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- PDB-3j3q: Atomic-level structure of the entire HIV-1 capsid -

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Basic information

Entry
Database: PDB / ID: 3j3q
TitleAtomic-level structure of the entire HIV-1 capsid
Componentscapsid proteinCapsid
KeywordsVIRUS / HIV-1 capsid / core / all-atom model / complete capsid
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein ...Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodELECTRON MICROSCOPY / electron tomography / cryo EM
AuthorsPerilla, J.R. / Zhao, G. / Zhang, P. / Schulten, K.J.
CitationJournal: Nature / Year: 2013
Title: Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
Authors: Gongpu Zhao / Juan R Perilla / Ernest L Yufenyuy / Xin Meng / Bo Chen / Jiying Ning / Jinwoo Ahn / Angela M Gronenborn / Klaus Schulten / Christopher Aiken / Peijun Zhang /
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, ...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.
History
DepositionApr 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jul 9, 2014Group: Other
SupersessionDec 10, 2014ID: 1VU4, 1VU5, 1VU6, 1VU7, 1VU8, 1VU9, 1VUA, 1VUC, 1VUD, 1VUE, 1VUF, 1VUG, 1VUH, 1VUI, 1VUJ, 1VUK, 1VUL, 1VUM, 1VUN, 1VUO, 1VUP, 1VUQ, 1VUR, 1VUS, 1VUT
Revision 1.3Dec 10, 2014Group: Other
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
g8: capsid protein
g9: capsid protein
ga: capsid protein
gb: capsid protein
gc: capsid protein
gd: capsid protein
ge: capsid protein
gf: capsid protein
gg: capsid protein
gh: capsid protein
1C: capsid protein
gi: capsid protein
gj: capsid protein
gk: capsid protein
gl: capsid protein
gm: capsid protein
gn: capsid protein
go: capsid protein
gp: capsid protein
gq: capsid protein
gr: capsid protein
1D: capsid protein
gs: capsid protein
gt: capsid protein
gu: capsid protein
gv: capsid protein
gw: capsid protein
gx: capsid protein
gy: capsid protein
gz: capsid protein
gA: capsid protein
gB: capsid protein
1E: capsid protein
gC: capsid protein
gD: capsid protein
gE: capsid protein
gF: capsid protein
gG: capsid protein
gH: capsid protein
gI: capsid protein
gJ: capsid protein
gK: capsid protein
gL: capsid protein
1F: capsid protein
gM: capsid protein
gN: capsid protein
gO: capsid protein
gP: capsid protein
gQ: capsid protein
gR: capsid protein
gS: capsid protein
gT: capsid protein
gU: capsid protein
gV: capsid protein
1G: capsid protein
gW: capsid protein
gX: capsid protein
gY: capsid protein
gZ: capsid protein
h0: capsid protein
h1: capsid protein
h2: capsid protein
h3: capsid protein
h4: capsid protein
h5: capsid protein
1H: capsid protein
h6: capsid protein
h7: capsid protein
h8: capsid protein
h9: capsid protein
ha: capsid protein
hb: capsid protein
hc: capsid protein
hd: capsid protein
he: capsid protein
hf: capsid protein
1I: capsid protein
hg: capsid protein
hh: capsid protein
hi: capsid protein
hj: capsid protein
hk: capsid protein
hl: capsid protein
hm: capsid protein
hn: capsid protein
ho: capsid protein
hp: capsid protein
1J: capsid protein
hq: capsid protein
hr: capsid protein
hs: capsid protein
ht: capsid protein
hu: capsid protein
hv: capsid protein
hw: capsid protein
hx: capsid protein
hy: capsid protein
hz: capsid protein
1K: capsid protein
hA: capsid protein
hB: capsid protein
hC: capsid protein
hD: capsid protein
hE: capsid protein
hF: capsid protein
hG: capsid protein
hH: capsid protein
hI: capsid protein
hJ: capsid protein
1L: capsid protein
hK: capsid protein
hL: capsid protein
hM: capsid protein
hN: capsid protein
hO: capsid protein
hP: capsid protein
hQ: capsid protein
hR: capsid protein
