› 8fwg

Electron Microscopy
3.45Å resolution

Structure of neck and portal vertex of Agrobacterium phage Milano, C5 symmetry

Released:
DOI: 10.2210/pdb8fwg/pdb
PDB entry 8fwg coloured by chain, front view.
PDB entry 8fwg coloured by chain, side view.
PDB entry 8fwg coloured by chain, top view.
Source organism: Agrobacterium phage Milano
Primary publication:
Neck and capsid architecture of the robust Agrobacterium phage Milano.
Sonani RR, Esteves NC, Horton AA, Kelly RJ, Sebastian AL, Wang F, Kreutzberger MAB, Leiman PG, Scharf BE, Egelman EH
OpenAccess logo Commun Biol 6 921 (2023)
PMID: 37684529
Related structures: EMD-29504

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 165-mer (preferred)
PDBe Complex ID:
PDB-CPX-236196 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Linking protein 2, gp128 Chains: a1, a2, a5, a6, a7, b1, b2, b5, b6, b7, c, d, d1, d2, d5, d6, d7, e, e1, e2, e5, e6, e7, f, g
Molecule details ›
Chains: a1, a2, a5, a6, a7, b1, b2, b5, b6, b7, c, d, d1, d2, d5, d6, d7, e, e1, e2, e5, e6, e7, f, g
Length: 38 amino acids
Theoretical weight: 3.94 KDa
Source organism: Agrobacterium phage Milano
Virion-associated protein Chains: f1, f2, f5, f6, f7
Molecule details ›
Chains: f1, f2, f5, f6, f7
Length: 217 amino acids
Theoretical weight: 22.91 KDa
Source organism: Agrobacterium phage Milano
UniProt:
  • Canonical: A0A482MFR0 (Residues: 1-217; Coverage: 100%)
Gene name: Milano_016
Major capsid protein Chains: g1, g2, g5, g6, g7, h1, h2, h5, h6, h7, k1, k2, k5, k6, k7, n1, n2, n5, n6, n7, o1, o2, o5, o6, o7, r1, r2, r5, r6, r7
Molecule details ›
Chains: g1, g2, g5, g6, g7, h1, h2, h5, h6, h7, k1, k2, k5, k6, k7, n1, n2, n5, n6, n7, o1, o2, o5, o6, o7, r1, r2, r5, r6, r7
Length: 465 amino acids
Theoretical weight: 52.04 KDa
Source organism: Agrobacterium phage Milano
UniProt:
  • Canonical: A0A482MFS6 (Residues: 1-465; Coverage: 100%)
Gene name: Milano_009
Sequence domains: Phage capsid family
Virion-associated protein Chains: l1, l2, l5, l6, l7, m1, m2, m5, m6, m7, p1, p2, p5, p6, p7, q1, q2, q5, q6, q7, s1, s2, s5, s6, s7, t1, t2, t5, t6, t7, u1, u2, u5, u6, u7, v1, v2, v5, v6, v7
Molecule details ›
Chains: l1, l2, l5, l6, l7, m1, m2, m5, m6, m7, p1, p2, p5, p6, p7, q1, q2, q5, q6, q7, s1, s2, s5, s6, s7, t1, t2, t5, t6, t7, u1, u2, u5, u6, u7, v1, v2, v5, v6, v7
Length: 137 amino acids
Theoretical weight: 14.55 KDa
Source organism: Agrobacterium phage Milano
UniProt:
  • Canonical: A0A482MFS0 (Residues: 1-137; Coverage: 100%)
Gene name: Milano_010
Virion-associated protein Chains: 03, 13, 23, 33, 43, 53, 63, 73, 83, 93, A3, B3, C3, D3, E3, F3, G3, J3, K3, L3, M3, N3, O3, P3, Q3, R3, S3, T3, U3, V3, W3, X3, Y3, Z3, a3, b3, c3, d3, e3, f3, g3, h3, i3, j3, k3, l3, m3, n3, o3, p3, q3, r3, s3, t3, u3, v3, w3, x3, y3, z3
Molecule details ›
Chains: 03, 13, 23, 33, 43, 53, 63, 73, 83, 93, A3, B3, C3, D3, E3, F3, G3, J3, K3, L3, M3, N3, O3, P3, Q3, R3, S3, T3, U3, V3, W3, X3, Y3, Z3, a3, b3, c3, d3, e3, f3, g3, h3, i3, j3, k3, l3, m3, n3, o3, p3, q3, r3, s3, t3, u3, v3, w3, x3, y3, z3
Length: 230 amino acids
Theoretical weight: 24.49 KDa
Source organism: Agrobacterium phage Milano
UniProt:
  • Canonical: A0A482MGH3 (Residues: 57-286; Coverage: 80%)
Gene name: Milano_013
Sequence domains: Bacterial Ig domain
Head-to-tail connector complex protein Chains: A4, B4, C4, D4, E4
Molecule details ›
Chains: A4, B4, C4, D4, E4
Length: 202 amino acids
Theoretical weight: 22.26 KDa
Source organism: Agrobacterium phage Milano
UniProt:
  • Canonical: A0A482MHL8 (Residues: 1-202; Coverage: 100%)
Gene name: Milano_014

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.45Å
Relevant EMDB volumes: EMD-29504

Quick links

Citations

1 mention without citation

Neck and capsid architecture of the robust Agrobacterium phage Milano.
Sonani et al. (2023)