6tba

Electron Microscopy
4.54Å resolution

Virion of native gene transfer agent (GTA) particle

Released:
Related structures: EMD-10443

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 288-mer (preferred)
PDBe Complex ID:
PDB-CPX-112666 (preferred)
Entry contents:
11 distinct polypeptide molecules
Macromolecules (11 distinct):
Phage major capsid protein, HK97 family Chains: A4, A5, A9, AA, AE, AF, AJ, AK, AO, AP, B4, B5, B9, BA, BE, BF, BJ, BK, BO, BP, C4, C5, C9, CA, CE, CF, CJ, CK, CO, CP, D4, D9, DE, DJ, DO, E4, E9, EE, EJ, EO, F4, F9, FE, FJ, FO, G4, G9, GE, GJ, GO, H4, H9, HE, HJ, HO, I4, I9, IE, IJ, IO, J4, J9, JE, JJ, JO, K4, K9, KE, KJ, KO, L4, L9, LE, LJ, LO, M4, M9, ME, MJ, MO, N4, N9, NE, NJ, NO, O4, O9, OE, OJ, OO, P4, P9, PE, PJ, PO, Q4, Q9, QE, QJ, QO, R4, R9, RE, RJ, RO, S4, S9, SE, SJ, SO, T4, T9, TE, TJ, TO, U4, U9, UE, UJ, UO, V4, V9, VE, VJ, VO, W4, W9, WE, WJ, WO, X4, X9, XE, XJ, XO, Y4, Y9, YE, YJ, YO, Z4, Z9, ZE, ZJ, ZO
Molecule details ›
Chains: A4, A5, A9, AA, AE, AF, AJ, AK, AO, AP, B4, B5, B9, BA, BE, BF, BJ, BK, BO, BP, C4, C5, C9, CA, CE, CF, CJ, CK, CO, CP, D4, D9, DE, DJ, DO, E4, E9, EE, EJ, EO, F4, F9, FE, FJ, FO, G4, G9, GE, GJ, GO, H4, H9, HE, HJ, HO, I4, I9, IE, IJ, IO, J4, J9, JE, JJ, JO, K4, K9, KE, KJ, KO, L4, L9, LE, LJ, LO, M4, M9, ME, MJ, MO, N4, N9, NE, NJ, NO, O4, O9, OE, OJ, OO, P4, P9, PE, PJ, PO, Q4, Q9, QE, QJ, QO, R4, R9, RE, RJ, RO, S4, S9, SE, SJ, SO, T4, T9, TE, TJ, TO, U4, U9, UE, UJ, UO, V4, V9, VE, VJ, VO, W4, W9, WE, WJ, WO, X4, X9, XE, XJ, XO, Y4, Y9, YE, YJ, YO, Z4, Z9, ZE, ZJ, ZO
Length: 385 amino acids
Theoretical weight: 40.89 KDa
Source organism: Rhodobacter capsulatus SB 1003
UniProt:
  • Canonical: D5ATZ3 (Residues: 13-397; Coverage: 97%)
Gene name: RCAP_rcc01687
Sequence domains: Phage capsid family
Uncharacterized protein Chains: A1, A2, A3, A6, A7, A8, AB, AC, AD, AG, AH, AI, AL, AM, AN, B2, B3, B7, B8, BC, BD, BH, BI, BM, BN, C2, C3, C7, C8, CC, CD, CH, CI, CM, CN, D2, D3, D7, D8, DC, DD, DH, DI, DM, DN, E2, E3, E7, E8, EC, ED, EH, EI, EM, EN
Molecule details ›
Chains: A1, A2, A3, A6, A7, A8, AB, AC, AD, AG, AH, AI, AL, AM, AN, B2, B3, B7, B8, BC, BD, BH, BI, BM, BN, C2, C3, C7, C8, CC, CD, CH, CI, CM, CN, D2, D3, D7, D8, DC, DD, DH, DI, DM, DN, E2, E3, E7, E8, EC, ED, EH, EI, EM, EN
Length: 84 amino acids
Theoretical weight: 9.1 KDa
Source organism: Rhodobacter capsulatus SB 1003
UniProt:
  • Canonical: D5AR33 (Residues: 1-84; Coverage: 100%)
Gene name: RCAP_rcc01079
Uncharacterized protein Chains: F2, F3, F7, F8, FC, FD, FH, FI, FM, FN
Molecule details ›
Chains: F2, F3, F7, F8, FC, FD, FH, FI, FM, FN
Length: 325 amino acids
Theoretical weight: 33 KDa
Source organism: Rhodobacter capsulatus SB 1003
UniProt:
  • Canonical: D5AR34 (Residues: 1-325; Coverage: 100%)
Gene name: RCAP_rcc01080
Gene transfer agent protein Chains: 2A, 2B, 2C, 2D, 2E, 2F, 2G, 2H, 2I, 2J, 2K, 2L
Molecule details ›
