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- PDB-5gzr: Zika virus E protein complexed with a neutralizing antibody Z23-Fab -

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Basic information

Entry
Database: PDB / ID: 5gzr
TitleZika virus E protein complexed with a neutralizing antibody Z23-Fab
Components
  • Z23 Fab heavy chain
  • Z23 Fab light chain
  • structural protein EStructure
  • strutural protein M
KeywordsVIRUS / Zika virus / Neutralizing antibody / Single Particle Reconstruction
Function / homology
Function and homology information


suppression by virus of host TYK2 activity / flavivirin / methyltransferase cap1 / suppression by virus of host STAT2 activity / mRNA (guanine-N7)-methyltransferase / suppression by virus of host innate immune response / host cell endoplasmic reticulum / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host STAT1 activity / mRNA (guanine-N7-)-methyltransferase activity ...suppression by virus of host TYK2 activity / flavivirin / methyltransferase cap1 / suppression by virus of host STAT2 activity / mRNA (guanine-N7)-methyltransferase / suppression by virus of host innate immune response / host cell endoplasmic reticulum / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host STAT1 activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / host cell membrane / suppression by virus of host type I interferon-mediated signaling pathway / double-stranded RNA binding / RNA helicase / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / viral capsid / induction by virus of host autophagy / RNA-directed RNA polymerase / clathrin-dependent endocytosis of virus by host cell / viral RNA genome replication / RNA helicase activity / fusion of virus membrane with host endosome membrane / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / serine-type endopeptidase activity / structural molecule activity / integral component of membrane / extracellular region / ATP binding / metal ion binding
Flavivirus envelope glycoprotein M / Flavivirus NS3, petidase S7 / Flavivirus glycoprotein central and dimerisation domain / DEAD box, Flavivirus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / Ribosomal RNA methyltransferase FtsJ domain / Flavivirus polyprotein propeptide / Helicase, C-terminal / Flaviviral glycoprotein E, central domain, subdomain 2 ...Flavivirus envelope glycoprotein M / Flavivirus NS3, petidase S7 / Flavivirus glycoprotein central and dimerisation domain / DEAD box, Flavivirus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / Ribosomal RNA methyltransferase FtsJ domain / Flavivirus polyprotein propeptide / Helicase, C-terminal / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS1 / Flavivirus capsid protein C / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4A / Flaviviral glycoprotein E, central domain, subdomain 1 / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, flavivirus / Flavivirus capsid protein C superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Envelope glycoprotein M superfamily, flavivirus / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Genome polyprotein, Flavivirus / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Envelope glycoprotein M, flavivirus
Genome polyprotein / Genome polyprotein
Biological speciesHomo sapiens (human)
Zika virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.4 Å
AuthorsGao, G.G. / Shi, Y. / Peng, R. / Liu, S.
Funding support China, 1items
OrganizationGrant numberCountry
China Ministry of Science and Technology Key Research and Development Program2016YFC1200300 China
CitationJournal: Sci Transl Med / Year: 2016
Title: Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus.
Authors: Qihui Wang / Huabing Yang / Xiaoqing Liu / Lianpan Dai / Tong Ma / Jianxun Qi / Gary Wong / Ruchao Peng / Sheng Liu / Junfu Li / Shihua Li / Jian Song / Jianying Liu / Jianhua He / Hui Yuan ...Authors: Qihui Wang / Huabing Yang / Xiaoqing Liu / Lianpan Dai / Tong Ma / Jianxun Qi / Gary Wong / Ruchao Peng / Sheng Liu / Junfu Li / Shihua Li / Jian Song / Jianying Liu / Jianhua He / Hui Yuan / Ying Xiong / Yong Liao / Jianhua Li / Jianping Yang / Zhou Tong / Bryan D Griffin / Yuhai Bi / Mifang Liang / Xiaoning Xu / Chuan Qin / Gong Cheng / Xinzheng Zhang / Peiyi Wang / Xiangguo Qiu / Gary Kobinger / Yi Shi / Jinghua Yan / George F Gao /
Abstract: The 2015-2016 outbreak of Zika virus (ZIKV) disease has affected many countries and is a major public health concern. ZIKV is associated with fetal microcephaly and neurological complications, and ...The 2015-2016 outbreak of Zika virus (ZIKV) disease has affected many countries and is a major public health concern. ZIKV is associated with fetal microcephaly and neurological complications, and countermeasures are needed to treat and prevent ZIKV infection. We report the isolation of 13 specific human monoclonal antibodies from a single patient infected with ZIKV. Two of the isolated antibodies (Z23 and Z3L1) demonstrated potent ZIKV-specific neutralization in vitro without binding or neutralizing activity against strains 1 to 4 of dengue virus, the closest relative to ZIKV. These two antibodies provided postexposure protection to mice in vivo. Structural studies revealed that Z23 and Z3L1 bound to tertiary epitopes in envelope protein domain I, II, or III, indicating potential targets for ZIKV-specific therapy. Our results suggest the potential of antibody-based therapeutics and provide a structure-based rationale for the design of future ZIKV-specific vaccines.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references

