[English] 日本語
Yorodumi
- PDB-1cov: COXSACKIEVIRUS B3 COAT PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cov
TitleCOXSACKIEVIRUS B3 COAT PROTEIN
Components(COXSACKIEVIRUS COAT ...) x 4
KeywordsVIRUS / COXSACKIEVIRUS B3 / Icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / 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 coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / PALMITIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus B3
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsMuckelbauer, J.K. / Rossmann, M.G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure determination of coxsackievirus B3 to 3.5 A resolution.
Authors: Muckelbauer, J.K. / Kremer, M. / Minor, I. / Tong, L. / Zlotnick, A. / Johnson, J.E. / Rossmann, M.G.
#1: Journal: Structure / Year: 1995
Title: The Structure of Coxsackievirus B3 at 3.5 Angstroms Resolution
Authors: Muckelbauer, J.K. / Kremer, M. / Minor, I. / Diana, G. / Dutko, F.J. / Groarke, J. / Pevear, D.C. / Rossmann, M.G.
History
DepositionOct 19, 1994Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Advisory
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: COXSACKIEVIRUS COAT PROTEIN
2: COXSACKIEVIRUS COAT PROTEIN
3: COXSACKIEVIRUS COAT PROTEIN
4: COXSACKIEVIRUS COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3206
Polymers93,8354
Non-polymers4852
Water0
1
1: COXSACKIEVIRUS COAT PROTEIN
2: COXSACKIEVIRUS COAT PROTEIN
3: COXSACKIEVIRUS COAT PROTEIN
4: COXSACKIEVIRUS COAT PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,659,212360
Polymers5,630,125240
Non-polymers29,088120
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
1: COXSACKIEVIRUS COAT PROTEIN
2: COXSACKIEVIRUS COAT PROTEIN
3: COXSACKIEVIRUS COAT PROTEIN
4: COXSACKIEVIRUS COAT PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 472 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)471,60130
Polymers469,17720
Non-polymers2,42410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: COXSACKIEVIRUS COAT PROTEIN
2: COXSACKIEVIRUS COAT PROTEIN
3: COXSACKIEVIRUS COAT PROTEIN
4: COXSACKIEVIRUS COAT PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 566 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)565,92136
Polymers563,01224
Non-polymers2,90912
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
1: COXSACKIEVIRUS COAT PROTEIN
2: COXSACKIEVIRUS COAT PROTEIN
3: COXSACKIEVIRUS COAT PROTEIN
4: COXSACKIEVIRUS COAT PROTEIN
hetero molecules
x 120


  • crystal asymmetric unit
  • 11.3 MDa, 480 polymers
Theoretical massNumber of molelcules
Total (without water)11,318,424720
Polymers11,260,249480
Non-polymers58,175240
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
transform to crystal frame1
point symmetry operation59
Unit cell
Length a, b, c (Å)574.620, 302.070, 521.610
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.80122195, -0.36352299, 0.47528059), (-0.25875514, 0.5056995, 0.82299516), (-0.53952347, -0.7823803, 0.31111254)-67.12188, -112.73127, 63.41869
3generate(0.47959502, -0.84694618, 0.22949333), (-0.78219784, -0.29409977, 0.54925105), (-0.39768565, -0.44292845, -0.80352922)-49.77931, -100.17801, 207.56159
4generate(0.47959669, -0.78219513, -0.39769215), (-0.8469481, -0.2941024, -0.44292725), (0.22949843, 0.54924462, -0.80352826)28.06085, 20.3116, 233.22812
