8, M8, N8, O8, P8, U8, V8, W8, X8, c8, d8, e8, f8, k8, l8, m8, n8, ED, FD, GD, HD, MD, ND, EE, GE, HE, IE, JE, OE, PE, QE, RE, WE, XE, YE, ZE, eE, fE, gE, hE, EG, FG, GG, HG, MG, NG, OG, PG, UG, VG, WG, XG, cG, dG, eG, fG, kG, lG, mG, nG, EJ, FJ, GJ, HJ, MJ, NJ, EK, FK, GK, HK, MK, NK, EL, FL, GL, HL, ML, NL, OL, PL, UL, VL, WL, XL, cL, dL, eL, fL, hL, iL, EP, FP, GP, HP, MP, NP, EQ, FQ, GQ, HQ, MQ, NQ, OQ, PQ, UQ, VQ, WQ, XQ, ZQ, aQ, fQ, gQ, hQ, iQ, ER, FR, GR, HR, MR, NR, OR, PR, UR, VR, WR, XR, cR, dR, eR, fR, kR, lR, mR, DS, ES, FS, GS, LS, MS
60Staphylococcus phage P68Mutation(s): 0 
Find proteins for Q859I2 (Staphylococcus phage P68)
Go to UniProtKB:  Q859I2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Portal protein
A2, A5, A9, AA, AB, AC, AF, AH, AI, AM, AN, AO
327N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Lower collar protein
B2, B5, B9, BA, BB, BC, BF, BH, BI, BM, BN, BO
251Staphylococcus phage P68Mutation(s): 0 
Find proteins for Q859I5 (Staphylococcus phage P68)
Go to UniProtKB:  Q859I5
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Minor structural protein
D2, E2, F2, C2, N2, O2, D5, E5, F5, C5, N5, O5, D9, E9, F9, C9, N9, O9, DA, EA, FA, CA, NA, OA, DB, EB, FB, CB, NB, OB, DC, EC, FC, CC, NC, OC, DF, EF, FF, CF, NF, OF, DH, EH, FH, CH, NH, OH, DI, EI, FI, CI, NI, OI, DM, EM, FM, CM, NM, OM, DN, EN, FN, CN, NN, ON, DO, EO, FO, CO, NO, OO
647Staphylococcus phage P68Mutation(s): 0 
Find proteins for Q859I6 (Staphylococcus phage P68)
Go to UniProtKB:  Q859I6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Tail fibre protein
G2, H2, I2, J2, K2, L2, G5, H5, I5, J5, K5, L5, G9, H9, I9, J9, K9, L9, GA, HA, IA, JA, KA, LA, GB, HB, IB, JB, KB, LB, GC, HC, IC, JC, KC, LC, GF, HF, IF, JF, KF, LF, GH, HH, IH, JH, KH, LH, GI, HI, II, JI, KI, LI, GM, HM, IM, JM, KM, LM, GN, HN, IN, JN, KN, LN, GO, HO, IO, JO, KO, LO
133Staphylococcus phage P68Mutation(s): 0 
Find proteins for Q859I1 (Staphylococcus phage P68)
Go to UniProtKB:  Q859I1
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Head fiber protein
ID, OD, SD, IJ, OJ, SJ, IK, OK, SK, IP, OP, SP, HS, NS, SS
55N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Inner core protein
PD, QD, RD, PJ, QJ, RJ, PK, QK, RK, PP, QP, RP, PS, QS, RS
17N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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