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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
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Structure viewerMolecule:
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Assembly

Deposited unit
A: structural protein E
B: structural protein E
C: structural protein E
D: strutural protein M
E: strutural protein M
F: strutural protein M
H: Z23 Fab heavy chain
L: Z23 Fab light chain
M: Z23 Fab heavy chain
N: Z23 Fab light chain


Theoretical massNumber of molelcules
Total (without water)282,69010
Polymers282,69010
Non-polymers00
Water0
1
A: structural protein E
B: structural protein E
C: structural protein E
D: strutural protein M
E: strutural protein M
F: strutural protein M
H: Z23 Fab heavy chain
L: Z23 Fab light chain
M: Z23 Fab heavy chain
N: Z23 Fab light chain
x 60


Theoretical massNumber of molelcules
Total (without water)16,961,372600
Polymers16,961,372600
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: structural protein E
B: structural protein E
C: structural protein E
D: strutural protein M
E: strutural protein M
F: strutural protein M
H: Z23 Fab heavy chain
L: Z23 Fab light chain
M: Z23 Fab heavy chain
N: Z23 Fab light chain
x 5


  • icosahedral pentamer
  • 1.41 MDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)1,413,44850
Polymers1,413,44850
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: structural protein E
B: structural protein E
C: structural protein E
D: strutural protein M
E: strutural protein M
F: strutural protein M
H: Z23 Fab heavy chain
L: Z23 Fab light chain
M: Z23 Fab heavy chain
N: Z23 Fab light chain
x 6


  • icosahedral 23 hexamer
  • 1.7 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,696,13760
Polymers1,696,13760
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: structural protein E
B: structural protein E
C: structural protein E
D: strutural protein M
E: strutural protein M
F: strutural protein M
H: Z23 Fab heavy chain
L: Z23 Fab light chain
M: Z23 Fab heavy chain
N: Z23 Fab light chain
x 60


