6Q3G image
Deposition Date 2018-12-04
Release Date 2019-11-06
Last Version Date 2024-05-15
Entry Detail
PDB ID:
6Q3G
Keywords:
VIRUS
Title:
Structure of native bacteriophage P68
Biological Source:
Source Organism:
Staphylococcus phage P68 (Taxon ID: 204090)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6Q3G validation report
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Portal protein
Chain IDs:NA (auth: A2), RD (auth: A5), VI (auth: A9), JJ (auth: AA), XJ (auth: AB), LK (auth: AC), ZM (auth: AF), BP (auth: AH), PP (auth: AI), WS (auth: AM), KT (auth: AN), YT (auth: AO)
Chain Length:327
Number of Molecules:12
Biological Source:Staphylococcus phage P68
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Lower collar protein
Chain IDs:OA (auth: B2), SD (auth: B5), WI (auth: B9), KJ (auth: BA), YJ (auth: BB), MK (auth: BC), AN (auth: BF), CP (auth: BH), QP (auth: BI), XS (auth: BM), LT (auth: BN), ZT (auth: BO)
Chain Length:251
Number of Molecules:12
Biological Source:Staphylococcus phage P68
UniProt ID:Q859I5
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Major head protein
Chain IDs:A (auth: C1), B (auth: A1), C (auth: B1), D (auth: D1), I (auth: I1), J (auth: J1), K (auth: K1), L (auth: L1), Q (auth: Q1), R (auth: R1), S (auth: S1), T (auth: T1), X (auth: X1), Y (auth: Y1), Z (auth: Z1), AA (auth: a1), FA (auth: f1), GA (auth: g1), HA (auth: h1), IA (auth: i1), BB (auth: C3), CB (auth: A3), DB (auth: B3), EB (auth: D3), JB (auth: I3), KB (auth: J3), LB (auth: K3), MB (auth: L3), RB (auth: Q3), SB (auth: R3), TB (auth: S3), UB (auth: T3), ZB (auth: Y3), CC (auth: b3), FC (auth: C4), GC (auth: A4), HC (auth: B4), IC (auth: D4), NC (auth: I4), OC (auth: J4), PC (auth: K4), QC (auth: L4), VC (auth: Q4), WC (auth: R4), XC (auth: S4), YC (auth: T4), CD (auth: X4), DD (auth: Y4), ED (auth: Z4), FD (auth: a4), KD (auth: f4), LD (auth: g4), MD (auth: h4), ND (auth: i4), FE (auth: C6), GE (auth: A6), HE (auth: B6), IE (auth: D6), NE (auth: I6), OE (auth: J6), PE (auth: K6), QE (auth: L6), VE (auth: Q6), WE (auth: R6), XE (auth: S6), YE (auth: T6), DF (auth: Y6), EF (auth: Z6), FF (auth: a6), GF (auth: b6), LF (auth: g6), MF (auth: h6), NF (auth: i6), OF (auth: j6), TF (auth: C7), UF (auth: A7), VF (auth: B7), WF (auth: D7), BG (auth: I7), CG (auth: J7), DG (auth: K7), EG (auth: L7), JG (auth: Q7), KG (auth: R7), LG (auth: S7), MG (auth: T7), RG (auth: Y7), SG (auth: Z7), TG (auth: a7), UG (auth: b7), ZG (auth: g7), AH (auth: h7), BH (auth: i7), CH (auth: j7), HH (auth: C8), IH (auth: A8), JH (auth: B8), KH (auth: D8), PH (auth: I8), QH (auth: J8), RH (auth: K8), SH (auth: L8), XH (auth: Q8), YH (auth: R8), ZH (auth: S8), AI (auth: T8), FI (auth: Y8), GI (auth: Z8), HI (auth: a8), II (auth: b8), NI (auth: g8), OI (auth: h8), PI (auth: i8), QI (auth: j8), ZK (auth: AD), AL (auth: BD), BL (auth: CD), CL (auth: DD), IL (auth: KD), JL (auth: LD), RL (auth: DE), UL (auth: AE), VL (auth: BE), WL (auth: CE), XL (auth: FE), BM (auth: