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- PDB-4aed: Crystal structure of Human enterovirus 71 -

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Basic information

Entry
Database: PDB / ID: 4aed
TitleCrystal structure of Human enterovirus 71
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / PICORNAVIRUS / CAPSID / PATHOGEN
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A ...Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures / Irregular / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
LAURIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesHUMAN ENTEROVIRUS 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsPlevka, P. / Perera, R. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: Science / Year: 2012
Title: Crystal Structure of Human Enterovirus 71.
Authors: Plevka, P. / Perera, R. / Cardosa, J. / Kuhn, R.J. / Rossmann, M.G.
History
DepositionJan 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,00210
Polymers94,6014
Non-polymers4016
Water00
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,700,130600
Polymers5,676,088240
Non-polymers24,042360
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 475 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)475,01150
Polymers473,00720
Non-polymers2,00430
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 570 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)570,01360
Polymers567,60924
Non-polymers2,40436
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 11.4 MDa, 480 polymers
Theoretical massNumber of molelcules
Total (without water)11,400,2601200
Polymers11,352,175480
Non-polymers48,085720
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z3
point symmetry operation118
transform to crystal frame1
Unit cell
Length a, b, c (Å)600.200, 610.600, 851.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.858329, 0.11723, 0.499471), (0.407904, 0.434525, -0.802964), (-0.311178, 0.892996, 0.325146)-102.33566, 195.72549, 51.26903
3generate(0.3091, -0.530936, 0.78901), (0.542665, 0.779767, 0.31215), (-0.780998, 0.331685, 0.529133)19.0947, -113.35406, 165.42949
4generate(0.32895, 0.55233, 0.765969), (-0.349495, 0.824701, -0.444595), (-0.877262, -0.121444, 0.464348)-146.38312, 173.44138, 263.56967
5generate(0.412769, -0.896693, 0.159717), (0.848317, 0.314666, -0.42584), (0.33159, 0.311264, 0.890565)192.95023, 68.48914, -74.74928
6generate(0.597161, 0.713118, -0.367163), (-0.738204, 0.309558, -0.599355), (-0.313752, 0.628952, 0.711282)27.8344, 344.0614, 10.89839
7generate(0.729691, -0.240845, 0.639913), (-0.425392, 0.572784, 0.700649), (-0.535318, -0.7835, 0.315526)-57.36563, -18.12088, 345.96289
8generate(0.597161, -0.738204, -0.313752), (0.713118, 0.309558, 0.628952), (-0.367163, -0.599355, 0.711282)240.78308, -133.20035, 208.6888
9generate(0.729691, -0.425392, -0.535318), (-0.240845, 0.572784, -0.7835), (0.639913, 0.700649, 0.315526)219.35567, 267.63092, -59.74034
10generate(0.412769, 0.848317, 0.33159), (-0.896693, 0.314666, 0.311264), (0.159717, -0.42584, 0.890565)-112.95352, 174.73872, 64.93156
11generate(0.32895, -0.349495, -0.877262), (0.55233, 0.824701, -0.121444), (0.765969, -0.444595, 0.464348)339.99924, -30.17218, 66.84761
12generate(0.3091, 0.542665, -0.780998), (-0.530936, 0.779767, 0.331685), (0.78901, 0.31215, 0.529133)184.80911, 43.66754, -67.21059
13generate(0.858329, 0.407904, -0.311178), (0.11723, 0.434525, 0.892996), (0.499471, -0.802964, 0.325146)23.96431, -118.83109, 191.61641
14generate(-0.196773, 0.51005, 0.837264), (0.686868, 0.681144, -0.253509), (-0.699595, 0.525209, -0.484371)-75.99722, -0.29451, 337.36365
15generate(-0.061171, -0.198474, 0.978176), (0.988983, -0.143991, 0.032649), (0.134378, 0.969427, 0.205161)-16.64487, 21.40457, -2.07664
