3D View: Structure
Global Stoichiometry: Homo 1176-mer - A1176
Total Structure Weight: 30226.13 kDa
Atom Count: 2116800
Residue Count: 271656
PDB format files are not available for large structures. Please use PDBx/mmCIF or PDBML/XML files.
Biological Assembly 1 (CIF Format)
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3J3Y
Atomic-level structure of the entire HIV-1 capsid (186 hexamers + 12 pentamers)
DOI: 10.2210/pdb3J3Y/pdb
Entry: 3J3Y supersedes: 1VUU, 1VUV, 1VUW, 1VUX, 1VUY, 1VUZ, 1VV0, 1VV1, 1VV2, 1VV3, 1VV4, 1VV5, 1VV6, 1VV7, 1VV8, 1VV9, 1VVA, 1VVB, 1VVF, 1VVG, 1VVH, 1VVI
EMDataResource: EMD-5639
Classification: VIRUS
Organism(s): Human immunodeficiency virus 1
Deposition Author(s): Perilla, J.R., Zhao, G., Zhang, P., Schulten, K.J.
Method: ELECTRON MICROSCOPY
Aggregation State: PARTICLE
Reconstruction Method: TOMOGRAPHY
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
Zhao, G., Perilla, J.R., Yufenyuy, E.L., Meng, X., Chen, B., Ning, J., Ahn, J., Gronenborn, A.M., Schulten, K., Aiken, C., Zhang, P.
(2013) Nature 497: 643-646
PubMed: 23719463 Search on PubMedSearch on PubMed Central
3J34, 3J3Y, 3J3Q, 3J4F
Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked ...
Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA.
capsid protein 0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 1A, 1B, 1C, 1D, 1E, 1F, 1G, 1H, 1I, 1J, 1K, 1L, 1M, 1N, 1O, 1P, 1Q, 1R, 1S, 1T, 1U, 1V, 1W, 1X, 1Y, 1Z, 1a, 1b, 1c, 1d, 1e, 1f, 1g, 1h, 1i, 1j, 1k, 1l, 1m, 1n, 1o, 1p, 1q, 1r, 1s, 1t, 1u, 1v, 1w, 1x, 1y, 1z, 2, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 2A, 2B, 2C, 2D, 2E, 2F, 2G, 2H, 2I, 2J, 2K, 2L, 2M, 2N, 2O, 2P, 2Q, 2R, 2S, 2T, 2U, 2V, 2W, 2X, 2Y, 2Z, 2a, 2b, 2c, 2d, 2e, 2f, 2g, 2h, 2i, 2j, 2k, 2l, 2m, 2n, 2o, 2p, 2q, 2r, 2s, 2t, 2u, 2v, 2w, 2x, 2y, 2z, 3, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 3A, 3B, 3C, 3D, 3E, 3F, 3G, 3H, 3I, 3J, 3K, 3L, 3M, 3N, 3O, 3P, 3Q, 3R, 3S, 3T, 3U, 3V, 3W, 3X, 3Y, 3Z, 3a, 3b, 3c, 3d, 3e, 3f, 3g, 3h, 3i, 3j, 3k, 3l, 3m, 3n, 3o, 3p, 3q, 3r, 3s, 3t, 3u, 3v, 3w, 3x, 3y, 3z, 4, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 4A, 4B, 4C, 4D, 4E, 4F, 4G, 4H, 4I, 4J, 4K, 4L, 4M, 4N, 4O, 4P, 4Q, 4R, 4S, 4T, 4U, 4V, 4W, 4X, 4Y, 4Z, 4a, 4b, 4c, 4d, 4e, 4f, 4g, 4h, 4i, 4j, 4k, 4l, 4m, 4n, 4o, 4p, 4q, 4r, 4s, 4t, 4u, 4v, 4w, 4x, 4y, 4z, 5, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 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, 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, 6, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 6A, 6B, 6C, 6D, 6E, 6F, 6G, 6H, 6I, 6J, 6K, 6L, 6M, 6N, 6O, 6P, 6Q, 6R, 6S, 6T, 6U, 6V, 6W, 6X, 6Y, 6Z, 6a, 6b, 6c, 6d, 6e, 6f, 6g, 6h, 6i, 6j, 6k, 6l, 6m, 6n, 6o, 6p, 6q, 6r, 6s, 6t, 6u, 6v, 6w, 6x, 6y, 6z, 7, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 7A, 7B, 7C, 7D, 7E, 7F, 7G, 7H, 7I, 7J, 7K, 7L, 7M, 7N, 7O, 7P, 7Q, 7R, 7S, 7T, 7U, 7V, 7W, 7X, 7Y, 7Z, 7a, 7b, 7c, 7d, 7e, 7f, 7g, 7h, 7i, 7j, 7k, 7l, 7m, 7n, 7o, 7p, 7q, 7r, 7s, 7t, 7u, 7v, 7w, 7x, 7y, 7z, 8, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 8A, 8B, 8C, 8D, 8E, 8F, 8G, 8H, 8I, 8J, 8K, 8L, 8M, 8N, 8O, 8P, 8Q, 8R, 