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- PDB-5c9a: Crystal structure of empty coxsackievirus A16 particle -

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Basic information

Entry
Database: PDB / ID: 5c9a
TitleCrystal structure of empty coxsackievirus A16 particle
Components
  • VP0
  • VP1
  • VP3
KeywordsVIRUS / HAND-FOOT-AND-MOUTH DISEASE / IMMUNOGENICITY / PICORNAVIRUS / 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 / 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Jelly Rolls - #20 / Picornavirus coat protein / 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 ...Jelly Rolls - #20 / Picornavirus coat protein / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / 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
: / SPHINGOSINE / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRen, J. / Wang, X. / Zhu, L. / Hu, Z. / Gao, Q. / Yang, P. / Li, X. / Wang, J. / Shen, X. / Fry, E.E. ...Ren, J. / Wang, X. / Zhu, L. / Hu, Z. / Gao, Q. / Yang, P. / Li, X. / Wang, J. / Shen, X. / Fry, E.E. / Rao, Z. / Stuart, D.I.
CitationJournal: J.Virol. / Year: 2015
Title: Structures of Coxsackievirus A16 Capsids with Native Antigenicity: Implications for Particle Expansion, Receptor Binding, and Immunogenicity.
Authors: Ren, J. / Wang, X. / Zhu, L. / Hu, Z. / Gao, Q. / Yang, P. / Li, X. / Wang, J. / Shen, X. / Fry, E.E. / Rao, Z. / Stuart, D.I.
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP0
C: VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,45212
Polymers94,8653
Non-polymers5879
Water1,02757
1
A: VP1
B: VP0
C: VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,727,101720
Polymers5,691,896180
Non-polymers35,206540
Water3,243180
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: VP0
C: VP3
hetero molecules
x 5


