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- PDB-4b03: 6A Electron cryomicroscopy structure of immature Dengue virus ser... -

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Basic information

Entry
Database: PDB / ID: 4b03
Title6A Electron cryomicroscopy structure of immature Dengue virus serotype 1
Components
  • DENGUE VIRUS 1 E PROTEIN
  • DENGUE VIRUS 1 PRM PROTEIN
KeywordsVIRUS / FLAVIVIRUS / PRM PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / channel activity / viral capsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / channel activity / viral capsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein, central and dimerisation domains / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesDENGUE VIRUS 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F
AuthorsKostyuchenko, V.A. / Zhang, Q. / Tan, L.C. / Ng, T.S. / Lok, S.M.
CitationJournal: J Virol / Year: 2013
Title: Immature and mature dengue serotype 1 virus structures provide insight into the maturation process.
Authors: Victor A Kostyuchenko / Qian Zhang / Joanne L Tan / Thiam-Seng Ng / Shee-Mei Lok /
Abstract: Dengue virus is a major human pathogen that has four serotypes (DENV1 to -4). Here we report the cryoelectron microscopy (cryo-EM) structures of immature and mature DENV1 at 6- and 4.5-Å resolution, ...Dengue virus is a major human pathogen that has four serotypes (DENV1 to -4). Here we report the cryoelectron microscopy (cryo-EM) structures of immature and mature DENV1 at 6- and 4.5-Å resolution, respectively. The subnanometer-resolution maps allow accurate placement of all of the surface proteins. Although the immature and mature viruses showed vastly different surface protein organizations, the envelope protein transmembrane (E-TM) regions remain in similar positions. The pivotal role of the E-TM regions leads to the identification of the start and end positions of all surface proteins during maturation.
History
DepositionJun 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Apr 19, 2017Group: Other
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.4May 8, 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 / em_3d_fitting_list / pdbx_initial_refinement_model / 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 / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • 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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  • Simplified surface model + fitted atomic model
  • EMDB-2141
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  • Superimposition on EM map
  • EMDB-2141
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Structure viewerMolecule:
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Assembly

Deposited unit
A: DENGUE VIRUS 1 E PROTEIN
B: DENGUE VIRUS 1 E PROTEIN
C: DENGUE VIRUS 1 E PROTEIN
D: DENGUE VIRUS 1 PRM PROTEIN
E: DENGUE VIRUS 1 PRM PROTEIN
F: DENGUE VIRUS 1 PRM PROTEIN


Theoretical massNumber of molelcules
Total (without water)216,9606
Polymers216,9606
Non-polymers00
Water00
1
A: DENGUE VIRUS 1 E PROTEIN
B: DENGUE VIRUS 1 E PROTEIN
C: DENGUE VIRUS 1 E PROTEIN
D: DENGUE VIRUS 1 PRM PROTEIN
E: DENGUE VIRUS 1 PRM PROTEIN
F: DENGUE VIRUS 1 PRM PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)13,017,608360
Polymers13,017,608360
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: DENGUE VIRUS 1 E PROTEIN
B: DENGUE VIRUS 1 E PROTEIN
C: DENGUE VIRUS 1 E PROTEIN
D: DENGUE VIRUS 1 PRM PROTEIN
E: DENGUE VIRUS 1 PRM PROTEIN
F: DENGUE VIRUS 1 PRM PROTEIN
x 5


  • icosahedral pentamer
  • 1.08 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,084,80130
Polymers1,084,80130
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: DENGUE VIRUS 1 E PROTEIN
B: DENGUE VIRUS 1 E PROTEIN
C: DENGUE VIRUS 1 E PROTEIN
D: DENGUE VIRUS 1 PRM PROTEIN
E: DENGUE VIRUS 1 PRM PROTEIN
F: DENGUE VIRUS 1 PRM PROTEIN
x 6


