9FO3: PDB entry 9FO3

Structure of a gp140 SpyTag-SpyCatcher mi3 nanoparticle including mi3 density only. Determined by electron microscopy at 5.3 Å resolution. Released 9 Oct 2024.

Method
Electron microscopy
Resolution
5.3 Å
Organism
Thermotoga maritima
Chains
60
Atoms
92,520
Mol. weight
2033.69 kDa
Released
9 Oct 2024

Explore 9FO3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FO3 contains 660 α-helices and 600 β-strands across 60 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains 0, 1, 2, 3, 5, 6, A, b, B, c, C, D, E, F, g, h, H, i, I, J, k, K, l, L, n, N, o, O, P, q, Q, r, R, s, t, T, u, U, v, W, X, y, Y, z and Z: 11 helices, 10 β-strands

ElementResiduesLengthSheet
α-helix116-1238
β-strand125-12955
α-helix134-14613
β-strand151-15555
α-helix161-1677
α-helix170-1734
β-strand177-18155
α-helix186-1949
β-strand199-20135
α-helix207-21610
β-strand219-22135
β-strand223-22426
α-helix227-2359
β-strand240-24346
α-helix246-25813
β-strand265-26846
β-strand26915
α-helix277-2837
β-strand288-29035
α-helix292-2954
α-helix299-31719
Chains 4, 7, a, d, e, f, G, j, m, M, p, S, V, w and x: 11 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix116-1238
β-strand125-129529
α-helix134-14613
β-strand151-155529
α-helix161-1677
α-helix170-1734
β-strand177-181529
α-helix186-1949
β-strand199-201329
α-helix207-21610
β-strand219-221329
β-strand223-224230
α-helix227-2359
β-strand240-243430
α-helix246-25712
β-strand265-268430
β-strand269129
α-helix277-2837
β-strand288-290329
α-helix292-2954
α-helix299-31719

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
CAP255 gp140 SpyTag-SpyCatcher mi3,2-dehydro-3-deoxyphosphogluconate…0, 1, 2, 3, 4, 5, 6, 7, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, zprotein318Thermotoga maritimaQ9WXS1 (AlphaFold model)
Sequence of entity 1 (0, 1, 2, 3, 4, 5, 6, 7, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z), FASTA
>9FO3_1 CAP255 gp140 SpyTag-SpyCatcher mi3,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (chains 0, 1, 2, 3, 4, 5, 6, 7, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z)
HHHHHHGSGDSATHIKFSKRDEDGKELAGATMELRDSSGKTISTWISDGQVKDFYLYPGK
YTFVETAAPDGYEVATAITFTVNEQGQVTVNGKATKGDAHIGGSGGSGGSGGSMKMEELF
KKHKIVAVLRANSVEEAKKKALAVFLGGVHLIEITFTVPDADTVIKELSFLKEMGAIIGA
GTVTSVEQARKAVESGAEFIVSPHLDEEISQFAKEKGVFYMPGVMTPTELVKAMKLGHTI
LKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPV
EVAEKAKAFVEKIRGCTE

Primary citation

Development of a Two-Component Nanoparticle Vaccine Displaying an HIV-1 Envelope Glycoprotein that Elicits Tier 2 Neutralising Antibodies. Malebo, K., Woodward, J., Ximba, P. et al. Vaccines (Basel) (2024) 12. DOI 10.3390/vaccines12091063 · PubMed

Other PDB entries of the same protein (UniProt Q9WXS1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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