KE), CM (auth: LE), DM (auth: ME), EM (auth: NE), JM (auth: SE), KM (auth: TE), LM (auth: UE), MM (auth: VE), RM (auth: aE), SM (auth: bE), TM (auth: cE), UM (auth: dE), NN (auth: CG), ON (auth: AG), PN (auth: BG), QN (auth: DG), VN (auth: IG), WN (auth: JG), XN (auth: KG), YN (auth: LG), DO (auth: QG), EO (auth: RG), FO (auth: SG), GO (auth: TG), LO (auth: YG), MO (auth: ZG), NO (auth: aG), OO (auth: bG), TO (auth: gG), UO (auth: hG), VO (auth: iG), WO (auth: jG), DQ (auth: AJ), EQ (auth: BJ), FQ (auth: CJ), GQ (auth: DJ), MQ (auth: KJ), NQ (auth: LJ), VQ (auth: AK), WQ (auth: BK), XQ (auth: CK), YQ (auth: DK), ER (auth: KK), FR (auth: LK), NR (auth: CL), OR (auth: AL), PR (auth: BL), QR (auth: DL), VR (auth: IL), WR (auth: JL), XR (auth: KL), YR (auth: LL), DS (auth: QL), ES (auth: RL), FS (auth: SL), GS (auth: TL), LS (auth: YL), MS (auth: ZL), NS (auth: aL), OS (auth: bL), TS (auth: gL), MU (auth: AP), NU (auth: BP), OU (auth: CP), PU (auth: DP), VU (auth: KP), WU (auth: LP), EV (auth: CQ), FV (auth: AQ), GV (auth: BQ), HV (auth: DQ), MV (auth: IQ), NV (auth: JQ), OV (auth: KQ), PV (auth: LQ), UV (auth: QQ), VV (auth: RQ), WV (auth: SQ), XV (auth: TQ), CW (auth: YQ), FW (auth: bQ), GW (auth: cQ), HW (auth: dQ), IW (auth: eQ), NW (auth: CR), OW (auth: AR), PW (auth: BR), QW (auth: DR), VW (auth: IR), WW (auth: JR), XW (auth: KR), YW (auth: LR), DX (auth: QR), EX (auth: RR), FX (auth: SR), GX (auth: TR), LX (auth: YR), MX (auth: ZR), NX (auth: aR), OX (auth: bR), TX (auth: gR), UX (auth: hR), VX (auth: iR), WX (auth: jR), AY (auth: AS), BY (auth: BS), CY (auth: CS), IY (auth: IS), JY (auth: JS), KY (auth: KS)
Chain Length:408
Number of Molecules:235
Biological Source:Staphylococcus phage P68
UniProt ID:Q859I3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Minor structural protein
Chain IDs:PA (auth: D2), QA (auth: E2), RA (auth: F2), YA (auth: C2), ZA (auth: N2), AB (auth: O2), TD (auth: D5), UD (auth: E5), VD (auth: F5), CE (auth: C5), DE (auth: N5), EE (auth: O5), XI (auth: D9), YI (auth: E9), ZI (auth: F9), GJ (auth: C9), HJ (auth: N9), IJ (auth: O9), LJ (auth: DA), MJ (auth: EA), NJ (auth: FA), UJ (auth: CA), VJ (auth: NA), WJ (auth: OA), ZJ (auth: DB), AK (auth: EB), BK (auth: FB), IK (auth: CB), JK (auth: NB), KK (auth: OB), NK (auth: DC), OK (auth: EC), PK (auth: FC), WK (auth: CC), XK (auth: NC), YK (auth: OC), BN (auth: DF), CN (auth: EF), DN (auth: FF), KN (auth: CF), LN (auth: NF), MN (auth: OF), DP (auth: DH), EP (auth: EH), FP (auth: FH), MP (auth: CH), NP (auth: NH), OP (auth: OH), RP (auth: DI), SP (auth: EI), TP (auth: FI), AQ (auth: CI), BQ (auth: NI), CQ (auth: OI), YS (auth: DM), ZS (auth: EM), AT (auth: FM), HT (auth: CM), IT (auth: NM), JT (auth: OM), MT (auth: DN), NT (auth: EN), OT (auth: FN), VT (auth: CN), WT (auth: NN), XT (auth: ON), AU (auth: DO), BU (auth: EO), CU (auth: FO), JU (auth: CO), KU (auth: NO), LU (auth: OO)
Chain Length:647
Number of Molecules:72
Biological Source:Staphylococcus phage P68