16generate(0.269316, 0.962577, -0.030236), (0.17461, -0.079681, -0.981408), (-0.947091, 0.259029, -0.189535)-32.65656, 347.87527, 353.36798
17generate(-0.404844, -0.363043, 0.839227), (-0.368006, 0.904882, 0.213918), (-0.837062, -0.222237, -0.499938)89.71254, 24.75394, 476.76544
18generate(-0.483771, -0.865441, 0.130302), (0.765549, -0.346294, 0.542231), (-0.424146, 0.362068, 0.830064)328.90479, -21.4259, 43.61528
19generate(0.6194, -0.577332, 0.532008), (0.270732, -0.479006, -0.83502), (0.736918, 0.661242, -0.140394)33.96584, 364.22565, 28.07785
20generate(0.91768, 0.051903, -0.393802), (-0.3209, -0.487253, -0.81215), (-0.234001, 0.871657, -0.430527)87.50822, 449.47372, 202.57991
21generate(0.028981, -0.996791, 0.074807), (-0.10286, 0.071487, 0.992154), (-0.994331, -0.036499, -0.100468)283.95502, -50.64825, 387.30707
22generate(-0.451634, 0.887305, 0.093051), (-0.678122, -0.273555, -0.68213), (-0.57988, -0.371241, 0.725289)61.14923, 442.61621, 202.41576
23generate(-0.237123, 0.126773, 0.963127), (-0.954844, 0.15232, -0.255188), (-0.17905, -0.980245, 0.084903)-37.30666, 328.18442, 371.59177
24generate(-0.451558, -0.678018, -0.579988), (0.887325, -0.273528, -0.371269), (0.09309, -0.682265, 0.725187)445.12604, 141.98477, 149.4776
25generate(-0.237212, -0.954844, -0.179138), (0.126689, 0.152376, -0.980147), (0.963186, -0.255196, 0.084936)371.06277, 318.9491, 88.11511
26generate(0.029002, -0.102902, -0.994212), (-0.996792, 0.071332, -0.036493), (0.074685, 0.992169, -0.100535)371.62274, 300.80487, 67.93256
27generate(0.91775, -0.320932, -0.234136), (0.052074, -0.487185, 0.871723), (-0.393863, -0.812142, -0.430465)111.37934, 37.84602, 486.70905
28generate(-0.483809, 0.765515, -0.424164), (-0.865433, -0.346369, 0.362015), (0.130211, 0.542231, 0.830078)194.03108, 261.45782, -67.43202
29generate(0.61946, 0.270805, 0.73684), (-0.577219, -0.479032, 0.661322), (0.53206, -0.834981, -0.140428)-140.34106, 175.47998, 290.00061
30generate(0.269316, 0.17461, -0.947091), (0.962577, -0.079681, 0.259029), (-0.030236, -0.981408, -0.189535)282.724, -32.37909, 407.39581
31generate(-0.404844, -0.368006, -0.837062), (-0.363043, 0.904882, -0.222237), (0.839227, 0.213918, -0.499938)444.51151, 116.12492, 157.76854
32generate(-0.061171, 0.988983, 0.134378), (-0.198474, -0.143991, 0.969427), (0.978176, 0.032649, 0.205161)-21.89673, 1.79454, 16.0013
33generate(-0.196773, 0.686868, -0.699595), (0.510051, 0.681144, 0.525209), (0.837264, -0.253509, -0.484371)221.26904, -138.21942, 226.99303
34generate(0.629282, 0.597565, 0.496972), (0.777234, -0.480499, -0.406304), (-0.004065, 0.64184, -0.766783)-141.63962, 197.88554, 274.59042
35generate(-0.808845, -0.316521, 0.495586), (0.346996, 0.423499, 0.836765), (-0.474735, 0.848877, -0.232654)215.74252, -139.73938, 200.44273
36generate(-0.756773, 0.544265, 0.362034), (-0.013124, 0.541222, -0.840779), (-0.653526, -0.641081, -0.402449)103.14111, 250.4238, 493.3385
37generate(-0.537298, -0.60256, 0.590062), (0.475918, -0.794278, -0.377635), (0.696322, 0.077906, 0.713575)199.22295, 285.53705, -56.06154
38generate(-0.054694, 0.415735, -0.907885), (-0.481211, -0.807594, -0.340866), (-0.874848, 0.418291, 0.244288)285.82397, 423.49402, 226.29504
39generate(0.292329, -0.815138, 0.500203), (-0.929158, -0.118351, 0.350127), (-0.226119, -0.567141, -0.791978)126.51755, 238.30504, 500.02942
40generate(-0.054694, -0.481211, -0.874848), (0.415735, -0.807594, 0.418291), (-0.907885, -0.340866, 0.244288)417.42474, 128.52835, 348.5437
41generate(0.292329, -0.929158, -0.226119), (-0.815138, -0.118351, -0.567141), (0.500203, 0.350127, -0.791978)297.53281, 414.91754, 249.29065
42generate(-0.537298, 0.475918, 0.696322), (-0.60256, -0.794278, 0.077906), (0.590062, -0.377635, 0.713575)10.15582, 351.20654, 30.26912
