8RQE

Composite map of bacteriophage JBD30 capsid - neck complex

• PDB DOI: https://doi.org/10.2210/pdb8RQE/pdb
• EM Map EMD-19439: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Pseudomonas phage JBD30
• Mutation(s): No 


• Deposited: 2024-01-18 Released: 2024-08-14 
• Deposition Author(s): Valentova, L., Fuzik, T., Plevka, P.
• Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic, European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 8.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and replication of Pseudomonas aeruginosa phage JBD30.

Valentova, L., Fuzik, T., Novacek, J., Hlavenkova, Z., Pospisil, J., Plevka, P.

(2024) EMBO J 

• PubMed: 39143239 
• DOI: https://doi.org/10.1038/s44318-024-00195-1
• Primary Citation of Related Structures:  
  8RK3, 8RK4, 8RK5, 8RK6, 8RK7, 8RK8, 8RK9, 8RKA, 8RKB, 8RKC, 8RKN, 8RKO, 8RKX, 8RQE


• PubMed Abstract: 
  

  Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection cycle of the siphophage Casadabanvirus JBD30. Using its baseplate, JBD30 attaches to Pseudomonas aeruginosa via the bacterial type IV pilus, whose subsequent retraction brings the phage to the bacterial cell surface. Cryo-electron microscopy structures of the baseplate-pilus complex show that the tripod of baseplate receptor-binding proteins attaches to the outer bacterial membrane. The tripod and baseplate then open to release three copies of the tape-measure protein, an event that is followed by DNA ejection. JBD30 major capsid proteins assemble into procapsids, which expand by 7% in diameter upon filling with phage dsDNA. The DNA-filled heads are finally joined with 180-nm-long tails, which bend easily because flexible loops mediate contacts between the successive discs of major tail proteins. It is likely that the structural features and replication mechanisms described here are conserved among siphophages that utilize the type IV pili for initial cell attachment.

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Organizational Affiliation: 

Central European Institute of Technology, Masaryk University, Brno, Czech Republic.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 871-mer - A420B415C12D12E6F6 