hS: capsid protein
hT: capsid protein
1M: capsid protein
hU: capsid protein
hV: capsid protein
hW: capsid protein
hX: capsid protein
hY: capsid protein
hZ: capsid protein
i0: capsid protein
i1: capsid protein
i2: capsid protein
i3: capsid protein
1N: capsid protein
i4: capsid protein
i5: capsid protein
i6: capsid protein
i7: capsid protein
i8: capsid protein
i9: capsid protein
ia: capsid protein
ib: capsid protein
ic: capsid protein
id: capsid protein
1O: capsid protein
ie: capsid protein
if: capsid protein
ig: capsid protein
ih: capsid protein
ii: capsid protein
ij: capsid protein
ik: capsid protein
il: capsid protein
im: capsid protein
in: capsid protein
1P: capsid protein
io: capsid protein
ip: capsid protein
iq: capsid protein
ir: capsid protein
is: capsid protein
it: capsid protein
iu: capsid protein
iv: capsid protein
iw: capsid protein
ix: capsid protein
1Q: capsid protein
iy: capsid protein
iz: capsid protein
iA: capsid protein
iB: capsid protein
iC: capsid protein
iD: capsid protein
iE: capsid protein
iF: capsid protein
iG: capsid protein
iH: capsid protein
1R: capsid protein
iI: capsid protein
iJ: capsid protein
iK: capsid protein
iL: capsid protein
iM: capsid protein
iN: capsid protein
iO: capsid protein
iP: capsid protein
iQ: capsid protein
iR: capsid protein
1S: capsid protein
iS: capsid protein
iT: capsid protein
iU: capsid protein
iV: capsid protein
iW: capsid protein
iX: capsid protein
iY: capsid protein
iZ: capsid protein
j0: capsid protein
j1: capsid protein
1T: capsid protein
j2: capsid protein
j3: capsid protein
j4: capsid protein
j5: capsid protein
j6: capsid protein
j7: capsid protein
j8: capsid protein
j9: capsid protein
ja: capsid protein
jb: capsid protein
1U: capsid protein
jc: capsid protein
jd: capsid protein
je: capsid protein
jf: capsid protein
jg: capsid protein
jh: capsid protein
ji: capsid protein
jj: capsid protein
jk: capsid protein
jl: capsid protein
1V: capsid protein
jm: capsid protein
jn: capsid protein
jo: capsid protein
jp: capsid protein
jq: capsid protein
jr: capsid protein
js: capsid protein
jt: capsid protein
ju: capsid protein
jv: capsid protein
1W: capsid protein
jw: capsid protein
jx: capsid protein
jy: capsid protein
jz: capsid protein
jA: capsid protein
jB: capsid protein
jC: capsid protein
jD: capsid protein
jE: capsid protein
jF: capsid protein
1X: capsid protein
jG: capsid protein
jH: capsid protein
jI: capsid protein
jJ: capsid protein
jK: capsid protein
jL: capsid protein
jM: capsid protein
jN: capsid protein
jO: capsid protein
jP: capsid protein
1Y: capsid protein
jQ: capsid protein
jR: capsid protein
jS: capsid protein
jT: capsid protein
jU: capsid protein
jV: capsid protein
jW: capsid protein
jX: capsid protein
jY: capsid protein
jZ: capsid protein
1Z: capsid protein
k0: capsid protein
k1: capsid protein
k2: capsid protein
k3: capsid protein
k4: capsid protein
k5: capsid protein
k6: capsid protein
k7: capsid protein
k8: capsid protein
k9: capsid protein
20: capsid protein
ka: capsid protein
kb: capsid protein
kc: capsid protein
kd: capsid protein
ke: capsid protein
kf: capsid protein
kg: capsid protein
kh: capsid protein
ki: capsid protein
kj: capsid protein
21: capsid protein
kk: capsid protein
kl: capsid protein
km: capsid protein
kn: capsid protein
ko: capsid protein
kp: capsid protein
kq: capsid protein
kr: capsid protein
ks: capsid protein
kt: capsid protein
22: capsid protein
ku: capsid protein
kv: capsid protein
kw: capsid protein
kx: capsid protein
ky: capsid protein
kz: capsid protein
kA: capsid protein
kB: capsid protein
kC: capsid protein
kD: capsid protein
23: capsid protein