  • icosahedral pentamer
  • 477 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)477,25860
Polymers474,32515
Non-polymers2,93445
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP0
C: VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 573 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)572,71072
Polymers569,19018
Non-polymers3,52154
Water32418
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
Unit cell
Length a, b, c (Å)491.400, 491.400, 708.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.5435, 0.3084, 0.7807), (-0.7728, 0.5469, 0.322), (-0.3276, -0.7783, 0.5356)-119.7, 93.66, 218.2
3generate(-0.1923, -0.2808, 0.9403), (-0.9489, -0.191, -0.2511), (0.2501, -0.9406, -0.2297)16.11, 307.7, 301.6
4generate(-0.1919, -0.9467, 0.2586), (-0.2819, -0.1992, -0.9385), (0.94, -0.253, -0.2287)218.4, 348.3, 131.6
5generate(0.5446, -0.7739, -0.3233), (0.3078, 0.543, -0.7813), (0.7802, 0.326, 0.5339)208.7, 156.3, -54.05
6generate(-0.9242, -0.3534, 0.1448), (-0.3549, 0.6547, -0.6673), (0.141, -0.6682, -0.7305)255.8, 204.2, 369.5
7generate(-0.2764, -0.5868, -0.7611), (-0.4772, 0.7712, -0.4213), (0.8342, 0.2467, -0.4932)364.3, 161.5, 130.3
8generate(0.5496, 0.1935, -0.8127), (-0.7204, 0.6023, -0.3438), (0.423, 0.7744, 0.4704)175.1, 198.7, -54
9generate(0.4136, 0.9085, 0.06011), (-0.7427, 0.3749, -0.5548), (-0.5266, 0.1848, 0.8298)-50.16, 266.4, 71.7
10generate(-0.4992, 0.5735, 0.6495), (-0.5094, 0.4121, -0.7554), (-0.7009, -0.708, 0.08644)-0.568, 268.1, 333.8
11generate(0.2667, 0.585, 0.7659), (0.5769, -0.7335, 0.3594), (0.772, 0.346, -0.5332)-116.9, 79.86, 133.5
12generate(-0.5535, -0.2033, 0.8076), (0.767, -0.5024, 0.3992), (0.3246, 0.8404, 0.434)74.6, 20.57, -42.8
13generate(-0.4061, -0.9112, -0.06934), (0.6722, -0.3493, 0.6528), (-0.6191, 0.2185, 0.7543)298.3, -31.59, 93.06
14generate(0.507, -0.5637, -0.6521), (0.421, -0.4982, 0.758), (-0.7521, -0.6588, -0.01527)245.6, -0.573, 352.8
15generate(0.923, 0.3601, -0.136), (0.3698, -0.7318, 0.5724), (0.1066, -0.5786, -0.8086)-10.89, 67.15, 377.4
16generate(-0.3428, -0.2306, -0.9107), (-0.2322, -0.9185, 0.32), (-0.9103, 0.3212, 0.2613)355.1, 209, 202.9
17generate(0.2851, 0.4836, -0.8276), (0.4818, -0.8187, -0.3124), (-0.8286, -0.3097, -0.4664)174.7, 220.1, 399.2
18generate(0.0487, 0.9969, -0.06166), (0.9974, -0.05187, -0.05082), (-0.05387, -0.05902, -0.9968)5.167, 16.22, 366.6
19generate(-0.7263, 0.6013, 0.3331), (0.5981, 0.314, 0.7374), (0.3388, 0.7348, -0.5876)80.28, -118.2, 148.1
20generate(-0.9686, -0.1569, -0.193), (-0.1563, -0.2197, 0.963), (-0.1934, 0.9629, 0.1883)296.6, 0.3957, 48.8
21generate(0.7227, -0.5519, 0.4161), (-0.6085, -0.2223, 0.7618), (-0.3279, -0.8037, -0.4965)29, 91.6, 403.9
22generate(0.6866, -0.403, 0.6052), (-0.4057, -0.9031, -0.1411), (0.6034, -0.1486, -0.7835)-18.28, 310.1, 258.8
23generate(0.4907, -0.4803, 0.727), (0.5236, -0.5044, -0.6866), (0.6965, 0.7176, 0.003973)-6.062, 242.6, 1.107
24generate(0.4069, -0.6782, 0.6119), (0.8959, 0.4271, -0.1224), (-0.1783, 0.598, 0.7814)49.02, -18.41, -13.31
25generate(0.549, -0.7222, 0.4208), (0.1955, 0.6004, 0.7754), (-0.8127, -0.3434, 0.4708)70.65, -111.7, 236.2
26generate(-0.5002, 0.4739, -0.7247), (-0.433, 0.588, 0.6833), (0.7499, 0.6555, -0.08889)254.7, -16.03, 18.51
27generate(-0.4049, 0.6711, -0.621), (-0.9116, -0.3492, 0.2169), (-0.0713, 0.654, 0.7532)200.3, 240.9, -28.39
28generate(-0.5396, 0.7262, -0.426), (-0.295, -0.637, -0.7122), (-0.7886, -0.2587, 0.5579)175.7, 363.9, 207.2
29generate(-0.7189, 0.5618, -0.4093), (0.5618, 0.123, -0.818), (-0.4092, -0.8181, -0.4041)215.3, 182.9, 398.9
30generate(-0.6939, 0.4058, -0.5949), (0.4764, 0.8782, 0.04332), (0.54, -0.2533, -0.8027)264.1, -51.33, 282.3
31generate(-0.4141, -0.8936, 0.1732), (0.7495, -0.4428, -0.4921), (0.5165, -0.07397, 0.8531)254.3, 172.1, -28.62
32generate(0.4104, -0.7463, -0.524), (0.9101, 0.3711, 0.1843), (0.05694, -0.5526, 0.8315)257.3, -66.77, 90.88
33generate(0.9707, 0.1308, -0.2016), (0.1476, 0.3376, 0.9296), (0.1896, -0.9322, 0.3084)23.19, -100.3, 213.7
34generate(0.4915, 0.5289, 0.6918), (-0.486, -0.4926, 0.7219), (0.7226, -0.6911, 0.01494)-124.9, 116.4, 170.7
35generate(-0.3638, -0.1067, 0.9253), (-0.1181, -0.9801, -0.1594), (0.924, -0.1673, 0.344)18.29, 286.4, 23.1
36generate(0.1912, 0.9723, 0.1342), (0.2949, 0.07351, -0.9527), (-0.9362, 0.2217, -0.2727)-43.91, 246.7, 312.3
37generate(-0.6926, 0.4774, 0.5407), (0.4116, 0.8772, -0.2472), (-0.5923, 0.05133, -0.8041)54.91, 8.995, 384.1
38generate(-0.9217, -0.3756, -0.09696), (-0.3748, 0.7977, 0.4724), (-0.1001, 0.4718, -0.876)300.9, -11.43, 284.9
39generate(-0.1793, -0.4096, -0.8945), (-0.9753, -0.04558, 0.2163), (-0.1294, 0.9111, -0.3913)354.1, 211, 149
40generate(0.5071, 0.4238, -0.7505), (-0.5654, -0.4935, -0.6608), (-0.6504, 0.7595, -0.01064)141, 370.7, 165
41generate(0.7223, -0.6096, -0.3267), (-0.5511, -0.2218, -0.8045), (0.4179, 0.7611, -0.4961)167.2, 360.5, 118.6
42generate(0.9704, 0.1463, 0.1923), (0.1338, 0.337, -0.9319), (-0.2011, 0.9301, 0.3075)-48.12, 230, 32.03
43generate(0.3526, 0.2286, 0.9074), (0.1182, 0.951, -0.2856), (-0.9283, 0.208, 0.3084)-108.5, 41.97, 210
44generate(-0.2756, -0.4803, 0.8327), (-0.5806, 0.7735, 0.254), (-0.7661, -0.4135, -0.492)70, 55.28, 408.3
45generate(-0.04766, -0.9964, 0.07012), (-0.9965, 0.04259, -0.07213), (0.06889, -0.07331, -0.9949)240, 254.1, 352.4
46generate(0.1899, 0.2892, -0.9382), (0.9727, 0.07418, 0.2198), (0.1332, -0.9544, -0.2673)230, -44.39, 324.8
47generate(0.1825, 0.949, -0.2572), (0.3958, 0.1685, 0.9027), (0.9, -0.2666, -0.3449)29.22, -105.7, 159.4
48generate(-0.5529, 0.7706, 0.3169), (-0.2105, -0.4972, 0.8417), (0.8062, 0.3987, 0.4371)40.8, 62.05, -48.36
49generate(-1, -0.000958, -0.00925), (-0.000189, -0.9924, 0.1232), (-0.009298, 0.1232, 0.9923)249, 223.8, -11.92
50generate(-0.5406, -0.2982, -0.7866), (0.725, -0.6395, -0.2558), (-0.4267, -0.7086, 0.5619)366, 158.1, 217.5
51generate(-0.4988, -0.4338, 0.7504), (0.4801, 0.5825, 0.6559), (-0.7216, 0.6874, -0.08232)106.5, -122.5, 195.6
52generate(-0.1793, -0.9749, -0.1318), (-0.4085, -0.04816, 0.9115), (-0.895, 0.2173, -0.3896)289.4, 19.06, 329
53generate(0.6992, -0.4793, -0.5305), (-0.4814, -0.8642, 0.1464), (-0.5286, 0.153, -0.835)189.9, 263.4, 369.9
54generate(0.9231, 0.3694, 0.1069), (0.3602, -0.7333, -0.5766), (-0.1346, 0.5708, -0.81)-54.89, 271.5, 265.6
55generate(0.1806, 0.4007, 0.8983), (0.9521, 0.1579, -0.2618), (-0.2467, 0.9025, -0.353)-106.9, 33.81, 157.6
56generate(-0.4122, 0.7528, 0.5132), (-0.8963, -0.4361, -0.08031), (0.1634, -0.4931, 0.8545)-9.128, 300.8, 66.38
57generate(-0.9726, -0.1221, 0.1979), (-0.1235, -0.4499, -0.8845), (0.197, -0.8847, 0.4224)223.9, 349.3, 186.5
58generate(-0.4997, -0.5183, -0.694), (0.5718, 0.4045, -0.7137), (0.6506, -0.7535, 0.09427)371.7, 128.8, 172.6
59generate(0.3534, 0.1083, -0.9292), (0.2315, 0.9523, 0.199), (0.9064, -0.2854, 0.3115)230.6, -57.65, 45.06
60generate(0.4079, 0.8945, -0.183), (-0.6797, 0.4313, 0.5933), (0.6096, -0.1176, 0.7839)-4.893, 49.05, -22.67