43generate(-0.756773, -0.013124, -0.653526), (0.544265, 0.541222, -0.641081), (0.362034, -0.840779, -0.402449)403.74399, 124.58334, 371.75635
44generate(-0.808845, 0.346996, -0.474735), (-0.316521, 0.423499, 0.848877), (0.495586, 0.836765, -0.232654)318.16089, -42.70374, 56.66901
45generate(0.629282, 0.777234, -0.004065), (0.597565, -0.480499, 0.64184), (0.496972, -0.406304, -0.766783)-63.57939, 3.48589, 361.32294
46generate(-0.437812, 0.780009, 0.447109), (0.780009, 0.082226, 0.620342), (0.447109, 0.620342, -0.644414)0.87485, -106.29959, 184.34637
47generate(-0.221418, 0.946243, -0.235717), (0.946246, 0.150035, -0.286584), (-0.235752, -0.286447, -0.928617)86.92367, 49.81454, 486.96637
48generate(-0.977619, 0.210428, 0.011206), (0.210386, 0.971895, 0.105506), (0.01128, 0.105453, -0.994376)261.96283, -49.51941, 403.22668
49generate(-0.890723, 0.201902, 0.407306), (0.202065, -0.626741, 0.752652), (0.407251, 0.752634, 0.517364)166.58069, 62.04144, -75.47768
50generate(0.13056, 0.296906, 0.945974), (0.296906, -0.922063, 0.248406), (0.945974, 0.248406, -0.208597)-115.15878, 199.9297, 74.88632
51generate(0.633187, 0.422913, -0.648201), (0.422913, -0.890487, -0.167851), (-0.648201, -0.167851, -0.742701)126.61847, 264.05109, 491.28644
52generate(-0.590215, -0.767953, -0.248625), (-0.767992, 0.439285, 0.466071), (-0.248755, 0.466112, -0.849071)409.84964, 103.47183, 355.8476
53generate(-0.720943, -0.374772, -0.5829), (-0.374772, -0.496635, 0.782843), (-0.5829, 0.782843, 0.217579)439.32434, 122.1469, 131.7915
54generate(0.931456, -0.221423, 0.288625), (-0.221423, -0.97459, -0.033097), (0.288625, -0.033097, -0.956867)-16.4594, 345.2998, 375.08105
55generate(-0.540292, 0.471069, -0.697255), (0.471069, -0.517261, -0.714479), (-0.697255, -0.714479, 0.057553)305.67804, 314.60724, 414.08981
56generate(-0.742541, -0.624941, 0.240886), (-0.624941, 0.517139, -0.584778), (0.240886, -0.584778, -0.774598)307.2337, 291.91064, 428.98639
57generate(-0.953892, 0.01112, -0.299855), (0.01112, -0.997318, -0.072315), (-0.299855, -0.072315, 0.95121)354.89053, 322.18951, 66.48549
58generate(-0.057683, -0.571483, 0.818567), (-0.571483, -0.653402, -0.496418), (0.818567, -0.496418, -0.288915)74.17104, 446.07385, 226.04861
59generate(0.405133, -0.636597, -0.65621), (-0.636597, -0.711589, 0.297297), (-0.65621, 0.297297, -0.693544)326.23529, 297.20468, 410.24127
60generate(-0.967237, -0.143577, 0.209374), (-0.143577, -0.3708, -0.917548), (0.209374, -0.917548, 0.338037)273.24509, 427.12546, 250.14052
61generate(0.923291, 0.139366, -0.357926), (-0.314425, 0.80946, -0.495894), (0.220616, 0.570396, 0.791187)216.77599, 330.16638, 137.66064
62generate(0.960714, -0.150831, 0.232873), (0.214614, -0.127961, -0.968252), (0.175828, 0.980241, -0.090564)131.21745, 495.35126, 267.28809
63generate(0.640558, -0.500253, 0.582598), (0.729369, 0.633649, -0.257805), (-0.24019, 0.590068, 0.770761)159.39662, 150.37137, 208.10229
64generate(0.569004, 0.668364, 0.479048), (0.048697, 0.55412, -0.83099), (-0.820857, 0.496174, 0.282777)11.4552, 385.88403, 412.82935
65generate(0.380648, -0.895464, -0.230639), (0.39246, 0.382298, -0.836546), (0.83729, 0.227928, 0.496942)431.22498, 362.00513, 160.15378
66generate(0.560772, 0.476438, -0.677115), (-0.62972, -0.285541, -0.722429), (-0.537561, 0.831515, 0.139886)286.52499, 594.51416, 348.67511
67generate(0.806036, 0.137892, 0.575538), (-0.308309, 0.927906, 0.209476), (-0.505197, -0.346316, 0.790462)37.45612, 161.97437, 388.39026
68generate(0.782155, -0.42391, -0.456616), (0.571553, 0.779901, 0.255042), (0.248008, -0.460491, 0.85229)345.8299, 43.15027, 279.91632
69generate(0.411109, -0.563714, -0.716383), (-0.741717, 0.249951, -0.622362), (0.529896, 0.78721, -0.315365)477.98642, 507.45706, 291.44373