  • icosahedral 23 hexamer
  • 1.3 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,301,76136
Polymers1,301,76136
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.309018, -0.951055, -0.001732), (0.951056, 0.309018, 0.000254), (0.000294, -0.001726, 0.999998)-5.72141, -0.52957, -0.00652
3generate(-0.809015, -0.587782, -0.002509), (0.587786, -0.809015, -0.001315), (-0.001257, -0.002538, 0.999996)-6.98578, -6.1346, -0.0138
4generate(-0.809015, 0.587786, -0.001257), (-0.587782, -0.809015, -0.002538), (-0.002509, -0.001315, 0.999996)-2.04578, -9.06914, -0.01179
5generate(0.309018, 0.951056, 0.000294), (-0.951055, 0.309018, -0.001726), (-0.001732, 0.000254, 0.999998)2.27167, -5.27775, -0.00326
6generate(0.362701, 0.260992, 0.894612), (-0.58849, 0.8085, 0.002721), (-0.722584, -0.527457, 0.446835)3.9937, -2.25602, -6.78743
7generate(0.360561, -0.265841, 0.894049), (0.587076, 0.809523, 0.003946), (-0.724802, 0.523452, 0.447951)1.7745, 0.68281, -2.37682
8generate(-0.141148, -0.426606, 0.893356), (0.951319, -0.308191, 0.003135), (0.273987, 0.850309, 0.449339)-0.15347, -3.10482, 1.48995
9generate(-0.449081, 0.000868, 0.893491), (0.000868, -0.999999, 0.001408), (0.893491, 0.001408, 0.44908)0.87418, -8.38453, -0.53086
10generate(-0.137686, 0.425827, 0.894267), (-0.950786, -0.309846, 0.001153), (0.277576, -0.850098, 0.447532)3.43728, -7.85994, -5.64657
11generate(-0.447818, 0.849425, 0.27917), (-0.525555, 0.002534, -0.850756), (-0.723361, -0.527703, 0.445285)1.3582, -9.76141, -6.79817
12generate(0.669549, 0.687906, 0.280161), (-0.160246, 0.502083, -0.849843), (-0.725276, 0.524117, 0.446403)3.46871, -6.75029, -2.38297
13generate(0.861221, -0.424687, 0.279176), (0.427741, 0.309022, -0.849437), (0.274473, 0.850968, 0.447793)-0.72818, -6.09379, 1.48617
14generate(-0.137686, -0.950786, 0.277576), (0.425827, -0.309846, -0.850098), (0.894267, 0.001153, 0.447532)-5.4325, -8.69919, -0.53776
15generate(-0.946717, -0.163342, 0.277572), (-0.163342, -0.499266, -0.850913), (0.277572, -0.850913, 0.445983)-4.14306, -10.9659, -5.65777
16generate(-0.638428, 0.264742, -0.722718), (0.264743, -0.806156, -0.529173), (-0.722717, -0.529173, 0.444585)-6.59427, -9.57419, -6.80625
17generate(0.054287, 0.690237, -0.721544), (-0.685045, -0.499988, -0.529836), (-0.726476, 0.523053, 0.445701)-3.07704, -10.65853, -2.39395
18generate(0.673018, 0.162912, -0.721461), (-0.687364, 0.497924, -0.528775), (0.273089, 0.851781, 0.447092)-3.74846, -6.47087, 1.48262
19generate(0.362701, -0.58849, -0.722584), (0.260992, 0.8085, -0.527457), (0.894613, 0.002721, 0.446834)-7.68065, -2.79841, -0.53382
20generate(-0.447818, -0.525555, -0.723361), (0.849425, 0.002534, -0.527703), (0.27917, -0.850756, 0.445285)-9.43946, -4.71637, -5.65662
21generate(0.054287, -0.685045, -0.726476), (0.690238, -0.499988, 0.523053), (-0.721543, -0.529836, 0.445701)-8.87367, -1.95308, -6.8005
22generate(-0.634954, -0.262067, -0.726743), (-0.262067, -0.811862, 0.521729), (-0.726742, 0.521729, 0.446816)-8.81675, -5.64085, -2.39458
23generate(-0.445665, 0.524147, -0.725708), (-0.852957, -0.002539, 0.521976), (0.271749, 0.851624, 0.448206)-5.0404, -3.71493, 1.48421
24generate(0.360561, 0.587075, -0.724802), (-0.265841, 0.809523, 0.523452), (0.894049, 0.003946, 0.447951)-2.7634, 1.16313, -0.52448
25generate(0.669549, -0.160246, -0.725276), (0.687906, 0.502082, 0.524117), (0.280161, -0.849844, 0.446403)-5.13249, 2.25201, -5.64472
26generate(0.673018, -0.687363, 0.27309), (0.162912, 0.497925, 0.851781), (-0.721461, -0.528775, 0.447092)-2.32994, 2.56979, -6.78888
27generate(-0.445665, -0.852957, 0.271749), (0.524147, -0.00254, 0.851624), (-0.725708, 0.521976, 0.448207)-5.81834, 1.36847, -2.38399
28generate(-0.948848, 0.159805, 0.272303), (0.159804, -0.500747, 0.850714), (0.272304, 0.850714, 0.449596)-2.81857, -1.6346, 1.48874
29generate(-0.141148, 0.951319, 0.273987), (-0.426606, -0.308191, 0.850309), (0.893356, 0.003135, 0.449339)2.52378, -2.28928, -0.52266
30generate(0.861221, 0.427741, 0.274473), (-0.424687, 0.309022, 0.850968), (0.279176, -0.849437, 0.447792)2.82577, 0.30918, -5.63851
