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- PDB-5wsn: Structure of Japanese encephalitis virus -

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Basic information

Entry
Database: PDB / ID: 5wsn
TitleStructure of Japanese encephalitis virus
Components
  • E protein
  • M protein
KeywordsVIRUS / Japanese encephalitis virus / Viral entry / Flavivirus / Neurotropism
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / host cell surface ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / host cell surface / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / viral translational frameshifting / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Polyprotein
Similarity search - Component
Biological speciesJapanese encephalitis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWang, X. / Zhu, L. / Li, S. / Yuan, S. / Qin, C. / Fry, E.E. / Stuart, I.D. / Rao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570717 China
CitationJournal: Nat Commun / Year: 2017
Title: Near-atomic structure of Japanese encephalitis virus reveals critical determinants of virulence and stability.
Authors: Xiangxi Wang / Shi-Hua Li / Ling Zhu / Qing-Gong Nian / Shuai Yuan / Qiang Gao / Zhongyu Hu / Qing Ye / Xiao-Feng Li / Dong-Yang Xie / Neil Shaw / Junzhi Wang / Thomas S Walter / Juha T ...Authors: Xiangxi Wang / Shi-Hua Li / Ling Zhu / Qing-Gong Nian / Shuai Yuan / Qiang Gao / Zhongyu Hu / Qing Ye / Xiao-Feng Li / Dong-Yang Xie / Neil Shaw / Junzhi Wang / Thomas S Walter / Juha T Huiskonen / Elizabeth E Fry / Cheng-Feng Qin / David I Stuart / Zihe Rao /
Abstract: Although several different flaviviruses may cause encephalitis, Japanese encephalitis virus is the most significant, being responsible for thousands of deaths each year in Asia. The structural and ...Although several different flaviviruses may cause encephalitis, Japanese encephalitis virus is the most significant, being responsible for thousands of deaths each year in Asia. The structural and molecular basis of this encephalitis is not fully understood. Here, we report the cryo-electron microscopy structure of mature Japanese encephalitis virus at near-atomic resolution, which reveals an unusual "hole" on the surface, surrounded by five encephalitic-specific motifs implicated in receptor binding. Glu138 of E, which is highly conserved in encephalitic flaviviruses, maps onto one of these motifs and is essential for binding to neuroblastoma cells, with the E138K mutation abrogating the neurovirulence and neuroinvasiveness of Japanese encephalitis virus in mice. We also identify structural elements modulating viral stability, notably Gln264 of E, which, when replaced by His264 strengthens a hydrogen-bonding network, leading to a more stable virus. These studies unveil determinants of neurovirulence and stability in Japanese encephalitis virus, opening up new avenues for therapeutic interventions against neurotropic flaviviruses.Japanese encephalitis virus (JEV) is a Flavivirus responsible for thousands of deaths every year for which there are no specific anti-virals. Here, Wang et al. report the cryo-EM structure of mature JEV at near-atomic resolution and identify structural elements that modulate stability and virulence.
History
DepositionDec 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell / em_software
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _em_software.name
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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Assembly

Deposited unit
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein


Theoretical massNumber of molelcules
Total (without water)185,2786
Polymers185,2786
Non-polymers00
Water00
1
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 60


Theoretical massNumber of molelcules
Total (without water)11,116,651360
Polymers11,116,651360
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: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 5


  • icosahedral pentamer
  • 926 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)926,38830
Polymers926,38830
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 6


  • icosahedral 23 hexamer
  • 1.11 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,111,66536
Polymers1,111,66536
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
6
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 60


