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- PDB-2zzq: Crystal structure analysis of the HEV capsid protein, PORF2 -

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Basic information

Entry
Database: PDB / ID: 2zzq
TitleCrystal structure analysis of the HEV capsid protein, PORF2
ComponentsProtein ORF3, Capsid protein
KeywordsVIRUS / Viral capsid protein / Virus-like particle / hepatitis E virus / HEV / Cytoplasm / Host-virus interaction / Phosphoprotein
Function / homology
Function and homology information


: / T=1 icosahedral viral capsid / host cell endoplasmic reticulum / host cell Golgi apparatus / host cell surface / membrane => GO:0016020 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / symbiont entry into host cell / structural molecule activity ...: / T=1 icosahedral viral capsid / host cell endoplasmic reticulum / host cell Golgi apparatus / host cell surface / membrane => GO:0016020 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / symbiont entry into host cell / structural molecule activity / RNA binding / extracellular region
Similarity search - Function
Hepatitis E virus Orf2, capsid / Hepatitis E virus ORF-2 (Putative capsid protein) / 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 ...Hepatitis E virus Orf2, capsid / Hepatitis E virus ORF-2 (Putative capsid protein) / 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
Secreted protein ORF2 / Protein ORF3
Similarity search - Component
Biological speciesHepatitis E virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.81 Å
AuthorsMiyazaki, N. / Xing, L. / Wang, C.-Y. / Li, T.-C. / Takeda, N. / Higashiura, A. / Nakagawa, A. / Tsukihara, T. / Miyamura, T. / Cheng, R.H.
CitationJournal: To be Published
Title: Role of protein domain-modularity in designating capsid assembly and antigenicity
Authors: Miyazaki, N. / Xing, L. / Wang, C.-Y. / Li, T.-C. / Takeda, N. / Higashiura, A. / Nakagawa, A. / Tsukihara, T. / Miyamura, T. / Cheng, R.H.
History
DepositionFeb 23, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 1.3Mar 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 / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ORF3, Capsid protein


Theoretical massNumber of molelcules
Total (without water)59,1781
Polymers59,1781
Non-polymers00
Water00
1
A: Protein ORF3, Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,550,69060
Polymers3,550,69060
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: Protein ORF3, Capsid protein
x 5


  • icosahedral pentamer
  • 296 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)295,8915
Polymers295,8915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Protein ORF3, Capsid protein
x 6