  • crystal asymmetric unit, crystal frame
  • 17 MDa, 600 polymers
Theoretical massNumber of molelcules
Total (without water)16,961,372600
Polymers16,961,372600
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.80143517, 0.51349197, 0.3066393), (-0.50609295, 0.30904479, 0.80520882), (0.31870299, -0.80051066, 0.50755403)-245.39278, 153.93894, 384.64172
3generate(0.48015053, 0.32475452, 0.81485579), (-0.30538362, -0.80894423, 0.50234458), (0.82231157, -0.49004463, -0.28924029)-245.06651, 635.42143, 378.43101
4generate(0.48015053, -0.30538361, 0.82231156), (0.32475452, -0.80894423, -0.49004463), (0.8148558, 0.50234459, -0.28924029)0.52791, 779.05504, -10.04915
5generate(0.80143517, -0.50609294, 0.31870299), (0.51349198, 0.30904479, -0.80051066), (0.3066393, 0.80520882, 0.50755403)151.98735, 386.343, -243.93238
6generate(-0.52368743, 0.30574217, 0.79515608), (0.30574217, -0.80374594, 0.5104059), (0.79515609, 0.5104059, 0.32743337)164.25637, 390.29395, -248.46278
7generate(-0.32101686, -0.81095218, 0.48918782), (0.81447058, -0.49998271, -0.29437219), (0.48330723, 0.30393065, 0.82099957)645.68132, 387.86263, -239.07247
8generate(0.3090486, -0.80706018, -0.50313299), (0.81196579, 0.49935512, -0.30225159), (0.49517727, -0.31511634, 0.80963027)787.78147, -2.1972, 4.90488
9generate(0.4957799, 0.31203955, -0.81045271), (0.30168935, 0.81321663, 0.49765676), (0.81436223, -0.49123317, 0.30903746)394.17924, -240.83612, 146.30086
10generate(-0.01887927, 0.99978922, -0.00806594), (-0.01117405, 0.00785588, 0.99990671), (0.99975934, 0.01896764, 0.01102339)8.81954, 1.73675, -10.28897
11generate(0.33203361, -0.80759354, -0.48738726), (-0.80759355, -0.51036721, 0.29549615), (-0.48738727, 0.29549615, -0.8216664)772.76515, 796.30319, 792.51118
12generate(0.51948904, 0.31107271, -0.79584226), (-0.29476512, -0.80896695, -0.50861184), (-0.80202536, 0.49880481, -0.32855607)379.49693, 1029.57558, 641.55368
13generate(0.00526777, 0.99996905, 0.0058413), (0.01108122, 0.00578265, -0.99992188), (-0.99992473, 0.00533208, -0.01105042)-6.20986, 781.74397, 788.77402
14generate(-0.49999387, 0.30706416, 0.80976399), (-0.31272377, 0.80792534, -0.4994602), (-0.80759518, -0.50295949, -0.30793146)148.67845, 395.30321, 1030.7187
15generate(-0.29804148, -0.81007096, 0.50493197), (-0.81869261, 0.48892718, 0.30115217), (-0.49082961, -0.32362823, -0.80891969)630.11149, 404.30131, 1033.02839
16generate(-0.80834618, 0.50185137, -0.30776882), (0.50185138, 0.31411315, -0.80590206), (-0.30776882, -0.80590206, -0.50576697)633.20252, 391.03777, 1031.93859
17generate(-0.99990735, -0.0136125, 1.514E-5), (-0.0136125, 0.99990487, -0.0022248), (1.514E-5, -0.0022248, -0.99999753)790.43858, 6.25775, 788.86406
18generate(-0.7944669, -0.51766339, -0.31756411), (-0.51766339, 0.30380646, 0.79982889), (-0.31756411, 0.79982889, -0.50933956)1033.71895, 162.6667, 403.87709
19generate(-0.47593655, -0.31372009, -0.82162284), (-0.3137201, -0.81219774, 0.49184807), (-0.82162285, 0.49184807, 0.2881343)1026.83844, 644.11277, 409.01659
20generate(-0.48451442, 0.31637468, -0.81556902), (0.31637469, -0.80582786, -0.50054823), (-0.81556903, -0.50054823, 0.29034228)779.30567, 785.25385, 797.17995
21generate(0.80196597, 0.51702829, -0.29921953), (0.49805646, -0.30214593, 0.81280232), (0.32983383, -0.80086802, -0.49982003)-8.2895, -2.17881, 777.3153
22generate(0.2856972, 0.81111641, 0.51035994), (0.81111642, -0.48828555, 0.3219742), (0.51035995, 0.3219742, -0.79741165)-240.58769, 141.72739, 380.84005
23generate(-0.01887927, -0.01117405, 0.99975932), (0.99978924, 0.00785589, 0.01896764), (-0.00806594, 0.99990671, 0.01102338)10.47241, -8.63617, -1.55203
24generate(0.30915088, -0.81346563, 0.4926453), (0.8033355, 0.50062777, 0.3225274), (-0.50899688, 0.29604982, 0.80825533)397.93427, -245.47216, 158.59193
25generate(0.81646114, -0.48701862, -0.31016778), (0.49324758, 0.30903611, 0.81314421), (-0.30016334, -0.81689016, 0.49253674)386.33878, -241.48129, 639.95841
26generate(-0.49982838, -0.32308799, 0.80360794), (0.29310005, 0.80998453, 0.50795416), (-0.8150239, 0.48942743, -0.31015615)399.57645, -240.24671, 643.10535
27generate(0.01904477, -0.99980324, -0.00554587), (-0.01314026, -0.00579669, 0.99989686), (-0.99973229, -0.01896993, -0.01324808)781.59605, 7.89717, 799.14927
28generate(0.51948903, -0.29476511, -0.80202535), (0.31107272, -0.80896695, 0.49880481), (-0.79584227, -0.50861183, -0.32855607)620.88078, 394.83141, 1036.46039
29generate(0.30990745, 0.81768766, -0.48512291), (0.81768767, -0.48957224, -0.30282981), (-0.48512293, -0.30282981, -0.82033521)139.53368, 385.82604, 1027.08279
30generate(-0.32006535, 0.80018316, 0.50721303), (0.80657996, 0.5109948, -0.29717521), (-0.49697783, 0.31399237, -0.80896343)2.76008, -6.67383, 783.97601
