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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 E
  • strutural protein M
KeywordsVIRUS / Zika virus / Neutralizing antibody / Single Particle Reconstruction
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 / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding ...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 / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / molecular adaptor activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / 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 / centrosome / lipid binding / viral envelope / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / 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 / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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 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 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 / : / Flavivirus NS3 helicase, C-terminal helical domain / 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
Similarity search - Component
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.
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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / em_software / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_software.name / _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: 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
Water00
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
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: 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
identity operation1_555x,y,z1
point symmetry operation4
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
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: 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
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(0.80143517, 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 / 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)
#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 FabCOMPLEXall0MULTIPLE SOURCES
2Zika virusCOMPLEX#1-#21NATURALZika virus strain ZIKA-SMGC-1 propagated in Aedes albopictus C6/36 cells
3Neutralizing antibody Z23 FabCOMPLEX#3-#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-HClTris-HCl1
2120 mMSodium ChlorideNaCl1
31 mMEthylenediaminetetraacetic acidEDTA1
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 FIELD / 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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