  • crystal asymmetric unit, crystal frame
  • 11.1 MDa, 360 polymers
Theoretical massNumber of molelcules
Total (without water)11,116,651360
Polymers11,116,651360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.3618034, -0.26286556, -0.89442719), (0.58778526, 0.80901699), (0.7236068, -0.52573111, 0.44721359)727.17319, -160.70491, 143.73885
3generate(-0.6708204, 0.16245984, -0.72360679), (0.68819096, 0.5, -0.52573112), (0.2763932, -0.8506508, -0.44721359)903.94678, 136.70377, 818.69585
4generate(-0.6708204, 0.68819095, 0.2763932), (0.16245984, 0.5, -0.85065081), (-0.7236068, -0.52573111, -0.44721359)286.02567, 481.21735, 1092.10337
5generate(0.3618034, 0.58778525, 0.7236068), (-0.26286556, 0.80901699, -0.52573111), (-0.89442719, 0.4472136)-272.64416, 396.72978, 586.12151
6generate(-0.30901698, 0.95105651, -1.0E-8), (0.95105653, 0.30901698, -2.0E-8), (-1.0E-8, -1)144.97399, -105.32976, 810.00003
7generate(0.44721359, 0.85065081, 0.27639318), (0.5257311, -0.85065082), (-0.72360681, 0.5257311, -0.44721359)-232.57433, 536.5925, 666.26118
8generate(0.86180339, 0.42532542, -0.27639321), (-0.42532543, 0.30901699, -0.8506508), (-0.27639321, 0.8506508, 0.44721361)-4.34791, 796.6185, -8.69583
9generate(0.3618034, 0.26286557, -0.89442719), (-0.58778526, 0.80901699, 2.0E-8), (0.7236068, 0.5257311, 0.4472136)514.25208, 315.40114, -282.10336
10generate(-0.36180339, 0.58778526, -0.72360679), (0.26286557, 0.80901699, 0.52573112), (0.89442719, -0.4472136)606.5381, -242.03354, 223.87851
11generate(-0.63819657, -0.26286557, 0.72360682), (-0.26286557, -0.80901699, -0.52573112), (0.72360681, -0.52573111, 0.44721356)476.8694, 1052.03355, 143.73886
12generate(0.13819662, -0.42532543, 0.89442718), (-0.95105653, -0.30901698, 2.0E-8), (0.27639318, -0.8506508, -0.44721362)159.04416, 915.32977, 818.69587
13generate(0.44721358, -0.85065082, 0.27639318), (-0.5257311, 0.85065082), (-0.72360682, -0.52573109, -0.44721358)456.45284, 273.40751, 1092.10337
14generate(-0.13819663, -0.95105651, -0.27639319), (0.42532542, -0.30901699, 0.8506508), (-0.89442718, 2.0E-8, 0.44721362)958.08677, 13.38151, 586.12149
15generate(-0.809017, -0.58778525, 4.0E-8), (0.58778526, -0.80901699, -2.0E-8), (4.0E-8, 1)970.70489, 494.59887, -2.0E-5
16generate(-0.05278644, -0.68819094, -0.7236068), (-0.68819095, -0.5, 0.52573113), (-0.72360681, 0.52573113, -0.44721356)998.15661, 673.29623, 666.26115
17generate(-0.94721361, -0.16245983, -0.27639317), (-0.16245983, -0.50000001, 0.85065081), (-0.27639317, 0.8506508, 0.44721361)966.35698, 328.78265, -8.69585
18generate(-0.63819657, 0.26286556, 0.72360682), (0.26286556, -0.809017, 0.5257311), (0.72360682, 0.5257311, 0.44721357)263.94829, 413.27024, -282.10335
19generate(0.44721363, -1.0E-8, 0.89442717), (-1.0E-8, -1), (0.89442718, -0.44721363)-138.36453, 810.00002, 223.87853
20generate(0.80901699, -0.58778526, -4.0E-8), (-0.58778527, -0.80901699, 1.0E-8), (-4.0E-8, 1.0E-8, -1)315.40117, 970.70491, 810.00003
21generate(-0.3618034, -0.58778524, -0.7236068), (-0.26286556, 0.809017, -0.5257311), (0.89442719, 1.0E-8, -0.4472136)1082.64416, 396.72977, 223.87851
22generate(-1), (1.0E-8, 1), (-1)809.99999, 810.00001
23generate(-0.36180339, 0.26286557, 0.89442719), (0.58778527, 0.80901699, -1.0E-8), (-0.72360679, 0.52573111, -0.44721359)82.8268, -160.70491, 666.26117
24generate(0.6708204, -0.16245983, 0.72360679), (0.68819095, 0.5, -0.52573113), (-0.2763932, 0.85065081, 0.44721359)-93.94679, 136.70378, -8.69583
25generate(0.6708204, -0.68819094, -0.27639321), (0.16245983, 0.50000001, -0.85065081), (0.7236068, 0.52573112, 0.44721358)523.97433, 481.21736, -282.10335
26generate(-0.44721359, -0.52573109, 0.72360682), (0.85065083, 0.52573109), (-0.27639318, 0.85065081, 0.44721359)505.98183, -152.43467, -8.69585
27generate(0.05278643, -0.68819095, 0.7236068), (0.68819095, -0.5, -0.52573114), (0.72360681, 0.52573111, 0.44721357)369.27807, 541.70379, -282.10335
28generate(0.13819662, -0.95105651, 0.27639318), (-0.42532543, -0.30901698, -0.8506508), (0.89442718, 1.0E-8, -0.44721362)622.26902, 1046.92226, 223.87852
29generate(-0.30901701, -0.95105651, -2.0E-8), (-0.95105652, 0.30901701, 3.0E-8), (-2.0E-8, 2.0E-8, -1)915.32978, 665.02599, 810.00001
30generate(-0.67082041, -0.68819094, 0.27639321), (-0.16245982, 0.5, 0.85065082), (-0.72360679, 0.52573113, -0.44721358)843.46035, -76.21736, 666.26115