kE: capsid protein
kF: capsid protein
kG: capsid protein
kH: capsid protein
kI: capsid protein
kJ: capsid protein
kK: capsid protein
kL: capsid protein
kM: capsid protein
kN: capsid protein
24: capsid protein
kO: capsid protein
kP: capsid protein
kQ: capsid protein
kR: capsid protein
kS: capsid protein
kT: capsid protein
kU: capsid protein
kV: capsid protein
kW: capsid protein
kX: capsid protein
25: capsid protein
kY: capsid protein
kZ: capsid protein
l0: capsid protein
l1: capsid protein
l2: capsid protein
l3: capsid protein
l4: capsid protein
l5: capsid protein
l6: capsid protein
l7: capsid protein
26: capsid protein
l8: capsid protein
l9: capsid protein
la: capsid protein
lb: capsid protein
lc: capsid protein
ld: capsid protein
le: capsid protein
lf: capsid protein
lg: capsid protein
lh: capsid protein
27: capsid protein
li: capsid protein
lj: capsid protein
lk: capsid protein
ll: capsid protein
lm: capsid protein
ln: capsid protein
lo: capsid protein
lp: capsid protein
lq: capsid protein
lr: capsid protein
28: capsid protein
ls: capsid protein
lt: capsid protein
lu: capsid protein
lv: capsid protein
lw: capsid protein
lx: capsid protein
ly: capsid protein
lz: capsid protein
lA: capsid protein
lB: capsid protein
29: capsid protein
lC: capsid protein
lD: capsid protein
lE: capsid protein
lF: capsid protein
lG: capsid protein
lH: capsid protein
lI: capsid protein
lJ: capsid protein
lK: capsid protein
lL: capsid protein
2a: capsid protein
lM: capsid protein
lN: capsid protein
lO: capsid protein
lP: capsid protein
lQ: capsid protein
lR: capsid protein
2b: capsid protein
2c: capsid protein
2d: capsid protein
2e: capsid protein
2f: capsid protein
2g: capsid protein
2h: capsid protein
2i: capsid protein
2j: capsid protein
2k: capsid protein
2l: capsid protein
2m: capsid protein
2n: capsid protein
2o: capsid protein
2p: capsid protein
2q: capsid protein
2r: capsid protein
2s: capsid protein
2t: capsid protein
2u: capsid protein
2v: capsid protein
2w: capsid protein
2x: capsid protein
2y: capsid protein
2z: capsid protein
2A: capsid protein
2B: capsid protein
2C: capsid protein
2D: capsid protein
2E: capsid protein
2F: capsid protein
2G: capsid protein
2H: capsid protein
2I: capsid protein
2J: capsid protein
2K: capsid protein
2L: capsid protein
2M: capsid protein
2N: capsid protein
2O: capsid protein
2P: capsid protein
2Q: capsid protein
2R: capsid protein
2S: capsid protein
2T: capsid protein
2U: capsid protein
2V: capsid protein
2W: capsid protein
2X: capsid protein
2Y: capsid protein
2Z: capsid protein
30: capsid protein
31: capsid protein
32: capsid protein
33: capsid protein
34: capsid protein
35: capsid protein
36: capsid protein
37: capsid protein
38: capsid protein
39: capsid protein
3a: capsid protein
3b: capsid protein
3c: capsid protein
3d: capsid protein
3e: capsid protein
3f: capsid protein
3g: capsid protein
3h: capsid protein
3i: capsid protein
3j: capsid protein
3k: capsid protein
3l: capsid protein
3m: capsid protein
3n: capsid protein
3o: capsid protein
3p: capsid protein
3q: capsid protein
3r: capsid protein
3s: capsid protein
3t: capsid protein
3u: capsid protein
3v: capsid protein
3w: capsid protein
3x: capsid protein
3y: capsid protein
3z: capsid protein
3A: capsid protein
3B: capsid protein
3C: capsid protein
3D: capsid protein
3E: capsid protein
3F: capsid protein
3G: capsid protein
3H: capsid protein
3I: capsid protein
3J: capsid protein
3K: capsid protein
3L: capsid protein
3M: capsid protein
3N: capsid protein
3O: capsid protein
3P: capsid protein
3Q: capsid protein
3R: capsid protein
3S: capsid protein
3T: capsid protein