Local Symmetry: Icosahedral - I  (Explore in 3D)
Local Stoichiometry: Homo 420-mer - A420 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 415-mer - B415 Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Hetero 12-mer - E6F6 Local Symmetry: Cyclic - C12  (Explore in 3D)
Local Stoichiometry: Hetero 24-mer - C12D12 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 20,209.71 kDa 
• Atom Count: 1,206,943 
• Modelled Residue Count: 154,887 
• Deposited Residue Count: 184,066 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mu-like prophage FluMu N-terminal domain-containing protein	A [auth aa], AA [auth aA], ABA [auth oa], ACA [auth oA], ADA [auth pa], AEA [auth pA], AF [auth da], AG [auth dA], AH [auth ea], AM [auth gA], AN [auth ha], AO [auth hA], AP [auth ia], AU [auth kA], AV [auth la], AW [auth lA], AX [auth ma], B [auth ab], BA [auth aB], BCA [auth oB], BDA [auth pb], BEA [auth pB], BF [auth db], BG [auth dB], BH [auth eb], BI [auth eB], BM [auth gB], BN [auth hb], BO [auth hB], BP [auth ib], BQ [auth iB], BV [auth lb], BW [auth lB], BX [auth mb], C [auth ac], CA [auth aC], CB [auth bc], CCA [auth oC], CDA [auth pc], CEA [auth pC], CFA [auth qc], CG [auth dC], CH [auth ec], CI [auth eC], CN [auth hc], CO [auth hC], CP [auth ic], CQ [auth iC], CV [auth lc], CW [auth lC], CX [auth mc], CY [auth mC], D [auth ad], DA [auth aD], DB [auth bd], DDA [auth pd], DEA [auth pD], DG [auth dD], DH [auth ed], DI [auth eD], DJ [auth fd], DN [auth hd], DO [auth hD], DP [auth id], DQ [auth iD], DR [auth jd], DW [auth lD], DX [auth md], DY [auth mD], E [auth ae], EA [auth aE], EB [auth be], EC [auth bE], EDA [auth pe], EEA [auth pE], EH [auth ee], EI [auth eE], EJ [auth fe], EO [auth hE], EP [auth ie], EQ [auth iE], ER [auth je], EW [auth lE], EX [auth me], EY [auth mE], EZ [auth ne], F [auth af], FA [auth aF], FB [auth bf], FC [auth bF], FD [auth cf], FEA [auth pF], FH [auth ef], FI [auth eF], FJ [auth ff], FK [auth fF], FP [auth if], FQ [auth iF], FR [auth jf], FS [auth jF], FX [auth mf], FY [auth mF], FZ [auth nf], GA [auth aG], GAA [auth nG], GB [auth bg], GC [auth bG], GD [auth cg], GEA [auth pG], GI [auth eG], GJ [auth fg], GK [auth fG], GQ [auth iG], GR [auth jg], GS [auth jG], GX [auth mg], GY [auth mG], GZ [auth ng], HAA [auth nH], HB [auth bh], HC [auth bH], HD [auth ch], HE [auth cH], HI [auth eH], HJ [auth fh], HK [auth fH], HL [auth gh], HQ [auth iH], HR [auth jh], HS [auth jH], HT [auth kh], HY [auth mH], HZ [auth nh], IAA [auth nI], IB [auth bi], IBA [auth oi], IC [auth bI], ID [auth ci], IE [auth cI], IJ [auth fi], IK [auth fI], IL [auth gi], IR [auth ji], IS [auth jI], IT [auth ki], IU [auth kI], IY [auth mI], IZ [auth ni], JAA [auth nJ], JBA [auth oj], JC [auth bJ], JD [auth cj], JE [auth cJ], JF [auth dj], JJ [auth fj], JK [auth fJ], JL [auth gj], JM [auth gJ], JR [auth jj], JS [auth jJ], JT [auth kj], JU [auth kJ], JZ [auth nj], KAA [auth nK], KBA [auth ok], KC [auth bK], KCA [auth oK], KD [auth ck], KE [auth cK], KF [auth dk], KK [auth fK], KL [auth gk], KM [auth gK], KS [auth jK], KT [auth kk], KU [auth kK], KV [auth lk], KZ [auth nk], LAA [auth nL], LBA [auth ol], LCA [auth oL], LD [auth cl], LE [auth cL], LF [auth dl], LG [auth dL], LK [auth fL], LL [auth gl], LM [auth gL], LN [auth hl], LO [auth hL], LS [auth jL], LT [auth kl], LU [auth kL], LV [auth ll], MAA [auth nM], MBA [auth om], MCA [auth oM], MDA [auth pm], ME [auth cM], MF [auth dm], MG [auth dM], ML [auth gm], MM [auth gM], MN [auth hm], MO [auth hM], MT [auth km], MU [auth kM], MV [auth lm], MW [auth lM], N [auth an], NBA [auth on], NCA [auth oN], NDA [auth pn], NE [auth cN], NF [auth dn], NG [auth dN], NH [auth en], NL [auth gn], NM [auth gN], NN [auth hn], NO [auth hN], NP [auth in], NT [auth kn], NU [auth kN], NV [auth ln], NW [auth lN], O [auth ao], OA [auth aO], OBA [auth oo], OCA [auth oO], ODA [auth po], OEA [auth pO], OF [auth do], OG [auth dO], OH [auth eo], OM [auth gO], ON [auth ho], OO [auth hO], OP [auth io], OU [auth kO], OV [auth lo], OW [auth lO], OX [auth mo], P [auth ap], PA [auth aP], PCA [auth oP], PDA [auth pp], PEA [auth pP], PF [auth dp], PG [auth dP], PH [auth ep], PI [auth eP], PM [auth gP], PN [auth hp], PO [auth hP], PP [auth ip], PQ [auth iP], PV [auth lp], PW [auth lP], PX [auth mp], Q [auth aq], QA [auth aQ], QB [auth bq], QCA [auth oQ], QDA [auth pq], QEA [auth pQ], QG [auth dQ], QH [auth eq], QI [auth eQ], QN [auth hq], QO [auth hQ], QP [auth iq], QQ [auth iQ], QV [auth lq], QW [auth lQ], QX [auth mq], QY [auth mQ], R [auth ar], RA [auth aR], RB [auth br], RC [auth bR], RDA [auth pr], REA [auth pR], RG [auth dR], RH [auth er], RI [auth eR], RJ [auth fr], RN [auth hr], RO [auth hR], RP [auth ir], RQ [auth iR], RR [auth jr], RW [auth lR], RX [auth mr], RY [auth mR], S [auth as], SA [auth aS], SB [auth bs], SC [auth bS], SDA [auth ps], SEA [auth pS], SH [auth es], SI [auth eS], SJ [auth fs], SP [auth is], SQ [auth iS], SR [auth js], SW [auth lS], SX [auth ms], SY [auth mS], SZ [auth ns], T [auth at], TA [auth aT], TB [auth bt], TC [auth bT], TD [auth ct], TEA [auth pT], TH [auth et], TI [auth eT], TJ [auth ft], TK [auth fT], TP [auth it], TQ [auth iT], TR [auth jt], TS [auth jT], TX [auth mt], TY [auth mT], TZ [auth nt], UA [auth aU], UAA [auth nU], UB [auth bu], UC [auth bU], UD [auth cu], UEA [auth pU], UI [auth eU], UJ [auth fu], UK [auth fU], UQ [auth iU], UR [auth ju], US [auth jU], UT [auth ku], UX [auth mu], UY [auth mU], UZ [auth nu], VAA [auth nV], VB [auth bv], VC [auth bV], VD [auth cv], VE [auth cV], VI [auth eV], VJ [auth fv], VK [auth fV], VL [auth gv], VQ [auth iV], VR [auth jv], VS [auth jV], VT [auth kv], VY [auth mV], VZ [auth nv], WAA [auth nW], WB [auth bw], WBA [auth ow], WC [auth bW], WD [auth cw], WE [auth cW], WJ [auth fw], WK [auth fW], WL [auth gw], WR [auth jw], WS [auth jW], WT [auth kw], WU [auth kW], WY [auth mW], WZ [auth nw], XAA [auth nX], XBA [auth ox], XC [auth bX], XD [auth cx], XE [auth cX], XF [auth dx], XJ [auth fx], XK [auth fX], XL [auth gx], XM [auth gX], XR [auth jx], XS [auth jX], XT [auth kx], XU [auth kX], XZ [auth nx], YAA [auth nY], YBA [auth oy], YCA [auth oY], YD [auth cy], YE [auth cY], YF [auth dy], YK [auth fY], YL [auth gy], YM [auth gY], YN [auth hy], YS [auth jY], YT [auth ky], YU [auth kY], YV [auth ly], YZ [auth ny], ZAA [auth nZ], ZBA [auth oz], ZCA [auth oZ], ZD [auth cz], ZE [auth cZ], ZF [auth dz], ZG [auth dZ], ZK [auth fZ], ZL [auth gz], ZM [auth gZ], ZN [auth hz], ZO [auth hZ], ZS [auth jZ], ZT [auth kz], ZU [auth kZ], ZV [auth lz]	113	Pseudomonas phage JBD30	Mutation(s): 0
UniProt
Find proteins for L7P800 (Pseudomonas phage JBD30) Explore L7P800  Go to UniProtKB:  L7P800