UniProt ID:Q859I6 Pfam ID:PF21311
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Arstotzka protein
Chain IDs:E (auth: E1), F (auth: F1), G (auth: G1), H (auth: H1), M (auth: M1), N (auth: N1), O (auth: O1), P (auth: P1), U (auth: U1), V (auth: V1), W (auth: W1), BA (auth: b1), CA (auth: c1), DA (auth: d1), EA (auth: e1), JA (auth: j1), KA (auth: k1), LA (auth: l1), MA (auth: m1), FB (auth: E3), GB (auth: F3), HB (auth: G3), IB (auth: H3), NB (auth: M3), OB (auth: N3), PB (auth: O3), QB (auth: P3), VB (auth: U3), WB (auth: V3), XB (auth: W3), YB (auth: X3), AC (auth: Z3), BC (auth: a3), DC (auth: c3), EC (auth: d3), JC (auth: E4), KC (auth: F4), LC (auth: G4), MC (auth: H4), RC (auth: M4), SC (auth: N4), TC (auth: O4), UC (auth: P4), ZC (auth: U4), AD (auth: V4), BD (auth: W4), GD (auth: b4), HD (auth: c4), ID (auth: d4), JD (auth: e4), OD (auth: j4), PD (auth: k4), QD (auth: l4), JE (auth: E6), KE (auth: F6), LE (auth: G6), ME (auth: H6), RE (auth: M6), SE (auth: N6), TE (auth: O6), UE (auth: P6), ZE (auth: U6), AF (auth: V6), BF (auth: W6), CF (auth: X6), HF (auth: c6), IF (auth: d6), JF (auth: e6), KF (auth: f6), PF (auth: k6), QF (auth: l6), RF (auth: m6), SF (auth: n6), XF (auth: E7), YF (auth: F7), ZF (auth: G7), AG (auth: H7), FG (auth: M7), GG (auth: N7), HG (auth: O7), IG (auth: P7), NG (auth: U7), OG (auth: V7), PG (auth: W7), QG (auth: X7), VG (auth: c7), WG (auth: d7), XG (auth: e7), YG (auth: f7), DH (auth: k7), EH (auth: l7), FH (auth: m7), GH (auth: n7), LH (auth: E8), MH (auth: F8), NH (auth: G8), OH (auth: H8), TH (auth: M8), UH (auth: N8), VH (auth: O8), WH (auth: P8), BI (auth: U8), CI (auth: V8), DI (auth: W8), EI (auth: X8), JI (auth: c8), KI (auth: d8), LI (auth: e8), MI (auth: f8), RI (auth: k8), SI (auth: l8), TI (auth: m8), UI (auth: n8), DL (auth: ED), EL (auth: FD), FL (auth: GD), GL (auth: HD), KL (auth: MD), LL (auth: ND), SL (auth: EE), TL (auth: GE), YL (auth: HE), ZL (auth: IE), AM (auth: JE), FM (auth: OE), GM (auth: PE), HM (auth: QE), IM (auth: RE), NM (auth: WE), OM (auth: XE), PM (auth: YE), QM (auth: ZE), VM (auth: eE), WM (auth: fE), XM (auth: gE), YM (auth: hE), RN (auth: EG), SN (auth: FG), TN (auth: GG), UN (auth: HG), ZN (auth: MG), AO (auth: NG), BO (auth: OG), CO (auth: PG), HO (auth: UG), IO (auth: VG), JO (auth: WG), KO (auth: XG), PO (auth: cG), QO (auth: dG), RO (auth: eG), SO (auth: fG), XO (auth: kG), YO (auth: lG), ZO (auth: mG), AP (auth: nG), HQ (auth: EJ), IQ (auth: FJ), JQ (auth: GJ), KQ (auth: HJ), OQ (auth: MJ), PQ (auth: NJ), ZQ (auth: EK), AR (auth: FK), BR (auth: GK), CR (auth: HK), GR (auth: MK), HR (auth: NK), RR (auth: EL), SR (auth: FL), TR (auth: GL), UR (auth: HL), ZR (auth: ML), AS (auth: NL), BS (auth: OL), CS (auth: PL), HS (auth: UL), IS (auth: VL), JS (auth: WL), KS (auth: XL), PS (auth: cL), QS (auth: dL), RS (auth: eL), SS (auth: fL), US (auth: hL), VS (auth: iL), QU (auth: EP), RU (auth: FP), SU (auth: GP), TU (auth: HP), XU (auth: MP), YU (auth: NP), IV (auth: EQ), JV (auth: FQ), KV (auth: GQ), LV (auth: HQ), QV (auth: MQ), RV (auth: NQ), SV (auth: OQ), TV (auth: PQ), YV (auth: UQ), ZV (auth: VQ), AW (auth: WQ), BW (auth: XQ), DW (auth: ZQ), EW (auth: aQ), JW (auth: fQ), KW (auth: gQ), LW (auth: hQ), MW (auth: iQ), RW (auth: ER), SW (auth: FR), TW (auth: GR), UW (auth: HR), ZW (auth: MR), AX (auth: NR), BX (auth: OR), CX (auth: PR), HX (auth: UR), IX (auth: VR), JX (auth: WR), KX (auth: XR), PX (auth: cR), QX (auth: dR), RX (auth: eR), SX (auth: fR), XX (auth: kR), YX (auth: lR), ZX (auth: mR), DY (auth: DS), EY (auth: ES), FY (auth: FS), GY (auth: GS), LY (auth: LS), MY (auth: MS)
Chain Length:408
Number of Molecules:235
Biological Source:Staphylococcus phage P68
UniProt ID:Q859I2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tail fibre protein
Chain IDs:SA (auth: G2), TA (auth: H2), UA (auth: I2), VA (auth: J2), WA (auth: K2), XA (auth: L2), WD (auth: G5), XD (auth: H5), YD (auth: I5), ZD (auth: J5), AE (auth: K5), BE (auth: L5), AJ (auth: G9), BJ (auth: H9), CJ (auth: I9), DJ (auth: J9), EJ (auth: K9), FJ (auth: L9), OJ (auth: GA), PJ (auth: HA), QJ (auth: IA), RJ (auth: JA), SJ (auth: KA), TJ (auth: LA), CK (auth: GB), DK (auth: HB), EK (auth: IB), FK (auth: JB), GK (auth: KB), HK (auth: LB), QK (auth: GC), RK (auth: HC), SK (auth: IC), TK (auth: JC), UK (auth: KC), VK (auth: LC), EN (auth: GF), FN (auth: HF), GN (auth: IF), HN (auth: JF), IN (auth: KF), JN (auth: LF), GP (auth: GH), HP (auth: HH), IP (auth: IH), JP (auth: JH), KP (auth: KH), LP (auth: LH), UP (auth: GI), VP (auth: HI), WP (auth: II), XP (auth: JI), YP (auth: KI), ZP (auth: LI), BT (auth: GM), CT (auth: HM), DT (auth: IM), ET (auth: JM), FT (auth: KM), GT (auth: LM), PT (auth: GN), QT (auth: HN), RT (auth: IN), ST (auth: JN), TT (auth: KN), UT (auth: LN), DU (auth: GO), EU (auth: HO), FU (auth: IO), GU (auth: JO), HU (auth: KO), IU (auth: LO)
Chain Length:133
Number of Molecules:72
Biological Source:Staphylococcus phage P68
UniProt ID:Q859I1
Polymer Type:polypeptide(L)
Molecule:Head fiber protein
Chain IDs:HL (auth: ID), ML (auth: OD), QL (auth: SD), LQ (auth: IJ), QQ (auth: OJ), UQ (auth: SJ), DR (auth: IK), IR (auth: OK), MR (auth: SK), UU (auth: IP), ZU (auth: OP), DV (auth: SP), HY (auth: HS), NY (auth: NS), RY (auth: SS)
Chain Length:55
Number of Molecules:15
Biological Source:Staphylococcus phage P68
Polymer Type:polypeptide(L)
Molecule:Inner core protein
Chain IDs:NL (auth: PD), OL (auth: QD), PL (auth: RD), RQ (auth: PJ), SQ (auth: QJ), TQ (auth: RJ), JR (auth: PK), KR (auth: QK), LR (auth: RK), AV (auth: PP), BV (auth: QP), CV (auth: RP), OY (auth: PS), PY (auth: QS), QY (auth: RS)
Chain Length:17
Number of Molecules:15
Biological Source:Staphylococcus phage P68
Ligand Molecules
NA
Primary Citation
Structure and genome ejection mechanism ofStaphylococcus aureusphage P68.
Sci Adv 5 eaaw7414 eaaw7414 (2019)
PMID: 31663016 DOI: 10.1126/sciadv.aaw7414

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6IAB
6IAV
6IAC