3U: capsid protein
3V: capsid protein
3W: capsid protein
3X: capsid protein
3Y: capsid protein
3Z: capsid protein
40: capsid protein
41: capsid protein
42: capsid protein
43: capsid protein
44: capsid protein
45: capsid protein
46: capsid protein
47: capsid protein
48: capsid protein
49: capsid protein
4a: capsid protein
4b: capsid protein
4c: capsid protein
4d: capsid protein
4e: capsid protein
4f: capsid protein
4g: capsid protein
4h: capsid protein
4i: capsid protein
4j: capsid protein
4k: capsid protein
4l: capsid protein
4m: capsid protein
4n: capsid protein
4o: capsid protein
4p: capsid protein
4q: capsid protein
4r: capsid protein
4s: capsid protein
4t: capsid protein
4u: capsid protein
4v: capsid protein
4w: capsid protein
4x: capsid protein
4y: capsid protein
4z: capsid protein
4A: capsid protein
4B: capsid protein
4C: capsid protein
4D: capsid protein
4E: capsid protein
4F: capsid protein
4G: capsid protein
4H: capsid protein
4I: capsid protein
4J: capsid protein
4K: capsid protein
4L: capsid protein
4M: capsid protein
4N: capsid protein
4O: capsid protein
4P: capsid protein
4Q: capsid protein
4R: capsid protein
4S: capsid protein
4T: capsid protein
4U: capsid protein
4V: capsid protein
4W: capsid protein
4X: capsid protein
4Y: capsid protein
4Z: capsid protein
50: capsid protein
51: capsid protein
52: capsid protein
53: capsid protein
54: capsid protein
55: capsid protein
56: capsid protein
57: capsid protein
58: capsid protein
59: capsid protein
5a: capsid protein
5b: capsid protein
5c: capsid protein
5d: capsid protein
5e: capsid protein
5f: capsid protein
5g: capsid protein
5h: capsid protein
5i: capsid protein
5j: capsid protein
5k: capsid protein
5l: capsid protein
5m: capsid protein
5n: capsid protein
5o: capsid protein
5p: capsid protein
5q: capsid protein
5r: capsid protein
5s: capsid protein
5t: capsid protein
5u: capsid protein
5v: capsid protein
5w: capsid protein
5x: capsid protein
5y: capsid protein
5z: capsid protein
5A: capsid protein
5B: capsid protein
5C: capsid protein
5D: capsid protein
5E: capsid protein
5F: capsid protein
5G: capsid protein
5H: capsid protein
5I: capsid protein
5J: capsid protein
5K: capsid protein
5L: capsid protein
5M: capsid protein
5N: capsid protein
5O: capsid protein
5P: capsid protein
5Q: capsid protein
5R: capsid protein
5S: capsid protein
5T: capsid protein
5U: capsid protein
5V: capsid protein
5W: capsid protein
5X: capsid protein
5Y: capsid protein
5Z: capsid protein
60: capsid protein
61: capsid protein
62: capsid protein
63: capsid protein
64: capsid protein
65: capsid protein
66: capsid protein
67: capsid protein
68: capsid protein
69: capsid protein
6a: capsid protein
6b: capsid protein
6c: capsid protein
6d: capsid protein
6e: capsid protein
6f: capsid protein
6g: capsid protein
6h: capsid protein
6i: capsid protein
6j: capsid protein
6k: capsid protein
6l: capsid protein
6m: capsid protein
6n: capsid protein
6o: capsid protein
6p: capsid protein
6q: capsid protein
6r: capsid protein
6s: capsid protein
6t: capsid protein
6u: capsid protein
6v: capsid protein
6w: capsid protein
6x: capsid protein
6y: capsid protein
6z: capsid protein
6A: capsid protein
6B: capsid protein
6C: capsid protein
6D: capsid protein
6E: capsid protein
6F: capsid protein
6G: capsid protein
6H: capsid protein
6I: capsid protein
6J: capsid protein
6K: capsid protein
6L: capsid protein
6M: capsid protein
6N: capsid protein
6O: capsid protein
6P: capsid protein
6Q: capsid protein
6R: capsid protein
6S: capsid protein
6T: capsid protein
6U: capsid protein
6V: capsid protein
6W: capsid protein
6X: capsid protein