31generate(-0.00543327, -0.99995504, 0.00777051), (0.01323309, -0.00784184, -0.99988169), (0.99989768, -0.00532979, 0.01327511)786.01831, 786.25702, -1.64733
32generate(0.50419227, -0.31804121, -0.80289472), (-0.30409112, 0.80478755, -0.50975051), (0.80828136, 0.50116542, 0.30905416)636.40844, 397.20633, -242.72931
33generate(0.30915089, 0.80333548, -0.50899687), (-0.81346564, 0.50062777, 0.29604982), (0.49264531, 0.3225274, 0.80825533)154.89756, 399.64492, -245.05172
34generate(-0.32101686, 0.81447056, 0.48330722), (-0.8109522, -0.49998271, 0.30393065), (0.48918783, -0.29437219, 0.82099957)6.91734, 790.20274, -5.40508
35generate(-0.51544056, -0.30002427, 0.80268702), (-0.30002428, -0.81423421, -0.49699908), (0.80268704, -0.49699907, 0.32967477)396.97142, 1029.14216, 145.02711
36generate(-0.29670432, 0.80601474, -0.51215892), (-0.8043896, -0.49999675, -0.32087478), (-0.51470761, 0.31677038, 0.79670108)392.91878, 1033.8034, 157.21368
37generate(-0.80893424, 0.50672804, 0.29808065), (-0.49388504, -0.31070531, -0.81212055), (-0.31890902, -0.80416969, 0.50160556)392.80724, 1030.80401, 638.72698
38generate(-0.80976065, -0.49739631, 0.3112629), (-0.49739632, 0.30048329, -0.81382228), (0.3112629, -0.81382227, -0.49072264)783.9733, 791.79474, 786.13035
39generate(-0.29804148, -0.8186926, -0.4908296), (-0.81007098, 0.48892718, -0.32362823), (0.50493198, 0.30115218, -0.80891969)1025.83876, 647.07828, 395.71735
40generate(0.01904477, -0.01314026, -0.99973227), (-0.99980326, -0.0057967, -0.01896993), (-0.00554587, 0.99989686, -0.01324807)784.15377, 796.64786, 7.02546
41generate(0.80196597, 0.49805645, 0.32983383), (0.51702829, -0.30214594, -0.80086802), (-0.29921954, 0.81280231, -0.49982003)-248.65182, 626.15455, 387.80832
42generate(0.4957799, 0.30168934, 0.81436222), (0.31203956, 0.81321663, -0.49123317), (-0.81045272, 0.49765675, 0.30903745)-241.91034, 144.72026, 394.10492
43generate(0.50419228, -0.30409111, 0.80828135), (-0.31804121, 0.80478755, 0.50116542), (-0.80289473, -0.50975051, 0.30905416)-3.89173, 4.38493, 788.46162
44generate(0.81557747, -0.48211692, 0.31999477), (-0.5024638, -0.31578447, 0.80486664), (-0.28699045, -0.81721688, -0.499793)136.47039, 399.08723, 1025.89086
45generate(0.99961174, 0.01363754, 0.02429794), (0.01363753, -0.99990699, 0.00016571), (0.02429794, 0.00016571, -0.99970475)-14.79966, 783.36198, 778.27351
46generate(-0.00543326, 0.0132331, 0.99989767), (-0.99995506, -0.00784184, -0.0053298), (0.00777051, -0.99988169, 0.0132751)-4.48681, 792.13991, 780.0781
47generate(0.3076188, -0.79912906, 0.51649144), (-0.79912907, -0.51162582, -0.315645), (0.51649145, -0.31564499, -0.79599298)383.48593, 1034.26444, 629.35671
48generate(0.81557747, -0.50246379, -0.28699044), (-0.48211693, -0.31578447, -0.81721689), (0.31999478, 0.80486663, -0.499793)383.64558, 1030.19557, 147.85127
49generate(0.81646114, 0.49324757, -0.30016333), (-0.48701864, 0.30903611, -0.81689016), (-0.31016779, 0.81314421, 0.49253674)-4.22849, 785.55635, 0.98593
50generate(0.30904861, 0.81196578, 0.49517726), (-0.8070602, 0.49935512, -0.31511635), (-0.503133, -0.30225159, 0.80963026)-244.1075, 638.42986, 391.7236
51generate(-0.29670433, -0.80438959, -0.51470761), (0.80601476, -0.49999675, 0.31677038), (-0.51215893, -0.32087478, 0.79670108)1029.08047, 150.39937, 407.70599
52generate(0.00526776, 0.01108122, -0.99992472), (0.99996907, 0.00578265, 0.00533209), (0.0058413, -0.99992188, -0.01105042)780.08468, -2.5167, 790.43545
53generate(-0.32006536, 0.80657994, -0.49697782), (0.80018318, 0.5109948, 0.31399238), (0.50721304, -0.29717521, -0.80896343)395.88507, -244.96077, 630.82468
54generate(-0.82310437, 0.48275437, 0.29907757), (0.48275439, 0.31745367, 0.81619322), (0.29907758, 0.81619322, -0.4943493)407.43245, -241.88338, 149.45033
55generate(-0.80866646, -0.51287955, 0.28811996), (0.4863585, -0.30737347, 0.81791012), (-0.33092894, 0.80154608, 0.49800594)798.76873, 2.46262, 11.5554
56generate(-0.49982838, 0.29310004, -0.81502389), (-0.32308799, 0.80998453, 0.48942743), (0.80360796, 0.50795415, -0.31015615)794.2822, 8.94108, 0.39458
57generate(-0.80866646, 0.48635849, -0.33092894), (-0.51287956, -0.30737347, 0.80154608), (0.28811997, 0.81791012, 0.49800594)648.56379, 401.16691, -237.91009
58generate(-0.99970439, -2.504E-5, -0.02431309), (-2.504E-5, -0.99999788, 0.00205909), (-0.02431308, 0.00205909, 0.99970227)794.58513, 788.01517, 8.84943
59generate(-0.80893425, -0.49388503, -0.31890902), (0.50672805, -0.31070531, -0.80416969), (0.29808066, -0.81212054, 0.50160556)1030.54969, 634.87471, 399.65986
60generate(-0.49999388, -0.31272377, -0.80759517), (0.30706416, 0.80792534, -0.50295949), (0.809764, -0.4994602, -0.30793146)1030.36247, 153.38044, 394.43448