31generate(-0.13819662, 0.95105651, -0.27639319), (-0.42532542, -0.30901699, -0.8506508), (-0.89442718, -2.0E-8, 0.44721362)187.73098, 1046.92227, 586.12151
32generate(0.309017, 0.95105651, 2.0E-8), (-0.95105652, 0.30901699, 2.0E-8), (-2.0E-8, 1)-105.32978, 665.026
33generate(0.67082041, 0.68819095, -0.2763932), (-0.16245984, 0.49999999, 0.85065082), (0.72360679, -0.52573113, 0.44721359)-33.46035, -76.21735, 143.73886
34generate(0.4472136, 0.52573109, -0.72360681), (0.85065082, 0.5257311), (0.27639318, -0.85065081, -0.44721359)304.01816, -152.43468, 818.69586
35generate(-0.05278643, 0.68819095, -0.72360681), (0.68819095, -0.5, -0.52573112), (-0.72360681, -0.52573112, -0.44721357)440.72193, 541.70378, 1092.10337
36generate(0.94721361, 0.16245982, 0.27639318), (-0.16245984, -0.5, 0.85065081), (0.27639317, -0.85065081, -0.44721361)-156.35698, 328.78266, 818.69587
37generate(0.63819657, -0.26286557, -0.72360682), (0.26286556, -0.80901699, 0.52573111), (-0.72360682, -0.5257311, -0.44721357)546.05171, 413.27023, 1092.10337
38generate(-0.44721363, -0.89442717), (-1), (-0.89442718, 0.44721363)948.36453, 810.00001, 586.12149
39generate(-0.80901699, 0.58778525, 4.0E-8), (-0.58778526, -0.809017), (3.0E-8, -2.0E-8, 1)494.59884, 970.70492
40generate(0.05278643, 0.68819094, 0.72360681), (-0.68819096, -0.5, 0.52573112), (0.7236068, -0.52573113, 0.44721357)-188.1566, 673.29624, 143.73887
41generate(-0.3618034, -0.26286556, 0.89442719), (-0.58778525, 0.809017, 1.0E-8), (-0.72360681, -0.5257311, -0.4472136)295.74791, 315.40113, 1092.10337
42generate(0.36180339, -0.58778525, 0.7236068), (0.26286557, 0.80901699, 0.52573111), (-0.89442719, 2.0E-8, 0.4472136)203.4619, -242.03354, 586.1215
43generate(0.30901699, -0.95105651, 1.0E-8), (0.95105652, 0.309017, -2.0E-8), (2.0E-8, 1.0E-8, 1)665.026, -105.32976, -1.0E-5
44generate(-0.44721359, -0.85065081, -0.27639319), (0.5257311, -0.85065082), (0.72360682, -0.5257311, 0.44721358)1042.57433, 536.5925, 143.73884
45generate(-0.86180339, -0.42532542, 0.27639321), (-0.42532542, 0.30901701, -0.8506508), (0.2763932, -0.85065079, -0.44721361)814.34792, 796.61849, 818.69585
46generate(-0.13819662, -0.42532542, -0.89442718), (0.95105652, -0.30901699, -2.0E-8), (-0.27639319, -0.8506508, 0.44721362)995.46944, 144.974, 680.33131
47generate(-0.9472136, 0.16245983, -0.27639318), (0.16245984, -0.49999999, -0.85065082), (-0.27639318, -0.85065081, 0.4472136)834.76451, 886.21736, 680.33132
48generate(-0.44721359, 0.52573109, 0.72360681), (-0.85065082, -0.5257311), (-0.2763932, -0.85065082, 0.44721358)80.13964, 962.43468, 680.33133
49generate(0.6708204, 0.16245982, 0.72360679), (-0.68819095, 0.5, 0.52573112), (-0.27639322, -0.85065081, 0.44721359)-225.53925, 268.29623, 680.33133
50generate(0.86180339, -0.42532542, -0.27639321), (0.42532542, 0.30901699, 0.8506508), (-0.27639321, -0.8506508, 0.44721361)340.16568, -236.92226, 680.33132
51generate(0.94721361, -0.16245984, 0.27639317), (0.16245982, -0.5, -0.85065082), (0.27639318, 0.85065081, -0.44721361)-24.76451, 886.21737, 129.66871
52generate(0.44721358, -0.52573109, -0.72360682), (-0.85065083, -0.52573109), (0.27639319, 0.85065082, -0.44721359)729.86036, 962.43468, 129.66869
53generate(-0.67082041, -0.16245982, -0.72360679), (-0.68819095, 0.5, 0.52573114), (0.27639321, 0.85065081, -0.44721358)1035.53925, 268.29622, 129.66868
54generate(-0.86180338, 0.42532542, 0.27639322), (0.42532543, 0.30901698, 0.8506508), (0.27639322, 0.8506508, -0.4472136)469.83431, -236.92226, 129.66869
55generate(0.13819663, 0.42532541, 0.89442718), (0.95105652, -0.309017, -3.0E-8), (0.2763932, 0.8506508, -0.44721362)-185.46945, 144.97401, 129.6687
56generate(-0.44721358, 0.85065082, -0.27639318), (-0.5257311, 0.85065082), (0.72360682, 0.52573109, 0.44721359)353.54715, 273.40751, -282.10335
57generate(0.13819663, 0.95105651, 0.2763932), (0.42532542, -0.30901701, 0.8506508), (0.89442718, -2.0E-8, -0.44721362)-148.08677, 13.38152, 223.87853
58generate(0.809017, 0.58778524, -4.0E-8), (0.58778525, -0.809017, -1.0E-8), (-3.0E-8, -1.0E-8, -1)-160.7049, 494.59887, 810.00003
59generate(0.63819657, 0.26286556, -0.72360682), (-0.26286557, -0.80901699, -0.52573111), (-0.72360682, 0.52573111, -0.44721357)333.1306, 1052.03355, 666.26117
60generate(-0.13819663, 0.42532542, -0.89442718), (-0.95105652, -0.309017, 2.0E-8), (-0.27639319, 0.85065079, 0.44721362)650.95585, 915.32977, -8.69584