31generate(-0.364421, 0.583144, 0.726044), (0.260492, 0.812368, -0.52173), (-0.894059, -0.001, -0.447948)2.68919, -2.75471, -9.49186
32generate(0.442204, 0.525533, 0.726822), (0.852951, 0.004195, -0.521974), (-0.277363, 0.850763, -0.446399)4.46064, -4.67189, -4.37312
33generate(0.636673, -0.259415, 0.726189), (0.267413, -0.809006, -0.523449), (0.723282, 0.527459, -0.445702)1.64756, -9.5508, -3.23384
34generate(-0.049762, -0.686928, 0.725019), (-0.686929, -0.503418, -0.524118), (0.725019, -0.524118, -0.446819)-1.86247, -10.64894, -7.64845
35generate(-0.668473, -0.166198, 0.724929), (-0.691206, 0.498646, -0.523055), (-0.274552, -0.850723, -0.448208)-1.21871, -6.44873, -11.51612
36generate(0.134868, 0.952809, -0.271966), (0.428624, -0.303565, -0.850958), (-0.89336, -0.001804, -0.449338)0.48001, -8.67018, -9.50045
37generate(0.947772, 0.166638, -0.271957), (-0.156504, -0.499983, -0.851777), (-0.277912, 0.849852, -0.447791)-0.79443, -10.95621, -4.38529
38generate(0.45128, -0.84942, -0.273556), (-0.524125, -0.004189, -0.851631), (0.722246, 0.527701, -0.447092)-6.3035, -9.79045, -3.24237
39generate(-0.668473, -0.691205, -0.274553), (-0.166198, 0.498646, -0.850723), (0.724929, -0.523055, -0.448208)-8.43386, -6.78395, -7.65118
40generate(-0.864026, 0.422633, -0.27357), (0.422633, 0.313622, -0.850307), (-0.27357, -0.850307, -0.449597)-4.24141, -6.09158, -11.51889
41generate(0.449059, 0.005727, -0.893484), (0.005727, -0.999977, -0.003531), (-0.893484, -0.003531, -0.449082)-5.82862, -8.3971, -9.50673
42generate(0.143952, -0.423768, -0.894258), (-0.949266, -0.314452, -0.003796), (-0.279592, 0.849435, -0.447535)-8.39508, -7.90029, -4.38994
43generate(-0.358806, -0.266315, -0.894614), (-0.592402, 0.805639, -0.002231), (0.721331, 0.529171, -0.446834)-8.98845, -2.3026, -3.23719
44generate(-0.364421, 0.260492, -0.894059), (0.583145, 0.812368, -0.001), (0.726044, -0.52173, -0.447948)-6.78871, 0.66016, -7.64154
45generate(0.134868, 0.428624, -0.89336), (0.952809, -0.303565, -0.001804), (-0.271966, -0.850958, -0.449338)-4.83582, -3.10645, -11.51633
46generate(0.143952, -0.949266, -0.279592), (-0.423769, -0.314451, 0.849435), (-0.894258, -0.003796, -0.447535)-7.51839, -2.31286, -9.50201
47generate(-0.858403, -0.429764, -0.280083), (-0.429764, 0.30439, 0.850088), (-0.280083, 0.850088, -0.445987)-7.83747, 0.27268, -4.38066
48generate(-0.674074, 0.684067, -0.278705), (0.156937, 0.501323, 0.850909), (0.7218, 0.529836, -0.445284)-2.69677, 2.5648, -3.22546
49generate(0.442204, 0.852951, -0.277363), (0.525533, 0.004194, 0.850763), (0.726822, -0.521974, -0.4464)0.79944, 1.39587, -7.63286
50generate(0.947772, -0.156505, -0.277911), (0.166637, -0.499983, 0.849852), (-0.271957, -0.851776, -0.447791)-2.18048, -1.61869, -11.51198
51generate(-0.358807, -0.592402, 0.72133), (-0.266315, 0.805639, 0.529171), (-0.894614, -0.002231, -0.446834)-2.2541, 1.17433, -9.49282
52generate(-0.674074, 0.156936, 0.7218), (0.684067, 0.501323, 0.529837), (-0.278704, 0.850909, -0.445284)0.10779, 2.26794, -4.37026
53generate(-0.058833, 0.688332, 0.723006), (0.688331, -0.496582, 0.528778), (0.723007, 0.528778, -0.444585)3.87664, -1.91483, -3.22338
54generate(0.636674, 0.267412, 0.723282), (-0.259416, -0.809006, 0.527459), (0.726189, -0.52345, -0.445702)3.84402, -5.59353, -7.63713
55generate(0.451281, -0.524125, 0.722246), (-0.849419, -0.00419, 0.527702), (-0.273555, -0.851631, -0.447093)0.05501, -3.68433, -11.51185
56generate(-0.999978, -0.006596, -7.0E-6), (-0.006596, 0.999976, 0.002123), (-7.0E-6, 0.002123, -0.999998)-5.00976, -0.00589, -10.01979
57generate(-0.315284, 0.948996, 0.001723), (0.948996, 0.315279, 0.002389), (0.001723, 0.002389, -0.999996)0.71503, -0.49771, -10.01435
58generate(0.805121, 0.593106, 0.002511), (0.593106, -0.805124, 0.000825), (0.002511, 0.000825, -0.999997)2.01633, -6.09429, -10.01896
59generate(0.812874, -0.582438, 0.001267), (-0.582438, -0.812875, -0.000407), (0.001267, -0.000407, -0.999999)-2.90421, -9.06134, -10.02724
60generate(-0.302738, -0.953074, -0.000289), (-0.953074, 0.302738, 0.000395), (-0.000289, 0.000395, -1)-7.24657, -5.29849, -10.02775

