8FXR image
Entry Detail
PDB ID:
8FXR
EMDB ID:
Keywords:
Title:
Structure of neck with portal vertex of capsid of Agrobacterium phage Milano
Biological Source:
PDB Version:
Deposition Date:
2023-01-25
Release Date:
2023-12-06
Method Details:
Experimental Method:
Resolution:
4.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Portal protein, gp7
Chain IDs:SF (auth: AA), TF (auth: AB), UF (auth: AC), VF (auth: AD), WF (auth: AE), XF (auth: AF), YF (auth: AG), ZF (auth: AH), AG (auth: AI), BG (auth: AJ), CG (auth: AK), DG (auth: AL)
Chain Length:420
Number of Molecules:12
Biological Source:Agrobacterium phage Milano
Polymer Type:polypeptide(L)
Description:Tail-terminator protein, gp18
Chain IDs:FG (auth: AQ), HG (auth: AR), LG (auth: AS), NG (auth: AT), QG (auth: AW), SG (auth: AX)
Chain Length:178
Number of Molecules:6
Biological Source:Agrobacterium phage Milano
Polymer Type:polypeptide(L)
Description:Tail-tube, gp21
Chain IDs:GG (auth: AU), JG (auth: AZ), MG (auth: AV), OG (auth: Aa), RG (auth: AY), TG (auth: Ab)
Chain Length:420
Number of Molecules:6
Biological Source:Agrobacterium phage Milano
Polymer Type:polypeptide(L)
Description:Neck 2 protein, gp15
Chain IDs:R (auth: H), S (auth: I), EG (auth: AM), IG (auth: AP), KG (auth: AN), PG (auth: AO)
Chain Length:141
Number of Molecules:6
Biological Source:Agrobacterium phage Milano
Polymer Type:polypeptide(L)
Description:Collar sheath protein, gp13
Chain IDs:FB (auth: J3), GB (auth: K3), HB (auth: L3), IB (auth: M3), JB (auth: N3), KB (auth: O3), LB (auth: P3), MB (auth: Q3), NB (auth: R3), OB (auth: S3), PB (auth: T3), QB (auth: U3), RB (auth: V3), SB (auth: W3), TB (auth: X3), UB (auth: Y3), VB (auth: Z3), WB (auth: a3), XB (auth: b3), YB (auth: c3), ZB (auth: d3), AC (auth: e3), BC (auth: f3), CC (auth: g3), DC (auth: h3), EC (auth: i3), FC (auth: j3), GC (auth: k3), HC (auth: l3), IC (auth: m3), JC (auth: n3), KC (auth: o3), LC (auth: p3), MC (auth: q3), NC (auth: r3), OC (auth: s3), PC (auth: t3), QC (auth: u3), RC (auth: v3), SC (auth: w3), TC (auth: x3), UC (auth: y3), VC (auth: z3), WC (auth: 13), XC (auth: 23), YC (auth: 33), ZC (auth: 43), AD (auth: 53), BD (auth: 63), CD (auth: 73), DD (auth: 83), ED (auth: 93), FD (auth: 03), GD (auth: A3), HD (auth: B3), ID (auth: C3), JD (auth: D3), KD (auth: E3), LD (auth: F3), MD (auth: G3)
Chain Length:230
Number of Molecules:60
Biological Source:Agrobacterium phage Milano
Polymer Type:polypeptide(L)
Description:Neck 1 protein, gp14
Chain IDs:F (auth: a), G (auth: b), H (auth: l), I (auth: n), J (auth: o), K (auth: p), L (auth: q), M (auth: h), N (auth: i), O (auth: j), P (auth: k), Q (auth: m)
Chain Length:202
Number of Molecules:12
Biological Source:Agrobacterium phage Milano
Polymer Type:polypeptide(L)
Description:Linking protein 2, gp128
Chain IDs:A (auth: c), B (auth: d), C (auth: e), D (auth: f), E (auth: g), T (auth: a1), U (auth: b1), V (auth: d1), W (auth: e1), MA (auth: a2), NA (auth: b2), OA (auth: d2), PA (auth: e2), ND (auth: a5), OD (auth: b5), PD (auth: d5), QD (auth: e5), GE (auth: a6), HE (auth: b6), IE (auth: d6), JE (auth: e6), ZE (auth: a7), AF (auth: b7), BF (auth: d7), CF (auth: e7)