6Y: capsid protein
6Z: capsid protein
70: capsid protein
71: capsid protein
72: capsid protein
73: capsid protein
74: capsid protein
75: capsid protein
76: capsid protein
77: capsid protein
78: capsid protein
79: capsid protein
7a: capsid protein
7b: capsid protein
7c: capsid protein
7d: capsid protein
7e: capsid protein
7f: capsid protein
7g: capsid protein
7h: capsid protein
7i: capsid protein
7j: capsid protein
7k: capsid protein
7l: capsid protein
7m: capsid protein
7n: capsid protein
7o: capsid protein
7p: capsid protein
7q: capsid protein
7r: capsid protein
7s: capsid protein
7t: capsid protein
7u: capsid protein
7v: capsid protein
7w: capsid protein
7x: capsid protein
7y: capsid protein
7z: capsid protein
7A: capsid protein
7B: capsid protein
7C: capsid protein
7D: capsid protein
7E: capsid protein
7F: capsid protein
7G: capsid protein
7H: capsid protein
7I: capsid protein
7J: capsid protein
7K: capsid protein
7L: capsid protein
7M: capsid protein
7N: capsid protein
7O: capsid protein
7P: capsid protein
7Q: capsid protein
7R: capsid protein
7S: capsid protein
7T: capsid protein
7U: capsid protein
7V: capsid protein
7W: capsid protein
7X: capsid protein
7Y: capsid protein
7Z: capsid protein
80: capsid protein
81: capsid protein
82: capsid protein
83: capsid protein
84: capsid protein
85: capsid protein
86: capsid protein
87: capsid protein
88: capsid protein
89: capsid protein
8a: capsid protein
8b: capsid protein
8c: capsid protein
8d: capsid protein
8e: capsid protein
8f: capsid protein
8g: capsid protein
8h: capsid protein
8i: capsid protein
8j: capsid protein
8k: capsid protein
8l: capsid protein
8m: capsid protein
8n: capsid protein
8o: capsid protein
8p: capsid protein
8q: capsid protein
8r: capsid protein
8s: capsid protein
8t: capsid protein
8u: capsid protein
8v: capsid protein
8w: capsid protein
8x: capsid protein
8y: capsid protein
8z: capsid protein
8A: capsid protein
8B: capsid protein
8C: capsid protein
8D: capsid protein
8E: capsid protein
8F: capsid protein
8G: capsid protein
8H: capsid protein
8I: capsid protein
8J: capsid protein
8K: capsid protein
8L: capsid protein
8M: capsid protein
8N: capsid protein
8O: capsid protein
8P: capsid protein
8Q: capsid protein
8R: capsid protein
8S: capsid protein
8T: capsid protein
8U: capsid protein
8V: capsid protein
8W: capsid protein
8X: capsid protein
8Y: capsid protein
8Z: capsid protein
90: capsid protein
91: capsid protein
92: capsid protein
93: capsid protein
94: capsid protein
95: capsid protein
96: capsid protein
97: capsid protein
98: capsid protein
99: capsid protein
9a: capsid protein
9b: capsid protein
9c: capsid protein
9d: capsid protein
9e: capsid protein
9f: capsid protein
9g: capsid protein
9h: capsid protein
9i: capsid protein
9j: capsid protein
9k: capsid protein
9l: capsid protein
9m: capsid protein
9n: capsid protein
9o: capsid protein
9p: capsid protein
9q: capsid protein
9r: capsid protein
9s: capsid protein
9t: capsid protein
9u: capsid protein
9v: capsid protein
9w: capsid protein
9x: capsid protein
9y: capsid protein
9z: capsid protein
9A: capsid protein
9B: capsid protein
9C: capsid protein
9D: capsid protein
9E: capsid protein
9F: capsid protein
9G: capsid protein
9H: capsid protein
9I: capsid protein
9J: capsid protein
9K: capsid protein
9L: capsid protein
9M: capsid protein
9N: capsid protein
9O: capsid protein
9P: capsid protein
Y: capsid protein
9Q: capsid protein
9R: capsid protein
9S: capsid protein
9T: capsid protein
9U: capsid protein
9V: capsid protein
9W: capsid protein
9X: capsid protein
9Y: capsid protein
9Z: capsid protein
Z: capsid protein