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Components

#1: Protein DENGUE VIRUS 1 E PROTEIN / Coordinate model: Cα atoms only


Mass: 53908.828 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) DENGUE VIRUS 1 / Strain: PVP159 (DEN1/SG/07K3640DK1/2008) / References: UniProt: G3F5K5
#2: Protein DENGUE VIRUS 1 PRM PROTEIN / Coordinate model: Cα atoms only


Mass: 18411.217 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) DENGUE VIRUS 1 / Strain: PVP159 (DEN1/SG/07K3640DK1/2008) / References: UniProt: G3F5K5
Sequence detailsLAB STRAIN HAS SEVERAL MUTATIONS COMPARED TO PUBLISHED SEQUENCE OF THE POLYPROTEIN

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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: DENGUE VIRUS 1 / Type: VIRUS
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Apr 11, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 75000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 17.7 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 838
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategoryDetails
1UCSF Chimeramodel fitting
2EMAN13D reconstruction
3EMAN23D reconstructionGPU-ADAPTED
CTF correctionDetails: WIENER FILTER WEIGHTING EACH PARTICLE DURING 3D RECONSTRUCTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: MPSA FOR ORIENTATION SEARCH, MAKE3D FROM EMAN1 FOR 3D RECONSTRUCTION
Resolution: 6 Å / Num. of particles: 7169 / Nominal pixel size: 1.2 Å / Actual pixel size: 1.2 Å
Details: DUE TO LOW RESOLUTION ONLY CALPHA ATOMS COORDINATES ARE DEPOSITED. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2141. (DEPOSITION ID: 10896).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 3C6E

3c6e


Accession code: 3C6E / Source name: PDB / Type: experimental model
RefinementHighest resolution: 6 Å
Refinement stepCycle: LAST / Highest resolution: 6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 0 0 1983

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