Chain Length:38
Number of Molecules:25
Biological Source:Agrobacterium phage Milano
Polymer Type:polypeptide(L)
Description:Linking protein 1, gp16
Chain IDs:X (auth: f1), QA (auth: f2), RD (auth: f5), KE (auth: f6), DF (auth: f7)
Chain Length:217
Number of Molecules:5
Biological Source:Agrobacterium phage Milano
Polymer Type:polypeptide(L)
Description:Major capsid protein, gp9
Chain IDs:Y (auth: g1), Z (auth: h1), AA (auth: k1), DA (auth: n1), EA (auth: o1), HA (auth: r1), RA (auth: g2), SA (auth: h2), TA (auth: k2), WA (auth: n2), XA (auth: o2), AB (auth: r2), SD (auth: g5), TD (auth: h5), UD (auth: k5), XD (auth: n5), YD (auth: o5), BE (auth: r5), LE (auth: g6), ME (auth: h6), NE (auth: k6), QE (auth: n6), RE (auth: o6), UE (auth: r6), EF (auth: g7), FF (auth: h7), GF (auth: k7), JF (auth: n7), KF (auth: o7), NF (auth: r7)
Chain Length:465
Number of Molecules:30
Biological Source:Agrobacterium phage Milano
Polymer Type:polypeptide(L)
Description:Minor capsid protein, gp10
Chain IDs:BA (auth: l1), CA (auth: m1), FA (auth: p1), GA (auth: q1), IA (auth: s1), JA (auth: t1), KA (auth: u1), LA (auth: v1), UA (auth: l2), VA (auth: m2), YA (auth: p2), ZA (auth: q2), BB (auth: s2), CB (auth: t2), DB (auth: u2), EB (auth: v2), VD (auth: l5), WD (auth: m5), ZD (auth: p5), AE (auth: q5), CE (auth: s5), DE (auth: t5), EE (auth: u5), FE (auth: v5), OE (auth: l6), PE (auth: m6), SE (auth: p6), TE (auth: q6), VE (auth: s6), WE (auth: t6), XE (auth: u6), YE (auth: v6), HF (auth: l7), IF (auth: m7), LF (auth: p7), MF (auth: q7), OF (auth: s7), PF (auth: t7), QF (auth: u7), RF (auth: v7)
Chain Length:137
Number of Molecules:40
Biological Source:Agrobacterium phage Milano
Ligand Molecules
Primary Citation
Neck and capsid architecture of the robust Agrobacterium phage Milano.
Commun Biol 6 921 921 (2023)
PMID: 37684529 DOI: 10.1038/s42003-023-05292-1

Abstact

Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the "neck" region, where the DNA-filled capsid is connected to the host-recognizing tail remains poorly understood. We describe cryo-EM structures of the neck, the neck-capsid and neck-tail junctions, and capsid of the Agrobacterium phage Milano. The Milano neck 1 protein connects the 12-fold symmetrical neck to a 5-fold vertex of the icosahedral capsid. Comparison of Milano neck 1 homologs leads to four proposed classes, likely evolved from the simplest one in siphophages to more complex ones in myo- and podophages. Milano neck is surrounded by the atypical collar, which covalently crosslinks the tail sheath to neck 1. The Milano capsid is decorated with three types of proteins, a minor capsid protein (mCP) and two linking proteins crosslinking the mCP to the major capsid protein. The extensive network of disulfide bonds within and between neck, collar, capsid and tail provides an exceptional structural stability to Milano.

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Primary Citation of related structures