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Components

#1: Protein E protein


Mass: 53508.684 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Japanese encephalitis virus / Strain: P3 / Organ: Homo sapiens
Cell line (production host): green monkey kidney (Vero) cells
Production host: Chlorocebus aethiops (grivet) / References: UniProt: A1E4C6
#2: Protein M protein


Mass: 8250.488 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Japanese encephalitis virus / Strain: P3 / Organ: Homo sapiens
Cell line (production host): green monkey kidney (Vero) cells
Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q82863, UniProt: P27395*PLUS
Has protein modificationY
Sequence detailsThis sequence is derived from Japanese encephalitis virus (P3 strain).

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Japanese encephalitis virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 11.8 MDa / Experimental value: NO
Source (natural)Organism: Japanese encephalitis virus / Strain: P3
Source (recombinant)Organism: Chlorocebus aethiops (grivet) / Cell: vero / Plasmid: no plasmids
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Envelope protein / Diameter: 500 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4 / Details: PBS buffer
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K / Details: blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3000 nm / Cs: 2 mm / C2 aperture diameter: 100 µm
Specimen holderSpecimen holder model: OTHER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 1.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 5 / Num. of real images: 2500
Image scansWidth: 3710 / Height: 3710 / Movie frames/image: 25 / Used frames/image: 2-18

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Processing

SoftwareName: PHENIX / Version: 1.10_2155: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EMAN2image acquisitionEMAN2 e2boxer.py was used to automatically select particle images
3RELION1.3image acquisitionRelion was used to reconstruct 3D structures
5Gctf5CTF correction
8CHIMERA2model fitting
10RELIONinitial Euler assignment
11RELION1.3final Euler assignment
12RELION1.3classification
13RELION1.33D reconstruction
14PHENIX3.Omodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 22000
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15260 / Num. of class averages: 120 / Symmetry type: POINT
Atomic model buildingB value: 120 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 3J57

3j57
PDB Unreleased entry


Pdb chain-ID: A / Accession code: 3J57 / Pdb chain residue range: 1-395 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01113367
ELECTRON MICROSCOPYf_angle_d1.0818150
ELECTRON MICROSCOPYf_dihedral_angle_d8.96110527
ELECTRON MICROSCOPYf_chiral_restr0.0512075
ELECTRON MICROSCOPYf_plane_restr0.0062297

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