5generate(0.80122465, -0.25875361, -0.53952682), (-0.36352324, 0.50569523, -0.78238307), (0.47528167, 0.82298947, 0.31111409)58.82616, 82.22501, 104.948
6generate(0.18614395, -0.49152027, -0.8507427), (-0.49152075, -0.79632117, 0.35253537), (-0.85073666, 0.35253252, -0.38982277)72.89507, -64.72146, 139.0267
7generate(0.73532168, 0.34937518, -0.58072492), (-0.37796613, -0.49983685, -0.77930057), (-0.56252996, 0.79252752, -0.23548482)61.85746, 80.39797, 131.66626
8generate(0.81206797, 0.36372025, 0.4563474), (0.24695154, 0.49434155, -0.83345345), (-0.52873232, 0.78951203, 0.31162446)-63.71303, 112.69279, 65.14755
9generate(0.31032207, -0.46830946, 0.82727555), (0.51961729, 0.81229327, 0.26491416), (-0.79605095, 0.34765336, 0.49541865)-130.28225, -12.46734, 31.39717
10generate(-0.07652026, -0.99687716, 0.01944943), (0.06321631, 0.01461984, 0.99789556), (-0.99506058, 0.07758517, 0.06190042)-45.8538, -122.11537, 77.057
11generate(-0.74179673, -0.35819657, 0.56695251), (-0.35819667, -0.50308599, -0.78651407), (0.56694834, -0.78650806, 0.24488271)-139.51178, 82.07164, 115.38917
12generate(-0.80754281, -0.35505214, -0.47096959), (0.26752386, 0.49115552, -0.82897565), (0.52564448, -0.79542691, -0.30164669)-13.38566, 112.9483, 181.52872
13generate(-0.30105031, 0.48248803, -0.82254016), (0.5345088, 0.79970025, 0.27346279), (0.78972417, -0.35732842, -0.49864995)50.97534, -12.94954, 216.78593
14generate(0.07772536, 0.99697188, -0.00190061), (0.07379404, -0.00385013, 0.9972688), (0.99423825, -0.0776498, -0.07387523)-35.37351, -121.63535, 172.43652
15generate(-0.19467091, 0.47740023, 0.85685308), (-0.47792828, -0.8090163, 0.34216707), (0.85655522, -0.34289742, 0.38565322)-153.10102, -62.90903, 109.76988
16generate(-0.44434722, 0.84971683, 0.28379019), (0.84971743, 0.29940715, 0.4339787), (0.28378832, 0.43397554, -0.85505994)-91.58057, -20.82514, 241.66609
17generate(-0.72900082, 0.36919995, 0.57641392), (0.36919741, -0.49701817, 0.78528106), (0.57640895, 0.78527968, 0.22601898)-139.5472, -84.08995, 119.46829
18generate(-0.99061268, 0.00073789, 0.13669943), (0.0007375, -0.99994203, 0.01073961), (0.1366938, 0.01074484, 0.9905547)-95.68027, -3.04019, 6.58689
19generate(-0.86764411, 0.2535327, -0.42768279), (0.25353677, -0.51434074, -0.8192557), (-0.42768573, -0.81924818, 0.38198485)-20.60237, 110.31613, 59.02015
20generate(-0.53003349, 0.77823054, -0.3367757), (0.77823521, 0.28870122, -0.55767955), (-0.33677631, -0.55767722, -0.75866774)-18.06862, 99.32443, 204.30708
21generate(-0.31860356, -0.50527421, 0.80199181), (-0.4726733, 0.81807081, 0.32763231), (-0.8216258, -0.27469899, -0.49946725)-152.05224, -59.48508, 153.23128
22generate(-0.55722328, -0.76715979, -0.3177546), (-0.76716158, 0.32919255, 0.55054639), (-0.31775055, 0.55053808, -0.77196926)-22.8455, -99.20251, 207.67195
23generate(-0.07651692, 0.06321609, -0.99506365), (-0.99687965, 0.01461673, 0.07758875), (0.01945228, 0.99789, 0.06190019)80.88769, -49.90455, 117.97983
24generate(0.45919567, 0.8383022, -0.29391724), (-0.84436497, 0.30907645, -0.43762922), (-0.27602017, 0.44913164, 0.84976185)15.79158, 20.2807, 8.10638
25generate(0.30957791, 0.48695587, 0.81672411), (-0.52038763, 0.80563837, -0.2830938), (-0.79583502, -0.33737161, 0.5028177)-128.17321, 14.35961, 29.89297
26generate(-0.49323721, 0.84168885, -0.21971205), (-0.76881287, -0.30361755, 0.56280373), (0.40699469, 0.44651591, 0.79685476)-31.07651, -101.33773, 41.67844