a0: capsid protein
a1: capsid protein
a2: capsid protein
a3: capsid protein
a4: capsid protein
a5: capsid protein
a6: capsid protein
a7: capsid protein
a8: capsid protein
a9: capsid protein
10: capsid protein
aa: capsid protein
ab: capsid protein
ac: capsid protein
ad: capsid protein
ae: capsid protein
af: capsid protein
ag: capsid protein
ah: capsid protein
ai: capsid protein
aj: capsid protein
11: capsid protein
ak: capsid protein
al: capsid protein
am: capsid protein
an: capsid protein
ao: capsid protein
ap: capsid protein
aq: capsid protein
ar: capsid protein
as: capsid protein
at: capsid protein
12: capsid protein
au: capsid protein
av: capsid protein
aw: capsid protein
ax: capsid protein
ay: capsid protein
az: capsid protein
aA: capsid protein
aB: capsid protein
aC: capsid protein
aD: capsid protein
13: capsid protein
aE: capsid protein
aF: capsid protein
aG: capsid protein
aH: capsid protein
aI: capsid protein
aJ: capsid protein
aK: capsid protein
aL: capsid protein
aM: capsid protein
aN: capsid protein
14: capsid protein
aO: capsid protein
aP: capsid protein
aQ: capsid protein
aR: capsid protein
aS: capsid protein
aT: capsid protein
aU: capsid protein
aV: capsid protein
aW: capsid protein
aX: capsid protein
15: capsid protein
aY: capsid protein
aZ: capsid protein
b0: capsid protein
b1: capsid protein
b2: capsid protein
b3: capsid protein
b4: capsid protein
b5: capsid protein
b6: capsid protein
b7: capsid protein
16: capsid protein
b8: capsid protein
b9: capsid protein
ba: capsid protein
bb: capsid protein
bc: capsid protein
bd: capsid protein
be: capsid protein
bf: capsid protein
bg: capsid protein
bh: capsid protein
17: capsid protein
bi: capsid protein
bj: capsid protein
bk: capsid protein
bl: capsid protein
bm: capsid protein
bn: capsid protein
bo: capsid protein
bp: capsid protein
bq: capsid protein
br: capsid protein
18: capsid protein
bs: capsid protein
bt: capsid protein
bu: capsid protein
bv: capsid protein
bw: capsid protein
bx: capsid protein
by: capsid protein
bz: capsid protein
bA: capsid protein
bB: capsid protein
19: capsid protein
bC: capsid protein
bD: capsid protein
bE: capsid protein
bF: capsid protein
bG: capsid protein
bH: capsid protein
bI: capsid protein
bJ: capsid protein
bK: capsid protein
bL: capsid protein
1a: capsid protein
bM: capsid protein
bN: capsid protein
bO: capsid protein
bP: capsid protein
bQ: capsid protein
bR: capsid protein
bS: capsid protein
bT: capsid protein
bU: capsid protein
bV: capsid protein
1b: capsid protein
bW: capsid protein
bX: capsid protein
bY: capsid protein
bZ: capsid protein
c0: capsid protein
c1: capsid protein
c2: capsid protein
c3: capsid protein
c4: capsid protein
c5: capsid protein
1c: capsid protein
c6: capsid protein
c7: capsid protein
c8: capsid protein
c9: capsid protein
ca: capsid protein
cb: capsid protein
cc: capsid protein
cd: capsid protein
ce: capsid protein
cf: capsid protein
1d: capsid protein
cg: capsid protein
ch: capsid protein
ci: capsid protein
cj: capsid protein
ck: capsid protein
cl: capsid protein
cm: capsid protein
cn: capsid protein
co: capsid protein
cp: capsid protein
1e: capsid protein
cq: capsid protein
cr: capsid protein
cs: capsid protein
ct: capsid protein
cu: capsid protein
cv: capsid protein
cw: capsid protein
cx: capsid protein
cy: capsid protein
cz: capsid protein
1f: capsid protein
cA: capsid protein
cB: capsid protein
cC: capsid protein
cD: capsid protein
cE: capsid protein
cF: capsid protein
cG: capsid protein
cH: capsid protein
cI: capsid protein
cJ: capsid protein
1g: capsid protein
cK: capsid protein
cL: capsid protein
cM: capsid protein