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriophage Mu GpT domain-containing protein	AAA [auth nA], AB [auth ba], AC [auth bA], AD [auth ca], AE [auth cA], AFA [auth qa], AI [auth eA], AJ [auth fa], AK [auth fA], AL [auth ga], AQ [auth iA], AR [auth ja], AS [auth jA], AT [auth ka], AY [auth mA], AZ [auth na], BAA [auth nB], BB [auth bb], BBA [auth ob], BC [auth bB], BD [auth cb], BE [auth cB], BFA [auth qb], BJ [auth fb], BK [auth fB], BL [auth gb], BR [auth jb], BS [auth jB], BT [auth kb], BU [auth kB], BY [auth mB], BZ [auth nb], CAA [auth nC], CBA [auth oc], CC [auth bC], CD [auth cc], CE [auth cC], CF [auth dc], CJ [auth fc], CK [auth fC], CL [auth gc], CM [auth gC], CR [auth jc], CS [auth jC], CT [auth kc], CU [auth kC], CZ [auth nc], DAA [auth nD], DBA [auth od], DC [auth bD], DCA [auth oD], DD [auth cd], DE [auth cD], DF [auth dd], DK [auth fD], DL [auth gd], DM [auth gD], DS [auth jD], DT [auth kd], DU [auth kD], DV [auth ld], DZ [auth nd], EAA [auth nE], EBA [auth oe], ECA [auth oE], ED [auth ce], EE [auth cE], EF [auth de], EG [auth dE], EK [auth fE], EL [auth ge], EM [auth gE], EN [auth he], ES [auth jE], ET [auth ke], EU [auth kE], EV [auth le], FAA [auth nF], FBA [auth of], FCA [auth oF], FDA [auth pf], FE [auth cF], FF [auth df], FG [auth dF], FL [auth gf], FM [auth gF], FN [auth hf], FO [auth hF], FT [auth kf], FU [auth kF], FV [auth lf], FW [auth lF], G [auth ag], GBA [auth og], GCA [auth oG], GDA [auth pg], GE [auth cG], GF [auth dg], GG [auth dG], GH [auth eg], GL [auth gg], GM [auth gG], GN [auth hg], GO [auth hG], GP [auth ig], GT [auth kg], GU [auth kG], GV [auth lg], GW [auth lG], H [auth ah], HA [auth aH], HBA [auth oh], HCA [auth oH], HDA [auth ph], HEA [auth pH], HF [auth dh], HG [auth dH], HH [auth eh], HM [auth gH], HN [auth hh], HO [auth hH], HP [auth ih], HU [auth kH], HV [auth lh], HW [auth lH], HX [auth mh], I [auth ai], IA [auth aI], ICA [auth oI], IDA [auth pi], IEA [auth pI], IF [auth di], IG [auth dI], IH [auth ei], II [auth eI], IM [auth gI], IN [auth hi], IO [auth hI], IP [auth ii], IQ [auth iI], IV [auth li], IW [auth lI], IX [auth mi], J [auth aj], JA [auth aJ], JB [auth bj], JCA [auth oJ], JDA [auth pj], JEA [auth pJ], JG [auth dJ], JH [auth ej], JI [auth eJ], JN [auth hj], JO [auth hJ], JP [auth ij], JQ [auth iJ], JV [auth lj], JW [auth lJ], JX [auth mj], JY [auth mJ], K [auth ak], KA [auth aK], KB [auth bk], KDA [auth pk], KEA [auth pK], KG [auth dK], KH [auth ek], KI [auth eK], KJ [auth fk], KN [auth hk], KO [auth hK], KP [auth ik], KQ [auth iK], KR [auth jk], KW [auth lK], KX [auth mk], KY [auth mK], L [auth al], LA [auth aL], LB [auth bl], LC [auth bL], LDA [auth pl], LEA [auth pL], LH [auth el], LI [auth eL], LJ [auth fl], LP [auth il], LQ [auth iL], LR [auth jl], LW [auth lL], LX [auth ml], LY [auth mL], LZ [auth nl], M [auth am], MA [auth aM], MB [auth bm], MC [auth bM], MD [auth cm], MEA [auth pM], MH [auth em], MI [auth eM], MJ [auth fm], MK [auth fM], MP [auth im], MQ [auth iM], MR [auth jm], MS [auth jM], MX [auth mm], MY [auth mM], MZ [auth nm], NA [auth aN], NAA [auth nN], NB [auth bn], NC [auth bN], ND [auth cn], NEA [auth pN], NI [auth eN], NJ [auth fn], NK [auth fN], NQ [auth iN], NR [auth jn], NS [auth jN], NX [auth mn], NY [auth mN], NZ [auth nn], OAA [auth nO], OB [auth bo], OC [auth bO], OD [auth co], OE [auth cO], OI [auth