27generate(-0.49444398, 0.77684308, 0.3899246), (-0.84107297, -0.31438464, -0.44018232), (-0.21936706, -0.54559253, 0.80882862)-106.78801, 20.1859, 14.55937
28generate(-0.80754498, 0.26752159, 0.52564889), (-0.3550488, 0.49115519, -0.79542893), (-0.47096886, -0.82897247, -0.30164419)-136.446, 84.16549, 142.08389
29generate(-0.99984528, 0.01758937, -0.00010552), (0.01759077, 0.99977326, -0.01199737), (-0.00010558, -0.01200248, -0.99992798)-79.06415, 2.18343, 248.01745
30generate(-0.80559238, 0.37244424, -0.46076392), (-0.23812949, 0.5085767, 0.82743657), (0.54250574, 0.7762927, -0.32101829)-13.94223, -112.46387, 185.96347
31generate(0.87201455, -0.26245396, 0.41316613), (0.24334786, -0.49993546, -0.83117603), (0.42470346, 0.82533578, -0.37207909)-56.53081, 111.40405, 187.67966
32generate(0.54367568, -0.77297321, 0.32699442), (0.7727755, 0.3090161, -0.55437523), (0.32746727, 0.55408976, 0.76534219)-59.27284, 98.71635, 42.53484
33generate(0.45919451, -0.84436478, -0.27602265), (0.83830364, 0.30907989, 0.44913087), (-0.29391969, -0.43762763, 0.84975958)12.11044, -23.14732, 6.62838
34generate(0.73532114, -0.37796793, -0.56253599), (0.34937462, -0.49983226, 0.79253095), (-0.58072176, -0.77929667, -0.23548888)58.96976, -85.77551, 129.58178
35generate(0.99045795, -0.01832726, -0.13659391), (-0.01832827, -0.99983123, 0.00125776), (-0.13658822, 0.00125764, -0.99062672)16.54714, -2.61819, 241.47762
36generate(-0.06017378, -0.07396069, -0.99544588), (0.99813832, -0.0145178, -0.05926001), (-0.01007236, -0.99715269, 0.07469158)81.46228, 45.94379, 113.49258
37generate(0.50799158, 0.76328993, -0.39916442), (0.83545904, -0.32382402, 0.44401116), (0.20965033, -0.55903531, -0.80220155)30.70907, -23.1747, 231.31579
38generate(0.42486739, 0.51362709, 0.7454374), (0.51362481, -0.81485181, 0.26870931), (0.74543628, 0.2687101, -0.61001558)-114.74941, -14.58858, 229.38986
39generate(-0.19467154, -0.47792364, 0.85655876), (0.47739958, -0.80901745, -0.34290436), (0.85684751, 0.34216751, 0.38565501)-153.89448, 59.83643, 110.37636
40generate(-0.49444348, -0.84107286, -0.21936628), (0.77684539, -0.31438384, -0.54560054), (0.38991751, -0.44017873, 0.80882731)-32.62898, 97.24749, 38.7479
41generate(-0.31859932, -0.47267426, -0.82163024), (-0.505276, 0.81806922, -0.2746953), (0.80199096, 0.32762625, -0.4994699)49.33865, 13.92647, 217.96781
42generate(0.31032694, 0.51961436, -0.79605217), (-0.46831327, 0.81229283, 0.34765798), (0.82727353, 0.26491368, 0.49541421)71.90209, -61.80125, 95.52722
43generate(0.54367671, 0.77277329, 0.32747066), (-0.77297745, 0.30901797, 0.55409361), (0.32699433, -0.55436856, 0.7653393)-57.98901, -99.88998, 41.55354
44generate(0.05896855, -0.06305452, 0.99626789), (-0.99823301, 0.00375338, 0.05932458), (-0.00747777, -0.99800027, -0.06272193)-160.82956, -47.70238, 130.63655
45generate(-0.47394734, -0.83278343, 0.28608447), (-0.8327844, 0.31836435, -0.45289514), (0.28608629, -0.45289749, -0.84441701)-94.49742, 22.64006, 239.66657
46generate(0.87201486, 0.24334716, 0.42470183), (-0.2624587, -0.49993147, 0.82534068), (0.41316802, -0.83116991, -0.37208339)-57.52205, -114.04227, 185.7849
47generate(0.4065735, -0.52621526, 0.74685534), (-0.52621851, -0.80313562, -0.27940886), (0.74685649, -0.27940757, -0.60343788)-116.55212, 12.27438, 228.15409
