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- PDB-2ztn: Hepatitis E virus ORF2 (Genotype 3) -

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Basic information

Entry
Database: PDB / ID: 2ztn
TitleHepatitis E virus ORF2 (Genotype 3)
ComponentsCapsid protein
KeywordsVIRUS / HEV
Function / homology
Function and homology information


viral capsid / host cell surface / host cell cytoplasm / structural molecule activity / RNA binding / cytoplasm
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #190 / Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / Jelly Rolls - #20 / Elongation Factor Tu (Ef-tu); domain 3 / Viral coat protein subunit / Jelly Rolls / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHepatitis E virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.56 Å
AuthorsYamashita, T. / Unno, H. / Mori, Y. / Li, T.C. / Takeda, N. / Matsuura, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Biological and immunological characteristics of hepatitis E virus-like particles based on the crystal structure
Authors: Yamashita, T. / Mori, Y. / Miyazaki, N. / Cheng, R.H. / Yoshimura, M. / Unno, H. / Shima, R. / Moriishi, K. / Tsukihara, T. / Li, T.C. / Takeda, N. / Miyamura, T. / Matsuura, Y.
History
DepositionOct 8, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)51,6101
Polymers51,6101
Non-polymers00
Water00
1
A: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,096,62460
Polymers3,096,62460
Non-polymers00
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: Capsid protein
x 5