eO], OJ [auth fo], OK [auth fO], OL [auth go], OQ [auth iO], OR [auth jo], OS [auth jO], OT [auth ko], OY [auth mO], OZ [auth no], PAA [auth nP], PB [auth bp], PBA [auth op], PC [auth bP], PD [auth cp], PE [auth cP], PJ [auth fp], PK [auth fP], PL [auth gp], PR [auth jp], PS [auth jP], PT [auth kp], PU [auth kP], PY [auth mP], PZ [auth np], QAA [auth nQ], QBA [auth oq], QC [auth bQ], QD [auth cq], QE [auth cQ], QF [auth dq], QJ [auth fq], QK [auth fQ], QL [auth gq], QM [auth gQ], QR [auth jq], QS [auth jQ], QT [auth kq], QU [auth kQ], QZ [auth nq], RAA [auth nR], RBA [auth or], RCA [auth oR], RD [auth cr], RE [auth cR], RF [auth dr], RK [auth fR], RL [auth gr], RM [auth gR], RS [auth jR], RT [auth kr], RU [auth kR], RV [auth lr], RZ [auth nr], SAA [auth nS], SBA [auth os], SCA [auth oS], SD [auth cs], SE [auth cS], SF [auth ds], SG [auth dS], SK [auth fS], SL [auth gs], SM [auth gS], SN [auth hs], SO [auth hS], SS [auth jS], ST [auth ks], SU [auth kS], SV [auth ls], TAA [auth nT], TBA [auth ot], TCA [auth oT], TDA [auth pt], TE [auth cT], TF [auth dt], TG [auth dT], TL [auth gt], TM [auth gT], TN [auth ht], TO [auth hT], TT [auth kt], TU [auth kT], TV [auth lt], TW [auth lT], U [auth au], UBA [auth ou], UCA [auth oU], UDA [auth pu], UE [auth cU], UF [auth du], UG [auth dU], UH [auth eu], UL [auth gu], UM [auth gU], UN [auth hu], UO [auth hU], UP [auth iu], UU [auth kU], UV [auth lu], UW [auth lU], V [auth av], VA [auth aV], VBA [auth ov], VCA [auth oV], VDA [auth pv], VEA [auth pV], VF [auth dv], VG [auth dV], VH [auth ev], VM [auth gV], VN [auth hv], VO [auth hV], VP [auth iv], VU [auth kV], VV [auth lv], VW [auth lV], VX [auth mv], W [auth aw], WA [auth aW], WCA [auth oW], WDA [auth pw], WEA [auth pW], WF [auth dw], WG [auth dW], WH [auth ew], WI [auth eW], WM [auth gW], WN [auth hw], WO [auth hW], WP [auth iw], WQ [auth iW], WV [auth lw], WW [auth lW], WX [auth mw], X [auth ax], XA [auth aX], XB [auth bx], XCA [auth oX], XDA [auth px], XEA [auth pX], XG [auth dX], XH [auth ex], XI [auth eX], XN [auth hx], XO [auth hX], XP [auth ix], XQ [auth iX], XV [auth lx], XW [auth lX], XX [auth mx], XY [auth mX], Y [auth ay], YA [auth aY], YB [auth by], YC [auth bY], YDA [auth py], YEA [auth pY], YG [auth dY], YH [auth ey], YI [auth eY], YJ [auth fy], YO [auth hY], YP [auth iy], YQ [auth iY], YR [auth jy], YW [auth lY], YX [auth my], YY [auth mY], Z [auth az], ZA [auth aZ], ZB [auth bz], ZC [auth bZ], ZDA [auth pz], ZEA [auth pZ], ZH [auth ez], ZI [auth eZ], ZJ [auth fz], ZP [auth iz], ZQ [auth iZ], ZR [auth jz], ZW [auth lZ], ZX [auth mz], ZY [auth mZ], ZZ [auth nz]	304	Pseudomonas phage JBD30	Mutation(s): 0
UniProt
Find proteins for L7P7W9 (Pseudomonas phage JBD30) Explore L7P7W9  Go to UniProtKB:  L7P7W9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stopper protein	DFA [auth qd], EFA [auth qe], FFA [auth qf], GFA [auth qg], HFA [auth qh], IFA [auth qi]	157	Pseudomonas phage JBD30	Mutation(s): 0
UniProt
Find proteins for L7P7R4 (Pseudomonas phage JBD30) Explore L7P7R4  Go to UniProtKB:  L7P7R4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Virion structural protein	JFA [auth qj], KFA [auth qk], LFA [auth ql], MFA [auth qm], NFA [auth qn], OFA [auth qo]	256	Pseudomonas phage JBD30	Mutation(s): 0
UniProt
Find proteins for L7P801 (Pseudomonas phage JBD30) Explore L7P801  Go to UniProtKB:  L7P801

