Atomic-level structure of the entire HIV-1 capsid

Experimental Data Snapshot

  • Aggregation State: PARTICLE 
  • Reconstruction Method: TOMOGRAPHY 

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history


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

  • DOI: 10.1038/nature12162
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 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.

    Organizational Affiliation

    Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
capsid protein0, 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, iY, iZ, 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, j0, j1, j2, j3, j4, j5, j6, j7, j8, j9, jA, jB, jC, jD, jE, jF, jG, jH, jI, jJ, jK, jL, jM, jN, jO, jP, jQ, jR, jS, jT, jU, jV, jW, jX, jY, jZ, ja, jb, jc, jd, je, jf, jg, jh, ji, jj, jk, jl, jm, jn, jo, jp, jq, jr, js, jt, ju, jv, jw, jx, jy, jz, k, k0, k1, k2, k3, k4, k5, k6, k7, k8, k9, kA, kB, kC, kD, kE, kF, kG, kH, kI, kJ, kK, kL, kM, kN, kO, kP, kQ, kR, kS, kT, kU, kV, kW, kX, kY, kZ, ka, kb, kc, kd, ke, kf, kg, kh, ki, kj, kk, kl, km, kn, ko, kp, kq, kr, ks, kt, ku, kv, kw, kx, ky, kz, l, l0, l1, l2, l3, l4, l5, l6, l7, l8, l9, lA, lB, lC, lD, lE, lF, lG, lH, lI, lJ, lK, lL, lM, lN, lO, lP, lQ, lR, la, lb, lc, ld, le, lf, lg, lh, li, lj, lk, ll, lm, ln, lo, lp, lq, lr, ls, lt, lu, lv, lw, lx, ly, lz, m, n, o, p, q, r, s, t, u, v, w, x, y, z231Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: gag
Find proteins for Q79791 (Human immunodeficiency virus 1)
Explore Q79791 
Go to UniProtKB:  Q79791
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Aggregation State: PARTICLE 
  • Reconstruction Method: TOMOGRAPHY 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-12
    Changes: Database references
  • Version 1.2: 2014-07-09
    Changes: Other
  • Version 1.3: 2014-12-10
    Changes: Other
  • Version 1.4: 2018-07-18
    Changes: Data collection