Chains: 2A, 2B, 2C, 2D, 2E, 2F, 2G, 2H, 2I, 2J, 2K, 2L
Length: 197 amino acids
Theoretical weight: 20.96 KDa
Source organism: Rhodobacter capsulatus SB 1003
UniProt:
  • Canonical: D5ATZ4 (Residues: 1-197; Coverage: 100%)
Gene name: RCAP_rcc01688
Phage portal protein, HK97 family Chains: 1A, 1B, 1C, 1D, 1E, 1F, 1G, 1H, 1I, 1J, 1K, 1L
Molecule details ›
Chains: 1A, 1B, 1C, 1D, 1E, 1F, 1G, 1H, 1I, 1J, 1K, 1L
Length: 396 amino acids
Theoretical weight: 42.85 KDa
Source organism: Rhodobacter capsulatus SB 1003
UniProt:
  • Canonical: D5ATZ0 (Residues: 1-396; Coverage: 100%)
Gene name: RCAP_rcc01684
Sequence domains: Phage portal protein
DUF3168 domain-containing protein Chains: 4A, 4B, 4C, 4D, 4E, 4F
Molecule details ›
Chains: 4A, 4B, 4C, 4D, 4E, 4F
Length: 135 amino acids
Theoretical weight: 13.87 KDa
Source organism: Rhodobacter capsulatus SB 1003
UniProt:
  • Canonical: D5ATZ6 (Residues: 1-135; Coverage: 100%)
Gene name: RCAP_rcc01690
Sequence domains: Protein of unknown function (DUF3168)
Head-tail adaptor protein Chains: 3A, 3B, 3C, 3D, 3E, 3F
Molecule details ›
Chains: 3A, 3B, 3C, 3D, 3E, 3F
Length: 112 amino acids
Theoretical weight: 12.4 KDa
Source organism: Rhodobacter capsulatus SB 1003
UniProt:
  • Canonical: D5ATZ5 (Residues: 1-112; Coverage: 100%)
Gene name: RCAP_rcc01689
Sequence domains: Phage head-tail joining protein
Phage major tail protein, TP901-1 family Chains: 50, 51, 52, 53, 5A, 5B, 5C, 5D, 5E, 5F, 5G, 5H, 5I, 5J, 5K, 5L, 5M, 5N, 5O, 5P, 5Q, 5R, 5S, 5T, 5U, 5V, 5W, 5X, 5Y, 5Z
Molecule details ›
Chains: 50, 51, 52, 53, 5A, 5B, 5C, 5D, 5E, 5F, 5G, 5H, 5I, 5J, 5K, 5L, 5M, 5N, 5O, 5P, 5Q, 5R, 5S, 5T, 5U, 5V, 5W, 5X, 5Y, 5Z
Length: 137 amino acids
Theoretical weight: 14.42 KDa
Source organism: Rhodobacter capsulatus SB 1003
UniProt:
  • Canonical: D5ATZ7 (Residues: 1-137; Coverage: 100%)
Gene name: RCAP_rcc01691
Sequence domains: Phage tail tube protein
DUF2163 domain-containing protein Chains: 7A, 7B, 7C
Molecule details ›
Chains: 7A, 7B, 7C
Length: 296 amino acids
Theoretical weight: 31.69 KDa
Source organism: Rhodobacter capsulatus SB 1003
UniProt:
  • Canonical: D5AU02 (Residues: 1-296; Coverage: 100%)
Gene name: RCAP_rcc01696
Sequence domains:
Host specificity protein Chains: 8A, 8B, 8C
Molecule details ›
Chains: 8A, 8B, 8C
Length: 1304 amino acids
Theoretical weight: 138.53 KDa
Source organism: Rhodobacter capsulatus SB 1003
UniProt:
  • Canonical: D5AU04 (Residues: 1-1304; Coverage: 100%)
Gene name: RCAP_rcc01698
Sequence domains:
DUF2460 domain-containing protein Chains: 6A, 6B, 6C, 6D, 6E, 6F
Molecule details ›
Chains: 6A, 6B, 6C, 6D, 6E, 6F
Length: 210 amino acids
Theoretical weight: 22.99 KDa
Source organism: Rhodobacter capsulatus SB 1003
UniProt:
  • Canonical: D5AU01 (Residues: 1-210; Coverage: 100%)
Gene name: RCAP_rcc01695
Sequence domains: Conserved hypothetical protein 2217 (DUF2460)

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.54Å
Relevant EMDB volumes: EMD-10443