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	BGA [auth qB], DGA [auth qD], FGA [auth qF], HGA [auth qH], JGA [auth qJ], LGA [auth qL], PFA [auth qp], RFA [auth qr], TFA [auth qt], VFA [auth qv], XFA [auth qx], ZFA [auth qz]	526	Pseudomonas phage JBD30	Mutation(s): 0
UniProt
Find proteins for L7P7R0 (Pseudomonas phage JBD30) Explore L7P7R0  Go to UniProtKB:  L7P7R0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF1320 domain-containing protein	AGA [auth qA], CGA [auth qC], EGA [auth qE], GGA [auth qG], IGA [auth qI], KGA [auth qK], MGA [auth qM], QFA [auth qq], SFA [auth qs], UFA [auth qu], WFA [auth qw], YFA [auth qy]	138	Pseudomonas phage JBD30	Mutation(s): 0
UniProt
Find proteins for L7P846 (Pseudomonas phage JBD30) Explore L7P846  Go to UniProtKB:  L7P846

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 8.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1

Structure Validation

Currently 8RQE does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Valentova, L., Fuzik, T., Plevka, P.

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Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LX22NPO5103
European Research Council (ERC)	European Union	101043452

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release
  
• Version 1.1: 2024-08-28
  Changes: Data collection, Database references