  • icosahedral pentamer
  • 258 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)258,0525
Polymers258,0525
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 310 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)309,6626
Polymers309,6626
Non-polymers00
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
Unit cell
Length a, b, c (Å)336.864, 349.423, 359.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.24738, -0.96068, -0.12606), (0.43495, -0.22636, 0.87154), (-0.86581, 0.16077, 0.47385)4.85432, -7.99233, 6.6926
3generate(-0.24733, 0.43491, -0.86584), (-0.96069, -0.22638, 0.16071), (-0.12612, 0.87155, 0.47381)10.47059, 1.78299, 4.41256
4generate(0.42815, 0.06538, -0.90134), (-0.55258, 0.80814, -0.20386), (0.71508, 0.58535, 0.38214)8.66324, 3.27993, 2.50986
5generate(-0.49756, -0.44703, -0.74337), (-0.82884, 0.49779, 0.25542), (0.25586, 0.74322, -0.6182)10.34348, 0.62574, 11.58599
6generate(-0.4975, -0.8289, 0.25577), (-0.44711, 0.49768, 0.74324), (-0.74337, 0.25541, -0.6182)2.68186, -4.27485, 14.67693
7generate(0.42828, -0.55251, 0.71506), (0.0652, 0.80813, 0.58538), (-0.90129, -0.20408, 0.38213)-3.69816, -4.70406, 7.54657
8generate(-0.7436, -0.46838, 0.47716), (0.64533, -0.6895, 0.32886), (0.17497, 0.55246, 0.81497)1.73745, -4.44848, 0.86518
9generate(0.33409, -0.86754, 0.36846), (0.93502, 0.35434, -0.0135), (-0.11885, 0.34902, 0.92955)-0.72594, -2.76966, 0.89094
10generate(0.70393, 0.66388, -0.25248), (-0.56931, 0.31481, -0.75946), (-0.42471, 0.67835, 0.59956)2.81302, 7.59638, 4.37278
11generate(0.22471, 0.50492, -0.8334), (-0.25731, -0.79417, -0.55053), (-0.93984, 0.33815, -0.04853)8.75348, 5.07152, 10.92129
12generate(-0.80137, 0.30042, 0.51726), (-0.47706, 0.20068, -0.85565), (-0.36086, -0.93246, -0.0175)1.59599, 8.04389, 8.93978
13generate(-0.80137, -0.47702, -0.36091), (0.30043, 0.20076, -0.93244), (0.51724, -0.85566, -0.01757)8.34764, 6.23231, 6.21667
14generate(-0.45952, -0.3173, 0.82956), (0.70709, 0.43451, 0.55787), (-0.53746, 0.84293, 0.02469)-1.84354, -6.42822, 9.10316
15generate(-0.45954, 0.70712, -0.53741), (-0.31726, 0.43447, 0.84296), (0.82956, 0.55787, 0.02469)8.61021, -5.45052, 4.9136
16generate(-0.77904, -0.06543, -0.62355), (-0.06535, -0.98065, 0.18455), (-0.62356, 0.18452, 0.75969)10.26939, -1.13865, 3.76746
17generate(0.33411, 0.93504, -0.11864), (-0.86748, 0.35428, 0.34925), (0.36859, -0.01377, 0.92949)2.9254, 0.03873, -0.57965
18generate(0.70395, -0.56924, -0.42476), (0.66385, 0.31471, 0.67842), (-0.25251, -0.75955, 0.59943)4.19864, -7.22183, 3.86981
19generate(0.22474, -0.25718, -0.93987), (0.50484, -0.79426, 0.33805), (-0.83344, -0.55046, -0.04867)9.59963, -4.07617, 10.61907
20generate(0.88046, 0.33421, -0.33629), (0.45365, -0.3877, 0.80243), (0.1378, -0.85906, -0.49297)2.9367, -7.47206, 11.05307
21generate(0.2819, 0.8924, 0.35236), (-0.14752, -0.32257, 0.93498), (0.94803, -0.31555, 0.04072)-0.51369, -6.68742, 4.45029
22generate(-0.74359, 0.64532, 0.17502), (-0.4683, -0.68948, 0.55256), (0.47725, 0.32892, 0.81489)4.01083, -2.7384, -0.05248
23generate(0.31199, 0.59537, 0.7404), (-0.66304, 0.69459, -0.27914), (-0.68047, -0.40383, 0.61147)-3.58217, 4.17695, 5.11572
24generate(-0.43411, 0.89664, -0.08705), (-0.74341, -0.41114, -0.52755), (-0.50882, -0.1643, 0.84505)5.05951, 6.38433, 2.75647
25generate(-0.4341, -0.74329, -0.509), (0.89664, -0.41115, -0.1643), (-0.08716, -0.52771, 0.84494)8.35653, -1.45754, 1.48976
26generate(0.31194, -0.66297, -0.68056), (0.5954, 0.69461, -0.40375), (0.7404, -0.27926, 0.61141)7.36536, 1.26703, 0.7036
27generate(0.28193, -0.14759, 0.94802), (0.8924, -0.32251, -0.3156), (0.35233, 0.93499, 0.04079)-5.05173, -0.27879, 6.25498
28generate(0.88047, 0.45366, 0.13773), (0.33408, -0.38755, -0.85918), (-0.3364, 0.80249, -0.49278)-0.70628, 5.61256, 12.47561
29generate(-0.13915, 0.49341, 0.85859), (-0.92693, -0.37, 0.06241), (0.34847, -0.78717, 0.50884)-3.07187, 2.45224, 2.70064
30generate(0.64472, -0.76436, 0.00982), (-0.30882, -0.24869, 0.91803), (-0.69926, -0.5949, -0.39639)1.05573, -6.04706, 12.86977
31generate(-0.84059, -0.53001, 0.1118), (-0.53003, 0.76223, -0.37159), (0.11173, -0.37161, -0.92164)4.85886, 4.49418, 14.38965
32generate(0.7019, -0.55424, 0.44738), (-0.14742, -0.72754, -0.67004), (0.69685, 0.40435, -0.59237)-2.48811, 5.63203, 10.02913
33generate(-0.12036, 0.78375, 0.6093), (0.94582, 0.27697, -0.16944), (-0.30156, 0.5559, -0.77462)-1.23857, -1.59688, 14.51142
34generate(-0.49517, 0.15767, 0.85437), (0.01334, 0.98466, -0.17398), (-0.8687, -0.07475, -0.48967)-1.92263, 1.29152, 14.09784