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein VP1


Mass: 33090.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A16 / Cell line: vero / References: UniProt: I3W9E1
#2: Protein VP0


Mass: 35120.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A16 / Cell line: vero / References: UniProt: I3W9E1
#3: Protein VP3


Mass: 26654.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A16 / Cell line: vero / References: UniProt: I3W9E1

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Non-polymers , 4 types, 66 molecules

#4: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.2 M Sodium chloride, 0.1 M Sodium acetate trihydrate pH 7.0

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 1437314 / % possible obs: 62.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.535 / Net I/σ(I): 1.4
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 0.4 / % possible all: 16.2

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C4W

5c4w


Resolution: 2.7→49.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 30503649.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.291 7095 0.5 %RANDOM
Rwork0.291 ---
obs0.291 1418902 61.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 8.44418 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0 Å20 Å2
2--1.01 Å20 Å2
3----2.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.5 Å
Luzzati d res low-50 Å
Luzzati sigma a0.64 Å0.63 Å
Refinement stepCycle: 1 / Resolution: 2.7→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6358 0 29 57 6444
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.696
X-RAY DIFFRACTIONc_mcangle_it9.7712
X-RAY DIFFRACTIONc_scbond_it10.868
X-RAY DIFFRACTIONc_scangle_it14.0616
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.397 178 0.6 %
Rwork0.405 31320 -
obs--13.7 %

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