  • icosahedral 23 hexamer
  • 355 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)355,0696
Polymers355,0696
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)337.000, 347.000, 354.000
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
1generate(1), (1), (1)
2generate(-0.39434, -0.898455, 0.193062), (0.436681, 0.001648, 0.899615), (-0.808582, 0.439061, 0.391688)-5.45386, -5.11386, 2.07684
3generate(-0.394282, 0.437587, -0.808121), (-0.898211, 0.002436, 0.439556), (0.194313, 0.899173, 0.392086)1.69156, -5.72305, 4.90218
4generate(0.370158, 0.036327, -0.928258), (-0.410705, 0.902675, -0.128451), (0.833249, 0.428787, 0.349052)1.91988, -0.43907, 4.54887
5generate(-0.654506, -0.352125, -0.669052), (-0.627283, 0.746912, 0.220542), (0.422064, 0.564031, -0.709741)-1.56966, -2.48005, 7.81926
6generate(-0.6546, -0.627671, 0.421341), (-0.353039, 0.746653, 0.563802), (-0.668478, 0.220315, -0.710352)-5.87308, -3.10052, 5.16709
7generate(0.367523, -0.40978, 0.834869), (0.034259, 0.903051, 0.428165), (-0.929384, -0.128759, 0.345931)-4.8905, -1.60449, 0.35824
8generate(-0.608766, -0.290502, 0.73825), (0.73241, -0.563447, 0.382234), (0.304925, 0.773393, 0.555774)-5.72525, -4.73637, 4.15855
9generate(0.385727, -0.741659, 0.548777), (0.910607, 0.401684, -0.097185), (-0.148356, 0.537207, 0.830301)-4.94474, 0.08918, 1.79993
10generate(0.621899, 0.658469, -0.423864), (-0.73969, 0.316237, -0.594014), (-0.257098, 0.682944, 0.683731)2.88832, -1.41987, 2.46462
11generate(0.0076, 0.329381, -0.944167), (-0.535947, -0.795786, -0.28193), (-0.844218, 0.508166, 0.170482)2.4502, -5.23731, 2.8866
12generate(-0.797362, 0.347802, 0.493202), (-0.541303, -0.050817, -0.839291), (-0.266844, -0.93619, 0.228786)-3.29958, -1.24538, -0.5956
13generate(-0.796111, -0.542453, -0.268239), (0.350594, -0.052148, -0.935075), (0.493246, -0.838466, 0.231696)-3.55728, 0.51547, 0.7052
14generate(-0.356366, 0.010025, 0.934293), (0.771339, 0.567469, 0.288122), (-0.527293, 0.823334, -0.209959)-5.10992, -1.0122, 5.5525
15generate(-0.359116, 0.770359, -0.526862), (0.006795, 0.566662, 0.823922), (0.933268, 0.292304, -0.208732)1.98243, -3.84304, 5.99437
16generate(-0.920363, -0.10552, -0.376561), (-0.106793, -0.858492, 0.501584), (-0.376202, 0.501854, 0.778855)-2.18963, -7.25541, 1.58702
17generate(0.384933, 0.910453, -0.151334), (-0.741128, 0.40264, 0.537224), (0.550051, -0.094637, 0.829752)2.31731, -4.67232, 1.09405
18generate(0.621528, -0.738237, -0.262125), (0.661145, 0.314817, 0.681012), (-0.420226, -0.596571, 0.683749)-2.01437, -3.2171, -1.42806
19generate(0.007312, -0.535866, -0.844272), (0.329572, -0.795829, 0.507974), (-0.944102, -0.281963, 0.170787)-0.48129, -6.42851, 0.39677
20generate(0.89153, 0.037899, -0.451373), (0.415771, -0.463902, 0.78226), (-0.179746, -0.885076, -0.42934)1.31396, -6.15409, 1.76049
21generate(0.512204, 0.819223, 0.257915), (0.034992, -0.319954, 0.946786), (0.858151, -0.475923, -0.192548)0.90692, -6.95259, 3.98155
22generate(-0.609732, 0.731567, 0.305019), (-0.289955, -0.564032, 0.773171), (0.737668, 0.382986, 0.556029)-1.27251, -7.5313, 3.67753
23generate(0.312391, 0.683198, 0.660039), (-0.757739, 0.598257, -0.260617), (-0.572925, -0.418724, 0.704577)-1.13603, -1.48631, -1.04271
24generate(-0.480035, 0.872774, -0.088498), (-0.846767, -0.487354, -0.213242), (-0.229242, -0.027426, 0.972983)0.37312, -5.16344, -0.41106
25generate(-0.481411, -0.84502, -0.232775), (0.871874, -0.488912, -0.028308), (-0.089886, -0.216578, 0.972118)-4.09544, -3.01561, -0.56106
26generate(0.311385, -0.758218, -0.572839), (0.684306, 0.597177, -0.418456), (0.659367, -0.261696, 0.704805)-1.44003, 1.32059, 1.30517
27generate(0.509602, 0.032379, 0.859801), (0.820488, -0.319149, -0.474282), (0.259048, 0.947151, -0.189206)-3.36282, -1.13246, 6.98273
28generate(0.890768, 0.415907, -0.183178), (0.034188, -0.463254, -0.885565), (-0.45317, 0.782572, -0.426871)1.79242, -1.31947, 6.23831
29generate(-0.028446, 0.495958, 0.867881), (-0.878476, -0.426665, 0.215029), (0.476939, -0.756296, 0.447824)-2.74131, -5.96977, 0.28361
30generate(0.444167, -0.888924, 0.111943), (-0.380277, -0.073914, 0.921915), (-0.811237, -0.452053, -0.370868)-3.90471, -6.73259, 1.85455
31generate(-0.903195, -0.40749, 0.134871), (-0.407111, 0.713701, -0.569992), (0.136009, -0.569722, -0.810505)-4.66392, 0.33593, 4.38165
32generate(0.751421, -0.586856, 0.301607), (-0.269081, -0.689913, -0.672024), (0.602464, 0.423816, -0.676327)-3.41878, -3.309, 7.42054
33generate(0.067511, 0.933452, 0.352293), (0.869237, 0.118302, -0.480033), (-0.489764, 0.338634, -0.803404)0.20933, 0.25942, 6.07759
34generate(-0.473534, 0.404009, 0.782651), (-0.016535, 0.884359, -0.466515), (-0.880621, -0.233852, -0.412094)-3.56663, 1.15988, 2.58297
35generate(0.640125, 0.398589, 0.656785), (0.291275, 0.665154, -0.687553), (-0.710915, 0.631425, 0.309682)-1.57676, 1.56336, 3.36879
36generate(0.904604, -0.420009, -0.072691), (0.090552, 0.355998, -0.930089), (0.416524, 0.834781, 0.36007)-1.23323, 1.1688, 5.15002
37generate(-0.051585, -0.918195, -0.392756), (-0.342522, 0.385692, -0.856692), (0.938092, 0.090335, -0.334398)-3.17746, 0.45527, 6.0478
38generate(0.768297, -0.377935, -0.516607), (-0.377715, -0.919272, 0.110773), (-0.516768, 0.110024, -0.849026)0.13622, -6.64179, 5.60208
39generate(0.028069, -0.999184, 0.029019), (-0.999129, -0.02894, -0.030044), (0.030859, -0.02815, -0.999127)-4.57428, -4.4731, 6.4051
40generate(-0.888434, 0.456327, 0.049493), (0.456145, 0.865735, 0.205996), (0.051153, 0.20559, -0.977301)-1.60235, -0.43968, 6.94594
41generate(-0.269482, 0.770261, 0.577995), (0.769913, -0.188201, 0.609766), (0.578458, 0.609327, -0.542317)-1.51504, -4.31205, 7.70439
42generate(0.645391, 0.292886, -0.70547), (0.394035, 0.663546, 0.635959), (0.654376, -0.688422, 0.312839)2.46435, -2.478, 1.08865
43generate(0.903754, 0.090353, 0.418407), (-0.421815, 0.354239, 0.834618), (-0.072805, -0.930779, 0.358257)-1.22756, -5.22053, -0.73477
44generate(0.443031, -0.379217, -0.812354), (-0.889484, -0.07274, -0.45114), (0.111988, 0.922445, -0.369534)0.6544, -3.24113, 7.24031
45generate(-0.064079, 0.996003, -0.062228), (-0.128091, -0.07005, -0.989286), (-0.98969, -0.055421, 0.132067)1.55696, -0.10954, 1.1504
46generate(0.823513, 0.513544, 0.241034), (0.513751, -0.855315, 0.067054), (0.240596, 0.068612, -0.968197)0.50088, -4.85895, 6.93376
47generate(-0.740071, 0.577055, -0.345403), (0.578261, 0.283774, -0.764909), (-0.343378, -0.76582, -0.543701)0.18086, 1.2411, 2.22792
48generate(-0.295253, -0.632685, 0.715916), (-0.630929, -0.433582, -0.643379), (0.717464, -0.64165, -0.271163)-6.11355, -3.15064, 3.32908
49generate(0.093779, 0.095316, 0.99102), (0.099933, -0.99128, 0.085885), (0.990565, 0.090982, -0.102486)-4.18522, -6.09546, 5.01691
50generate(-0.882255, -0.081791, 0.463613), (-0.077157, -0.946354, -0.313784), (0.464407, -0.312609, 0.828615)-4.46969, -4.94734, 0.27139
51generate(-0.760947, 0.227649, -0.607567), (0.231224, -0.77979, -0.581776), (-0.606214, -0.583185, 0.54074)-0.05651, -3.11648, -1.00969
52generate(0.294487, 0.594899, -0.747912), (0.592104, -0.727884, -0.345829), (-0.750126, -0.340999, -0.566594)3.1259, -2.74677, 2.776
53generate(-0.47294, -0.015162, -0.880964), (0.404184, 0.884712, -0.23221), (0.78292, -0.465892, -0.412287)0.39387, 1.013, 4.409
54generate(0.06869, 0.869518, -0.489102), (0.933553, 0.116857, 0.338858), (0.351797, -0.479878, -0.803713)2.66226, -2.24009, 4.97156
55generate(0.748684, -0.274749, 0.603312), (-0.590623, -0.689746, 0.418827), (0.30106, -0.669899, -0.678674)-3.13873, -7.18942, 3.91611
56generate(-0.053503, -0.342792, 0.937887), (-0.920234, 0.381584, 0.086971), (-0.387695, -0.858421, -0.335865)-5.61642, -3.11143, 1.23488
57generate(-0.357165, -0.674544, -0.646083), (-0.673859, -0.292901, 0.678324), (-0.646798, 0.677642, -0.349934)-2.10742, -7.00625, 5.42911
58generate(-0.999066, 0.032821, 0.028094), (0.032953, 0.158376, 0.986829), (0.02794, 0.986833, -0.15931)-2.92126, -5.53012, 6.75045
59generate(-0.063467, -0.127504, -0.989805), (0.996103, -0.068969, -0.054986), (-0.061254, -0.989437, 0.131384)1.01471, -1.41617, -0.12803
60generate(-0.02467, -0.878632, 0.476861), (0.499224, -0.424099, -0.755589), (0.866122, 0.21942, 0.449097)-5.79982, -1.05245, 3.72436