48generate(0.05897053, -0.99823053, -0.00748006), (-0.06305471, 0.00375124, -0.99800578), (0.99626487, 0.05932213, -0.06272178)-37.1566, 120.41391, 171.25241
49generate(0.30958142, -0.52038957, -0.79583848), (0.48695607, 0.8056389, -0.33737353), (0.81671924, -0.28309374, 0.50281365)70.94261, 60.93116, 93.71605
50generate(0.81207045, 0.24694763, -0.52873538), (0.36371764, 0.49434586, 0.78951655), (0.45634558, -0.83344809, 0.31161766)58.35607, -83.97073, 102.69762
51generate(-0.06017562, 0.9981358, -0.01006877), (-0.07395564, -0.01452096, -0.99715858), (-0.99544254, -0.05925749, 0.07469659)-39.81337, 119.86185, 75.33603
52generate(-0.30105446, 0.53450961, 0.7897281), (0.48249296, 0.79969857, -0.3573289), (-0.8225378, 0.27345864, -0.49864411)-148.93394, 63.22436, 153.56933
53generate(-0.8055954, -0.23812625, 0.54250779), (0.37244517, 0.50857697, 0.77629809), (-0.46076396, 0.82742863, -0.32101555)-138.89902, -81.97384, 146.32892
54generate(-0.87654002, -0.25201527, -0.41007963), (-0.2520167, -0.4855656, 0.83708841), (-0.41008018, 0.83708479, 0.36210562)-23.57654, -115.07377, 63.62079
55generate(-0.41584526, 0.51203669, -0.75159072), (-0.52790758, -0.8088579, -0.25896808), (-0.74052972, 0.28908263, 0.60666918)37.66176, 9.66754, 19.74477
56generate(-0.49323991, -0.7688087, 0.40699719), (0.84169034, -0.30361678, 0.44651319), (-0.21971644, 0.56280116, 0.7968567)-110.20051, -23.22101, 16.99322
57generate(-0.41584598, -0.5279087, -0.74053127), (0.51203882, -0.80885577, 0.28907979), (-0.75159222, -0.25896474, 0.60666778)35.38669, -17.17246, 18.83132
58generate(0.20294816, 0.46358349, -0.86249839), (0.46358699, -0.82134618, -0.33238592), (-0.86249524, -0.33238219, -0.38160197)75.84735, 57.97494, 136.9471
59generate(0.50799005, 0.83545936, 0.20965022), (0.76329363, -0.32382669, -0.55903946), (-0.39916129, 0.44400921, -0.80219734)-44.73379, 98.37003, 208.10857
60generate(0.07772215, 0.07379911, 0.99424164), (0.99697434, -0.00385232, -0.07765333), (-0.00190215, 0.99726295, -0.07386984)-159.71768, 48.18817, 133.973
61generate(0.99973361, -0.00041514, -0.02320947), (0.00041031, 0.99999739, -0.00048809), (0.02319826, 0.00048554, 0.99973175)210.61915, 0.10145, 249.81899
62generate(0.81363798, -0.34547746, 0.46759156), (-0.25816237, 0.5059309, 0.82303617), (-0.52091743, -0.79035799, 0.32245436)142.09004, -112.68802, 311.60882
63generate(0.48902205, -0.83631833, 0.24785366), (-0.78180491, -0.29423032, 0.54973598), (-0.38683299, -0.46260011, -0.79772315)156.07729, -100.19804, 456.12147
64generate(0.474494, -0.79461234, -0.37875286), (-0.84686112, -0.29469066, -0.44269707), (0.24015145, 0.53080892, -0.81275354)233.251, 20.31067, 483.64536
65generate(0.79013109, -0.27799577, -0.54627909), (-0.36342552, 0.50518605, -0.78275426), (0.49356469, 0.8170116, 0.29813468)266.95972, 82.29916, 356.14342
66generate(0.20604355, -0.49924083, -0.84161484), (-0.49102785, -0.79669283, 0.35237565), (-0.84642889, 0.34064889, -0.40928278)280.29494, -64.65779, 390.46801
67generate(0.74833872, 0.33109547, -0.57478122), (-0.37738887, -0.50007902, -0.77942187), (-0.54550439, 0.80017714, -0.24927184)269.37085, 80.46032, 382.92394
68generate(0.82402071, 0.34509398, 0.4493392), (0.24754217, 0.49410414, -0.83341613), (-0.50963202, 0.79797794, 0.32172267)145.36427, 112.736, 313.52574