70generate(0.19897, 0.979517, 0.030778), (-0.934825, 0.19915, -0.29393), (-0.29404, 0.029717, 0.955302)113.59904, 474.92664, 263.78448
71generate(0.106532, -0.048617, -0.993096), (-0.036181, 0.997925, -0.052739), (0.993644, 0.041543, 0.104578)502.56262, 165.68976, 248.34888
72generate(-0.071013, 0.497984, -0.864253), (-0.918226, 0.30577, 0.251657), (0.389604, 0.811465, 0.435535)417.55075, 340.73438, 150.16412
73generate(0.630051, 0.724575, -0.279232), (-0.422672, 0.621661, 0.659449), (0.651404, -0.297454, 0.697962)153.75641, 131.4209, 226.77133
74generate(0.164451, 0.377867, 0.911076), (0.964788, 0.130538, -0.228265), (-0.205136, 0.916585, -0.343115)25.81604, 186.52664, 387.64429
75generate(0.033255, -0.5503, 0.834259), (0.753139, -0.534883, -0.382873), (0.656934, 0.64108, 0.396746)205.13431, 353.75592, 144.55457
76generate(0.61198, 0.78492, -0.096853), (0.526317, -0.495608, -0.690915), (-0.590314, 0.371851, -0.716419)108.62688, 446.79242, 608.46283
77generate(-0.12547, -0.12954, 0.983604), (0.244501, 0.956821, 0.157201), (-0.961497, 0.260216, -0.088379)132.40967, 85.57057, 548.78302
78generate(-0.188156, -0.976909, -0.101226), (0.982123, -0.187743, -0.013679), (-0.005641, -0.101991, 0.994769)501.85361, 187.77866, 232.50899
79generate(0.345855, -0.836478, 0.425075), (-0.341041, -0.534115, -0.773571), (0.874114, 0.122575, -0.47)288.84735, 600.38922, 375.12155
80generate(0.886318, -0.331974, -0.322683), (-0.432257, -0.842981, -0.320086), (-0.165724, 0.423168, -0.890754)287.70435, 566.02454, 573.6228
81generate(0.36832, -0.897302, 0.243301), (0.40071, 0.389381, 0.829409), (-0.83898, -0.20801, 0.502935)333.26294, 7.82281, 477.84863
82generate(-0.303942, 0.913993, -0.268753), (-0.119349, -0.316326, -0.941081), (-0.945229, -0.254002, 0.205284)262.4704, 568.84296, 563.76624
83generate(-0.28792, 0.489132, 0.823292), (-0.609561, 0.569534, -0.551498), (-0.738614, -0.660707, 0.134098)95.06648, 423.2785, 610.62378
84generate(-0.326576, -0.419927, -0.846803), (0.814072, 0.330106, -0.477781), (0.480157, -0.8454, 0.234033)594.0426, 231.01376, 435.1149
85generate(-0.546109, -0.769021, -0.332397), (-0.300503, 0.550119, -0.779184), (0.781991, -0.325648, -0.531392)572.28687, 427.97598, 471.16577
86generate(-0.138873, -0.440191, -0.887049), (-0.853019, -0.401915, 0.33292), (-0.503077, 0.802977, -0.319696)577.49902, 423.12131, 444.97177
87generate(0.995582, -0.073524, 0.059388), (-0.051097, 0.109289, 0.992708), (-0.079447, -0.991248, 0.104994)150.67996, 84.42456, 568.89795
88generate(-0.613915, 0.464442, -0.638281), (-0.612983, -0.789958, 0.014773), (-0.497354, 0.400324, 0.769662)456.49719, 514.23718, 276.25006
89generate(0.301058, 0.482132, 0.822747), (-0.925855, -0.058843, 0.37327), (0.228379, -0.87412, 0.428669)7.85754, 372.52747, 436.23694
90generate(0.39363, 0.501383, -0.7705), (0.709482, 0.367274, 0.601452), (0.584543, -0.783406, -0.211152)327.48218, 13.03616, 503.89166
91generate(-0.724766, -0.290233, -0.624883), (-0.582744, 0.742095, 0.331217), (0.367592, 0.604202, -0.706977)586.90375, 206.16304, 426.7887
92generate(-0.434254, 0.881365, 0.185743), (-0.626495, -0.443706, 0.640722), (0.647217, 0.161886, 0.744924)191.08176, 330.56894, 146.51349
93generate(-0.410273, 0.819845, -0.399364), (0.059542, 0.461105, 0.885302), (0.909952, 0.339482, -0.237993)320.56171, 36.14624, 287.23044
94generate(0.690785, 0.25503, 0.676677), (0.433294, -0.895119, -0.104903), (0.578945, 0.365574, -0.728783)15.29688, 398.71399, 436.53815
95generate(-0.528519, -0.537055, 0.657459), (0.770619, 0.021374, 0.636875), (-0.356124, 0.843354, 0.402548)324.75034, 49.81975, 264.138
96generate(-0.466636, 0.807403, 0.361133), (0.551404, 0.584876, -0.594838), (-0.691504, -0.078431, -0.718119)170.32701, 255.80063, 693.57898