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Components

#1: Protein structural protein E / Structure / Coordinate model: Cα atoms only


Mass: 54444.051 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Zika virus / Cell line: Aedes albopictus C6/36 cells / Strain: isolate ZIKV_SMGC-1 / References: UniProt: A0A024B7W1, UniProt: A0A1B0XTC8*PLUS
#2: Protein strutural protein M / Coordinate model: Cα atoms only


Mass: 8496.883 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Zika virus / Cell line: Aedes albopictus C6/36 cells / Strain: ZIKV_SMGC-1 / References: UniProt: A0A024B7W1, UniProt: A0A1B0XTC8*PLUS
#3: Antibody Z23 Fab heavy chain / IgG heavy chain / Coordinate model: Cα atoms only


Mass: 23516.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCAGGS / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / Antibody class: IGG (SACS)
#4: Antibody Z23 Fab light chain / IgG light chain / Coordinate model: Cα atoms only


Mass: 23416.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCAGGS / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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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

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Zika virus in complex with a neutralizing antibody Z23 FabCOMPLEX1, 2, 3, 40MULTIPLE SOURCES
2Zika virusCOMPLEX1, 21NATURALZika virus strain ZIKA-SMGC-1 propagated in Aedes albopictus C6/36 cells
3Neutralizing antibody Z23 FabCOMPLEX3, 41RECOMBINANT
Molecular weight
IDEntity assembly-IDUnitsExperimental value
11MEGADALTONSNO
21NO
31NO
Source (natural)Organism: Zika virus / Strain: ZIKA-SMGC-1
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T / Plasmid: pCAGGS
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
112 mMTris-HClTrisTris-HClTris1
2120 mMSodium ChlorideNaClSodium chloride1
31 mMEthylenediaminetetraacetic acidEDTAEthylenediaminetetraacetic acid1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 230 divisions/in. / Grid type: Zhongjikeyi ultra-thin carbon-coated copper grid
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 3 uL Zika virus-Z23 Fab complex sample was transferred onto a glow-discharged ultra-thin carbon-coated copper grid (Purchased from Zhongjingkeyi Company, China) followed by 60s waiting and ...Details: 3 uL Zika virus-Z23 Fab complex sample was transferred onto a glow-discharged ultra-thin carbon-coated copper grid (Purchased from Zhongjingkeyi Company, China) followed by 60s waiting and blotted for 2s with filter paper before plugging into liquid ethane using the FEI Vitrobot Mark IV

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 41139 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Num. of grids imaged: 1 / Num. of real images: 566

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2particle selectione2boxer.py
4CTFFIND3CTF correction
7Chimera1.11model fitting
9Relion1.4initial Euler assignment
10Relion1.4final Euler assignment
11Relion1.4classification
12Relion1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 17024
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3369 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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