69generate(0.3284996, -0.47659077, 0.81544679), (0.52013181, 0.81192931, 0.26501109), (-0.78838618, 0.33709054, 0.51460573)79.64807, -12.43464, 278.17936
70generate(-0.05343129, -0.99841837, 0.01759331), (0.06367043, 0.01417291, 0.99787072), (-0.9965381, 0.05444564, 0.06281952)163.03981, -122.07003, 325.7323
71generate(-0.75460899, -0.33963786, 0.5614444), (-0.35877683, -0.50284775, -0.78639892), (0.54941395, -0.79485088, 0.25758745)68.43234, 82.05931, 361.98062
72generate(-0.81963867, -0.33670001, -0.46349893), (0.26693525, 0.4913968, -0.8290195), (0.50689978, -0.80321166, -0.31289395)192.97699, 112.95536, 431.04333
73generate(-0.31952108, 0.49032092, -0.81086117), (0.53399842, 0.80007054, 0.27336797), (0.78278801, -0.3456514, -0.51746491)256.5548, -12.93295, 467.72301
74generate(0.05459827, 0.99851011, -0.0005995), (0.07334046, -0.00340314, 0.99730147), (0.99581047, -0.05450283, -0.0734153)171.3034, -121.63226, 421.32959
75generate(-0.21430083, 0.48556737, 0.84753197), (-0.47842499, -0.80865094, 0.34232952), (0.85157737, -0.33212339, 0.40559341)55.03733, -62.92381, 355.97719
76generate(-0.45116817, 0.83929384, 0.30337992), (0.84939437, 0.2995432, 0.43451136), (0.27381668, 0.45371645, -0.84803642)113.46269, -20.87917, 489.28563
77generate(-0.74233803, 0.351082, 0.57068859), (0.36861599, -0.49724867, 0.7854052), (0.55952204, 0.79339251, 0.23971143)68.37124, -84.10386, 365.97715
78generate(-0.99352168, 0.00090343, 0.11366831), (0.00026432, -0.99994436, 0.01031218), (0.113677, 0.01027356, 0.99346539)114.81276, -2.98121, 254.18302
79generate(-0.85759187, 0.272693, -0.43609442), (0.25338885, -0.5138355, -0.81961549), (-0.44757574, -0.81339663, 0.37156311)188.60665, 110.38003, 308.39893
80generate(-0.52239897, 0.79084676, -0.31884619), (0.77818008, 0.28929198, -0.55744598), (-0.34860397, -0.53933385, -0.76654761)187.77226, 99.31849, 453.70033
81generate(-0.29925296, -0.4991036, 0.81323452), (-0.47240176, 0.81799543, 0.3282043), (-0.82902595, -0.28594958, -0.48056937)55.07569, -59.52065, 399.45293
82generate(-0.54938154, -0.77986978, -0.29998151), (-0.76723311, 0.3286082, 0.55079137), (-0.33096441, 0.53275346, -0.77886623)183.00096, -99.21154, 456.85709
83generate(-0.07653417, 0.04003269, -0.99626745), (-0.99691794, 0.01415557, 0.07715005), (0.01718798, 0.99909592, 0.03883751)288.76776, -49.82737, 369.61939
84generate(0.46583016, 0.82752647, -0.31337979), (-0.84403963, 0.30920039, -0.43816344), (-0.26570356, 0.46860838, 0.84250305)226.20997, 20.38462, 258.29937
85generate(0.32818238, 0.49432191, 0.80495393), (-0.5198708, 0.80600074, -0.28300337), (-0.78869254, -0.32559341, 0.52149195)81.78033, 14.39384, 276.73751
86generate(-0.50223278, 0.83122727, -0.23838174), (-0.7692119, -0.30348935, 0.56232317), (0.39506999, 0.46577443, 0.79181733)178.62566, -101.26911, 290.71612
87generate(-0.48887171, 0.78942956, 0.37123098), (-0.84116658, -0.31379877, -0.44041596), (-0.23118682, -0.52757741, 0.8174435)103.5133, 20.23638, 261.90696
88generate(-0.79625152, 0.28648644, 0.53284008), (-0.35514934, 0.49166829, -0.79506394), (-0.48974855, -0.82230559, -0.28975534)70.87687, 84.14139, 388.74032
89generate(-0.99958377, 0.01744821, 0.02310729), (0.01718053, 0.99978373, -0.01150932), (-0.02329168, -0.01110579, -0.99966803)125.8188, 2.13137, 495.93681
90generate(-0.81787019, 0.35411656, -0.45353401), (-0.23872421, 0.50834928, 0.82740204), (0.52355625, 0.78497145, -0.33121935)192.41122, -112.45861, 435.35453