cN: capsid protein
cO: capsid protein
cP: capsid protein
cQ: capsid protein
cR: capsid protein
cS: capsid protein
cT: capsid protein
1h: capsid protein
cU: capsid protein
cV: capsid protein
cW: capsid protein
cX: capsid protein
cY: capsid protein
cZ: capsid protein
d0: capsid protein
d1: capsid protein
d2: capsid protein
d3: capsid protein
1i: capsid protein
d4: capsid protein
d5: capsid protein
d6: capsid protein
d7: capsid protein
d8: capsid protein
d9: capsid protein
da: capsid protein
db: capsid protein
dc: capsid protein
dd: capsid protein
1j: capsid protein
de: capsid protein
df: capsid protein
dg: capsid protein
dh: capsid protein
di: capsid protein
dj: capsid protein
dk: capsid protein
dl: capsid protein
dm: capsid protein
dn: capsid protein
1k: capsid protein
do: capsid protein
dp: capsid protein
dq: capsid protein
dr: capsid protein
ds: capsid protein
dt: capsid protein
du: capsid protein
dv: capsid protein
dw: capsid protein
dx: capsid protein
1l: capsid protein
dy: capsid protein
dz: capsid protein
dA: capsid protein
dB: capsid protein
dC: capsid protein
dD: capsid protein
dE: capsid protein
dF: capsid protein
dG: capsid protein
dH: capsid protein
1m: capsid protein
dI: capsid protein
dJ: capsid protein
dK: capsid protein
dL: capsid protein
dM: capsid protein
dN: capsid protein
dO: capsid protein
dP: capsid protein
dQ: capsid protein
dR: capsid protein
1n: capsid protein
dS: capsid protein
dT: capsid protein
dU: capsid protein
dV: capsid protein
dW: capsid protein
dX: capsid protein
dY: capsid protein
dZ: capsid protein
e0: capsid protein
e1: capsid protein
1o: capsid protein
e2: capsid protein
e3: capsid protein
e4: capsid protein
e5: capsid protein
e6: capsid protein
e7: capsid protein
e8: capsid protein
e9: capsid protein
ea: capsid protein
eb: capsid protein
1p: capsid protein
ec: capsid protein
ed: capsid protein
ee: capsid protein
ef: capsid protein
eg: capsid protein
eh: capsid protein
ei: capsid protein
ej: capsid protein
ek: capsid protein
el: capsid protein
1q: capsid protein
em: capsid protein
en: capsid protein
eo: capsid protein
ep: capsid protein
eq: capsid protein
er: capsid protein
es: capsid protein
et: capsid protein
eu: capsid protein
ev: capsid protein
1r: capsid protein
ew: capsid protein
ex: capsid protein
ey: capsid protein
ez: capsid protein
eA: capsid protein
eB: capsid protein
eC: capsid protein
eD: capsid protein
eE: capsid protein
eF: capsid protein
1s: capsid protein
eG: capsid protein
eH: capsid protein
eI: capsid protein
eJ: capsid protein
eK: capsid protein
eL: capsid protein
eM: capsid protein
eN: capsid protein
eO: capsid protein
eP: capsid protein
1t: capsid protein
eQ: capsid protein
eR: capsid protein
eS: capsid protein
eT: capsid protein
eU: capsid protein
eV: capsid protein
eW: capsid protein
eX: capsid protein
eY: capsid protein
eZ: capsid protein
1u: capsid protein
f0: capsid protein
f1: capsid protein
f2: capsid protein
f3: capsid protein
f4: capsid protein
f5: capsid protein
f6: capsid protein
f7: capsid protein
f8: capsid protein
f9: capsid protein
1v: capsid protein
fa: capsid protein
fb: capsid protein
fc: capsid protein
fd: capsid protein
fe: capsid protein
ff: capsid protein
fg: capsid protein
fh: capsid protein
fi: capsid protein
fj: capsid protein
1w: capsid protein
fk: capsid protein
fl: capsid protein
fm: capsid protein
fn: capsid protein
fo: capsid protein
fp: capsid protein
fq: capsid protein
fr: capsid protein
fs: capsid protein
ft: capsid protein
1x: capsid protein
fu: capsid protein
fv: capsid protein
fw: capsid protein
fx: capsid protein
fy: capsid protein
fz: capsid protein