97generate(-0.678987, -0.694919, 0.236762), (0.208874, -0.492109, -0.845068), (0.703846, -0.524349, 0.479348)460.57684, 526.45728, 300.12628
98generate(0.195568, 0.121575, -0.973185), (0.061508, -0.991861, -0.111598), (-0.978716, -0.037983, -0.201445)458.69846, 470.87946, 621.31891
99generate(0.221345, -0.566109, 0.794098), (-0.731901, 0.441741, 0.518875), (-0.644398, -0.696054, -0.316539)187.82645, 235.32285, 697.11755
100generate(0.332397, -0.434844, -0.836881), (0.803933, -0.333377, 0.492523), (-0.49324, -0.8365, 0.238863)495.3399, 130.11551, 578.82666
101generate(-0.022734, -0.999697, -0.004344), (-0.999785, 0.022724, 0.004757), (-0.004705, 0.004522, -0.999983)460.08313, 448.85223, 637.20392
102generate(-0.791257, 0.463881, 0.398358), (-0.611417, -0.60531, -0.509737), (0.004615, -0.646837, 0.762629)264.26501, 596.25061, 364.17636
103generate(-0.752451, 0.364248, -0.548692), (0.498979, 0.859162, -0.113873), (0.429927, -0.359399, -0.828261)473.8504, 119.71275, 591.92383
104generate(-0.968295, 0.0799, -0.236741), (-0.247649, -0.181245, 0.951773), (0.033115, 0.980152, 0.195389)484.2962, 167.45999, 228.32986
105generate(0.486411, 0.796075, 0.36015), (0.039398, -0.431843, 0.901066), (0.872877, -0.424066, -0.241463)29.23254, 173.80099, 411.49646
106generate(-0.455553, 0.509598, 0.729919), (0.547327, -0.48632, 0.681122), (0.702072, 0.709791, -0.057372)136.7867, 152.42967, 223.07335
107generate(0.011823, 0.997094, 0.074801), (0.952476, -0.034027, 0.302633), (0.304362, 0.067703, -0.950179)129.67618, 101.67447, 570.53302
108generate(-0.877343, 0.291991, 0.380964), (0.472093, 0.668253, 0.574985), (-0.086751, 0.684221, -0.724086)307.41702, 7.75702, 486.23608
109generate(-0.940001, -0.17032, 0.295778), (0.241675, -0.944032, 0.224617), (0.24096, 0.282527, 0.9285)406.24036, 365.43839, 150.08218
110generate(-0.176665, 0.056715, 0.982691), (-0.269821, -0.962911, 0.00708), (0.9466, -0.263902, 0.185347)111.51067, 491.07458, 285.54285
111generate(0.875564, 0.326447, -0.356039), (0.464681, -0.770551, 0.436242), (-0.131929, -0.54743, -0.826361)194.63712, 260.46713, 704.90784
112generate(-0.562936, -0.814656, 0.139306), (-0.312725, 0.365905, 0.87649), (-0.765082, 0.449925, -0.46078)482.23959, 108.59311, 568.64209
113generate(-0.509235, -0.695438, -0.506962), (0.212377, -0.672377, 0.709063), (-0.834003, 0.253416, 0.490078)592.25159, 225.55043, 408.52649
114generate(0.725839, -0.328417, 0.60436), (-0.615233, -0.702858, 0.356963), (0.307552, -0.630937, -0.712264)115.45096, 428.84753, 627.74628
115generate(-0.183629, 0.618575, -0.763943), (0.896957, -0.212512, -0.387648), (-0.402161, -0.756404, -0.515826)394.6377, 283.37097, 712.17139
116generate(-0.858896, -0.295623, 0.418158), (-0.391845, 0.905088, -0.164976), (-0.329694, -0.305567, -0.893264)387.57898, 257.12271, 711.35449
117generate(-0.771844, -0.102842, -0.627395), (0.457625, -0.774925, -0.435954), (-0.441343, -0.623627, 0.645184)565.54858, 446.40991, 452.33316
118generate(-0.42589, -0.441026, 0.790002), (-0.850379, -0.103044, -0.515937), (0.308942, -0.891536, -0.331152)266.51636, 555.828, 587.30927
119generate(0.52021, -0.793346, -0.316201), (-0.317273, -0.523269, 0.790903), (-0.792918, -0.311113, -0.523917)412.57013, 264.72906, 703.73535
120generate(-0.987992, 0.144175, -0.055554), (0.084076, 0.200003, -0.976182), (-0.129629, -0.96913, -0.209723)439.05566, 465.94922, 639.48138
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR ICOSAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = I). THERE ARE 120 OPERATORS (BIOMT + MTRIX) TO GENERATE 2 PARTICLES THAT FORM THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. AUTHOR PROVIDED MATRIX TO BRING THE MODEL TO STANDARD ORIENTATION 0.838212 -0.379679 -0.391463 15.52176 0.530128 0.735679 0.421593 -282.27505 0.127921 -0.560910 0.817934 -105.28804