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Components

#1: Protein Protein ORF3, Capsid protein / pORF3 / pORF2


Mass: 59178.164 Da / Num. of mol.: 1
Fragment: UNP residues 61-114 of Protein ORF3, UNP residues 112-608 of Capsid protein
Source method: isolated from a genetically manipulated source
Details: Fusion protein comprises N-terminal initiating methionine, Residues 58-111 of s tructural protein 1, and residues 112-608 of structural protein 2
Source: (gene. exp.) Hepatitis E virus / Strain: genotype 1 (isolate Human/Burma) / Gene: ORF3, ORF2 / Cell line (production host): BTL-Tn 5B1-4 (Tn5) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P69616, UniProt: P29326

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 6% PEG 8000, 20% glycerol, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jul 6, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.8→70 Å / Num. all: 406649 / Num. obs: 278024 / % possible obs: 68.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1 / Num. unique all: 278024 / Rsym value: 0.626 / % possible all: 24.8

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.81→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 11879682.62 / 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
Rfree0.245 13665 5 %RANDOM
Rwork0.242 ---
obs0.242 275008 68.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.108 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 140.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.98 Å20 Å20 Å2
2---23.02 Å20 Å2
3---28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.63 Å
Luzzati d res low-5 Å
Luzzati sigma a1.04 Å1.07 Å
Refinement stepCycle: LAST / Resolution: 3.81→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 0 0 3658
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it1.462
X-RAY DIFFRACTIONc_scangle_it2.552.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.8→4.04 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 1174 4.9 %
Rwork0.375 22557 -
obs--35.7 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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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

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