35generate(0.5721, 0.19901, 0.79567), (0.46159, 0.72378, -0.51292), (-0.67797, 0.66071, 0.32221)-4.77571, 2.51513, 7.26726
36generate(0.88537, -0.46466, 0.01426), (0.19374, 0.34094, -0.9199), (0.42258, 0.81722, 0.39188)0.26572, 6.45297, 3.33357
37generate(0.01306, -0.91378, -0.40599), (-0.41763, 0.36393, -0.83255), (0.90852, 0.18043, -0.37687)6.22329, 7.65637, 7.74774
38generate(0.92671, -0.1405, -0.34854), (-0.14051, -0.98975, 0.02536), (-0.34853, 0.02547, -0.93695)2.90261, 0.29402, 15.90852
39generate(0.22017, -0.97526, 0.01967), (-0.97526, -0.22049, -0.01578), (0.01972, -0.01571, -0.99968)2.2862, 3.16905, 15.26841
40generate(-0.9718, 0.2268, 0.06459), (0.2268, 0.8239, 0.51938), (0.06458, 0.51938, -0.8521)5.58824, -4.67866, 13.96983
41generate(-0.54967, 0.57557, 0.60546), (0.57566, -0.26425, 0.77381), (0.60537, 0.77388, -0.18609)0.11335, -7.66578, 7.20758
42generate(0.57207, 0.46176, -0.67788), (0.1989, 0.7237, 0.66083), (0.79572, -0.51287, 0.32216)6.47575, -5.64454, 2.7223
43generate(0.88612, 0.1952, 0.42035), (-0.46316, 0.34014, 0.81841), (0.01678, -0.91989, 0.39181)-2.89946, -4.80737, 4.63711
44generate(0.64488, -0.30892, -0.69906), (-0.76421, -0.24836, -0.59523), (0.01026, 0.91809, -0.39625)6.44603, 6.95197, 10.64154
45generate(-0.04886, 0.98219, 0.18144), (0.13065, 0.18638, -0.97375), (-0.99022, -0.02388, -0.13743)1.819, 7.07775, 11.7748
46generate(0.61977, 0.59495, 0.51179), (0.595, -0.78146, 0.1879), (0.51173, 0.18806, -0.83831)-2.76743, -3.21724, 12.5181
47generate(-0.78984, 0.58, -0.1994), (0.57993, 0.60048, -0.55054), (-0.19958, -0.55047, -0.81065)7.02356, 2.43324, 14.49716
48generate(-0.33757, -0.64911, 0.68169), (-0.64909, -0.36396, -0.66799), (0.68171, -0.66797, -0.29847)-1.08593, 7.18996, 7.86184
49generate(-0.15806, 0.03164, 0.98692), (0.03169, -0.99881, 0.0371), (0.98692, 0.03714, 0.15687)-3.98805, -0.33554, 3.41759
50generate(-0.95494, -0.08646, 0.28392), (-0.08647, -0.83407, -0.54484), (0.28391, -0.54484, 0.78902)3.85881, 4.4952, 0.76042
51generate(-0.67049, 0.39978, -0.62499), (0.39967, -0.5151, -0.75825), (-0.62507, -0.75819, 0.18559)9.90772, 4.63097, 8.20831
52generate(0.30263, 0.8209, -0.48429), (0.82087, -0.4827, -0.30525), (-0.48435, -0.30516, -0.81993)5.82734, -0.13499, 15.43793
53generate(-0.49525, 0.01336, -0.86865), (0.15775, 0.98464, -0.0748), (0.85431, -0.17407, -0.48975)11.27146, 0.079, 8.77428
54generate(-0.12031, 0.94589, -0.30137), (0.78382, 0.2768, 0.55588), (0.60922, -0.16934, -0.77471)5.757, -6.61513, 11.72813
55generate(0.70194, -0.1475, 0.6968), (-0.55423, -0.72757, 0.40431), (0.44733, -0.66999, -0.59246)-4.41332, -1.33167, 10.85125
56generate(0.01317, -0.41766, 0.90851), (-0.91383, 0.36378, 0.18048), (-0.40588, -0.8326, -0.37688)-3.89958, 1.46594, 11.83476
57generate(-0.05528, -0.61535, -0.78631), (-0.61554, -0.59906, 0.51209), (-0.78616, 0.51232, -0.34566)9.30061, -1.9774, 12.73899
58generate(-0.96515, -0.17182, -0.19738), (-0.17178, -0.153, 0.97318), (-0.19741, 0.97317, 0.11815)7.58174, -6.89642, 7.34042
59generate(-0.04894, 0.13078, -0.9902), (0.98221, 0.18624, -0.02395), (0.18128, -0.97376, -0.13757)10.81796, -2.81667, 8.19261
60generate(-0.13923, -0.92701, 0.34824), (0.49346, -0.36984, -0.78722), (0.85855, 0.06224, 0.50893)0.91661, 4.55633, 1.12896

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Components

#1: Protein Capsid protein


Mass: 51610.402 Da / Num. of mol.: 1 / Fragment: UNP residues 129-606
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus / Strain: Genotype 3 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Tn5 / References: UniProt: Q1AHU7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 12

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Sample preparation

Crystal growTemperature: 293 K / Method: evaporation / pH: 8
Details: 5% PEG10000, 100mM Tris, pH8.0, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 26, 2008 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.56→50 Å / Num. all: 503674 / Num. obs: 503674 / % possible obs: 99.9 % / Observed criterion σ(I): 9.8 / Redundancy: 5.6 % / Rmerge(I) obs: 0.131
Reflection shellResolution: 3.56→3.68 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3.2 / Num. unique all: 44942 / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.56→20 Å / σ(I): 3.2
RfactorNum. reflection% reflection
Rfree0.309 --
Rwork0.305 --
obs-503674 99 %
Refinement stepCycle: LAST / Resolution: 3.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3590 0 0 0 3590

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