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein VP1


Mass: 32775.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ENTEROVIRUS 71 / Strain: MY104-9-SAR-97 / References: UniProt: A9X4C2
#2: Protein VP2


Mass: 27800.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ENTEROVIRUS 71 / Strain: MY104-9-SAR-97 / References: UniProt: A9X4C2
#3: Protein VP3


Mass: 26524.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GENBANK DQ341368.1 / Source: (natural) HUMAN ENTEROVIRUS 71 / Strain: MY104-9-SAR-97 / References: UniProt: A9X4C2
#4: Protein VP4


Mass: 7501.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GENBANK DQ341368.1 / Source: (natural) HUMAN ENTEROVIRUS 71 / Strain: MY104-9-SAR-97 / References: UniProt: A9X4C2

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Non-polymers , 2 types, 6 molecules

#5: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca

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Details

Sequence detailsGENBANK: DQ341368.1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 8
Details: 2.5% W/W PEG800, 2.5% W/W GLYCEROL, 600MM NACL, 150MM CACL2, 100MM TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.033
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 459113 / % possible obs: 31.7 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 2.41
Reflection shellResolution: 3.8→3.97 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.19 / % possible all: 11.5

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Processing

Software
NameClassification
CCP4model building
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
PHASERphasing
GLRFphasing
CCP4phasing
USFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X5I

2x5i


Resolution: 3.8→50 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: ONE B-FACTOR PER RESIDUE / Cross valid method: NONE / σ(F): 0 / Stereochemistry target values: CRYSTALLOGRAPHIC RESIDUAL
RfactorNum. reflection% reflection
Rwork0.2792 --
obs0.2792 451044 31.7 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.8494 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 82.7 Å2
Baniso -1Baniso -2Baniso -3
1--34.14 Å20 Å20 Å2
2--45.15 Å20 Å2
3----11.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.63 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 1 Å
Refinement stepCycle: LAST / Resolution: 3.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 19 0 6471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINTS - MATRICES ARE LISTED IN ATTACHED FILE MTRIX.PDB
LS refinement shellResolution: 3.8→3.97 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.3672 21982 -
obs--11.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DAO_XPLOR_PAR.TXTDAO_XPLOR_TOP.TXT

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