fA: capsid protein
fB: capsid protein
fC: capsid protein
fD: capsid protein
1y: capsid protein
fE: capsid protein
fF: capsid protein
fG: capsid protein
fH: capsid protein
fI: capsid protein
fJ: capsid protein
fK: capsid protein
fL: capsid protein
fM: capsid protein
fN: capsid protein
1z: capsid protein
fO: capsid protein
fP: capsid protein
fQ: capsid protein
fR: capsid protein
fS: capsid protein
fT: capsid protein
fU: capsid protein
fV: capsid protein
fW: capsid protein
fX: capsid protein
1A: capsid protein
fY: capsid protein
fZ: capsid protein
g0: capsid protein
g1: capsid protein
g2: capsid protein
g3: capsid protein
g4: capsid protein
g5: capsid protein
g6: capsid protein
g7: capsid protein
1B: capsid protein
0: capsid protein
a: capsid protein
b: capsid protein
c: capsid protein
d: capsid protein
e: capsid protein
f: capsid protein
g: capsid protein
h: capsid protein
i: capsid protein
j: capsid protein
1: capsid protein
k: capsid protein
l: capsid protein
m: capsid protein
n: capsid protein
o: capsid protein
p: capsid protein
q: capsid protein
r: capsid protein
s: capsid protein
t: capsid protein
2: capsid protein
u: capsid protein
v: capsid protein
w: capsid protein
x: capsid protein
y: capsid protein
z: capsid protein
A: capsid protein
B: capsid protein
C: capsid protein
D: capsid protein
3: capsid protein
E: capsid protein
F: capsid protein
G: capsid protein
H: capsid protein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
M: capsid protein
N: capsid protein
4: capsid protein
O: capsid protein
P: capsid protein
Q: capsid protein
R: capsid protein
S: capsid protein
T: capsid protein
U: capsid protein
V: capsid protein
W: capsid protein
X: capsid protein
5: capsid protein
6: capsid protein
7: capsid protein
8: capsid protein
9: capsid protein


Theoretical massNumber of molelcules
Total (without water)34,852,5761356
Polymers34,852,5761356
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • 1356-MERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein ...
capsid protein / Capsid / CA


Mass: 25702.490 Da / Num. of mol.: 1356 / Fragment: UNP residues 133-363 / Mutation: A92E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q79791

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: electron tomography

-
Sample preparation

ComponentName: HIV-1 core with A14C/E45C cross-linked capsid protein / Type: VIRUS
Details of virusEmpty: NO / Enveloped: YES / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA / pH: 8 / Details: 10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA
SpecimenConc.: 0.011 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 200 mesh holey carbon copper grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Sep 11, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Nominal defocus max: 8000 nm / Nominal defocus min: 8000 nm / Cs: 2 mm
Specimen holderSpecimen holder model: SIDE ENTRY, EUCENTRIC / Temperature: 82 K / Temperature (max): 85 K / Temperature (min): 80 K / Tilt angle max: 66 ° / Tilt angle min: -70 °
Image recordingElectron dose: 120 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 53

-
Processing

EM software
IDNameCategory
1MDmodel fitting
2TOMO3D3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: SIRTSirte / Nominal pixel size: 6.25 Å / Actual pixel size: 6.25 Å / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: REFINEMENT PROTOCOL--FLEXIBLE DETAILS--The model was built using hexamer of hexamers (PDB entry 3J34) and pentamer of hexamers (computer-based MD model available upon request).
Atomic model buildingPDB-ID: 3J34

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