91generate(0.86182408, -0.2813321, 0.42203687), (0.24349772, -0.50044468, -0.83082272), (0.44493691, 0.81878317, -0.36279811)149.70121, 111.3904, 436.19097
92generate(0.5356097, -0.78575571, 0.30937427), (0.77283673, 0.30842769, -0.55461318), (0.34036697, 0.53615953, 0.77245342)150.33391, 98.77246, 291.01532
93generate(0.46554588, -0.83411105, -0.29585804), (0.83863333, 0.30894623, 0.44860168), (-0.28278131, -0.45694796, 0.84334646)222.58214, -23.04408, 256.71529
94generate(0.74845846, -0.35957268, -0.55724958), (0.34995887, -0.49960567, 0.792413), (-0.56333818, -0.78809851, -0.24809077)266.60129, -85.71289, 380.69235
95generate(0.99337185, -0.01793649, -0.11356612), (-0.01785516, -0.99983676, 0.00168523), (-0.11358358, 0.00034669, -0.99352911)221.5584, -2.62781, 491.61443
96generate(-0.06033834, -0.05079157, -0.99688965), (0.99811594, -0.0140614, -0.05970475), (-0.01098095, -0.99860801, 0.05155015)289.40656, 46.02315, 365.19321
97generate(0.50264355, 0.77619594, -0.38062374), (0.83556296, -0.32323712, 0.44423777), (0.22178426, -0.54133558, -0.81103069)235.96095, -23.1735, 481.77387
98generate(0.40723981, 0.50759192, 0.7592854), (0.51343395, -0.81477009, 0.26931222), (0.75534188, 0.28015764, -0.59242863)90.58235, -14.64614, 476.47824
99generate(-0.21470485, -0.485402, 0.84752208), (0.47690023, -0.80937845, -0.34274024), (0.85233342, 0.33059592, 0.40525574)54.17906, 59.8207, 356.6247
100generate(-0.50368404, -0.83050197, -0.23785379), (0.77645017, -0.31451327, -0.54608391), (0.37871987, -0.45972472, 0.80325651)177.05917, 97.31639, 287.84677
101generate(-0.33691847, -0.48049199, -0.8097049), (-0.50579685, 0.81771322, -0.27478792), (0.79413955, 0.31697034, -0.51852968)254.87996, 13.94174, 468.87966
102generate(0.29123811, 0.51299022, -0.80748274), (-0.4685885, 0.81237461, 0.34708863), (0.83402328, 0.27729116, 0.47698309)280.31061, -61.71677, 346.95858
103generate(0.53626341, 0.78530574, 0.30939028), (-0.77291196, 0.30960482, 0.55385297), (0.33914366, -0.53614282, 0.77299978)151.72263, -99.83234, 289.96763
104generate(0.0595408, -0.03987622, 0.99743361), (-0.99820255, 0.00421462, 0.05976382), (-0.00659248, -0.99919349, -0.03956462)46.82023, -47.73056, 376.66637
105generate(-0.48011527, -0.82218224, 0.30579475), (-0.83311633, 0.31824288, -0.45236441), (0.27461045, -0.47194055, -0.83777373)110.57497, 22.58569, 487.24008
106generate(0.8623021, 0.26278089, 0.43288191), (-0.26230188, -0.49942462, 0.8256944), (0.43315898, -0.82554446, -0.3617305)148.8478, -114.05481, 434.16426
107generate(0.38934951, -0.51925677, 0.76077784), (-0.52641485, -0.80321306, -0.27880716), (0.75583245, -0.29192985, -0.58608592)88.79765, 12.21662, 475.21402
108generate(0.03585822, -0.999343, -0.00560801), (-0.06351662, 0.00331269, -0.99797563), (0.99733502, 0.03615082, -0.06336304)169.44779, 120.41622, 420.22195
109generate(0.29034118, -0.51401494, -0.80715646), (0.48668319, 0.80556145, -0.33794462), (0.82391834, -0.29469876, 0.4840529)279.34247, 61.01582, 345.18523
110generate(0.80111159, 0.26602051, -0.53615477), (0.36382715, 0.4948527, 0.78914544), (0.47523838, -0.82725574, 0.29965167)266.61098, -83.89524, 353.80205
111generate(-0.0370252, 0.99925126, -0.01138579), (-0.07349426, -0.01408246, -0.99719656), (-0.99660739, -0.03609363, 0.07395882)169.01812, 119.90987, 324.2694