8S, 8T, 8U, 8V, 8W, 8X, 8Y, 8Z, 8a, 8b, 8c, 8d, 8e, 8f, 8g, 8h, 8i, 8j, 8k, 8l, 8m, 8n, 8o, 8p, 8q, 8r, 8s, 8t, 8u, 8v, 8w, 8x, 8y, 8z, 9, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 9A, 9B, 9C, 9D, 9E, 9F, 9G, 9H, 9I, 9J, 9K, 9L, 9M, 9N, 9O, 9P, 9Q, 9R, 9S, 9T, 9U, 9V, 9W, 9X, 9Y, 9Z, 9a, 9b, 9c, 9d, 9e, 9f, 9g, 9h, 9i, 9j, 9k, 9l, 9m, 9n, 9o, 9p, 9q, 9r, 9s, 9t, 9u, 9v, 9w, 9x, 9y, 9z, 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, a0, a1, a2, a3, a4, a5, a6, a7, a8, a9, aA, aB, aC, aD, aE, aF, aG, aH, aI, aJ, aK, aL, aM, aN, aO, aP, aQ, aR, aS, aT, aU, aV, aW, aX, aY, aZ, aa, ab, ac, ad, ae, af, ag, ah, ai, aj, ak, al, am, an, ao, ap, aq, ar, as, at, au, av, aw, ax, ay, az, b, b0, b1, b2, b3, b4, b5, b6, b7, b8, b9, bA, bB, bC, bD, bE, bF, bG, bH, bI, bJ, bK, bL, bM, bN, bO, bP, bQ, bR, bS, bT, bU, bV, bW, bX, bY, bZ, ba, bb, bc, bd, be, bf, bg, bh, bi, bj, bk, bl, bm, bn, bo, bp, bq, br, bs, bt, bu, bv, bw, bx, by, bz, c, c0, c1, c2, c3, c4, c5, c6, c7, c8, c9, cA, cB, cC, cD, cE, cF, cG, cH, cI, cJ, cK, cL, cM, cN, cO, cP, cQ, cR, cS, cT, cU, cV, cW, cX, cY, cZ, ca, cb, cc, cd, ce, cf, cg, ch, ci, cj, ck, cl, cm, cn, co, cp, cq, cr, cs, ct, cu, cv, cw, cx, cy, cz, d, d0, d1, d2, d3, d4, d5, d6, d7, d8, d9, dA, dB, dC, dD, dE, dF, dG, dH, dI, dJ, dK, dL, dM, dN, dO, dP, dQ, dR, dS, dT, dU, dV, dW, dX, dY, dZ, da, db, dc, dd, de, df, dg, dh, di, dj, dk, dl, dm, dn, do, dp, dq, dr, ds, dt, du, dv, dw, dx, dy, dz, e, e0, e1, e2, e3, e4, e5, e6, e7, e8, e9, eA, eB, eC, eD, eE, eF, eG, eH, eI, eJ, eK, eL, eM, eN, eO, eP, eQ, eR, eS, eT, eU, eV, eW, eX, eY, eZ, ea, eb, ec, ed, ee, ef, eg, eh, ei, ej, ek, el, em, en, eo, ep, eq, er, es, et, eu, ev, ew, ex, ey, ez, f, f0, f1, f2, f3, f4, f5, f6, f7, f8, f9, fA, fB, fC, fD, fE, fF, fG, fH, fI, fJ, fK, fL, fM, fN, fO, fP, fQ, fR, fS, fT, fU, fV, fW, fX, fY, fZ, fa, fb, fc, fd, fe, ff, fg, fh, fi, fj, fk, fl, fm, fn, fo, fp, fq, fr, fs, ft, fu, fv, fw, fx, fy, fz, g, g0, g1, g2, g3, g4, g5, g6, g7, g8, g9, gA, gB, gC, gD, gE, gF, gG, gH, gI, gJ, gK, gL, gM, gN, gO, gP, gQ, gR, gS, gT, gU, gV, gW, gX, gY, gZ, ga, gb, gc, gd, ge, gf, gg, gh, gi, gj, gk, gl, gm, gn, go, gp, gq, gr, gs, gt, gu, gv, gw, gx, gy, gz, h, h0, h1, h2, h3, h4, h5, h6, h7, h8, h9, hA, hB, hC, hD, hE, hF, hG, hH, hI, hJ, hK, hL, hM, hN, hO, hP, hQ, hR, hS, hT, hU, hV, hW, hX, hY, hZ, ha, hb, hc, hd, he, hf, hg, hh, hi, hj, hk, hl, hm, hn, ho, hp, hq, hr, hs, ht, hu, hv, hw, hx, hy, hz, i, i0, i1, i2, i3, i4, i5, i6, i7, i8, i9, iA, iB, iC, iD, iE, iF, iG, iH, iI, iJ, iK, iL, iM, iN, iO, iP, iQ, iR, iS, iT, iU, iV, iW, iX, ia, ib, ic, id, ie, if, ig, ih, ii, ij, ik, il, im, in, io, ip, iq, ir, is, it, iu, iv, iw, ix, iy, iz, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z 231 Human immunodeficiency virus 1 Mutation(s): 1
Gene Names: gag
Find proteins for Q79791 (Human immunodeficiency virus 1)
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Go to UniProtKB: Q79791
This entry supersedes: 1VUU, 1VUV, 1VUW, 1VUX, 1VUY, 1VUZ, 1VV0, 1VV1, 1VV2, 1VV3, 1VV4, 1VV5, 1VV6, 1VV7, 1VV8, 1VV9, 1VVA, 1VVB, 1VVF, 1VVG, 1VVH, 1VVI
Changes: Other
Changes: Data collection