112generate(-0.2820839, 0.5276884, 0.80123933), (0.48276965, 0.79978232, -0.35676055), (-0.82906683, 0.28617326, -0.48036352)58.13438, 63.18958, 399.92281
113generate(-0.79484132, -0.25747812, 0.5494916), (0.37233855, 0.50807407, 0.77667534), (-0.47914794, 0.82192949, -0.30796728)68.39495, -82.00059, 392.84663
114generate(-0.86668415, -0.27117485, -0.41872218), (-0.25217554, -0.48607631, 0.83674122), (-0.43042674, 0.83077817, 0.35290179)185.62006, -115.01275, 312.8199
115generate(-0.39832802, 0.50552662, -0.76536347), (-0.52771538, -0.80878679, -0.2595719), (-0.75023428, 0.30049071, 0.5889451)247.8086, 9.77478, 270.43684
116generate(-0.48835844, -0.78154016, 0.38820878), (0.841593, -0.30420614, 0.44629008), (-0.23069114, 0.54466775, 0.80630137)100.06324, -23.17301, 264.23992
117generate(-0.39850372, -0.52142185, -0.75453444), (0.5122337, -0.80894387, 0.28847907), (-0.7607889, -0.27153456, 0.58946636)245.56648, -17.06563, 269.45783
118generate(0.2227197, 0.47151538, -0.85327386), (0.46409003, -0.82099159, -0.33255269), (-0.85733074, -0.32193749, -0.40166946)283.24376, 58.04051, 388.51703
119generate(0.51680217, 0.82506602, 0.22844503), (0.7636949, -0.32369976, -0.55856043), (-0.38689912, 0.46311408, -0.79739007)161.02636, 98.35129, 456.88175
120generate(0.07733171, 0.05063511, 0.99572349), (0.99700456, -0.00430879, -0.07720912), (0.00038545, 0.99870558, -0.05082305)47.81457, 48.15857, 380.07427

-
Components

-
COXSACKIEVIRUS COAT ... , 4 types, 4 molecules 1234

#1: Protein COXSACKIEVIRUS COAT PROTEIN


Mass: 31380.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HUMAN HELA CELLS / Source: (natural) Human coxsackievirus B3 / Genus: Enterovirus / Species: Human enterovirus B / Strain: GAUNTT / References: UniProt: Q66282
#2: Protein COXSACKIEVIRUS COAT PROTEIN


Mass: 28877.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HUMAN HELA CELLS / Source: (natural) Human coxsackievirus B3 / Genus: Enterovirus / Species: Human enterovirus B / Strain: GAUNTT / References: UniProt: Q66282
#3: Protein COXSACKIEVIRUS COAT PROTEIN


Mass: 26198.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HUMAN HELA CELLS / Source: (natural) Human coxsackievirus B3 / Genus: Enterovirus / Species: Human enterovirus B / Strain: GAUNTT / References: UniProt: Q66282
#4: Protein COXSACKIEVIRUS COAT PROTEIN


Mass: 7379.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM HUMAN HELA CELLS / Source: (natural) Human coxsackievirus B3 / Genus: Enterovirus / Species: Human enterovirus B / Strain: GAUNTT / References: UniProt: Q66282

-
Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlvirus1drop
250 mMMES1drop
30.75 M1dropNaCl
42 Mammonium sulfate1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 185662 / % possible obs: 55 % / Observed criterion σ(F): 3
Reflection
*PLUS
Num. all: 3345935 / Num. obs: 1856628 / Num. measured all: 3113647 / Rmerge(I) obs: 0.128
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.5 Å / % possible obs: 44 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.5→10 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.264 --
obs0.264 125208 55 %
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6376 0 33 0 6409
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Num. reflection obs: 1252081
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more