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- EMDB-27058: Structures of Zika Virus in Complex with Antibodies Targeting E D... -

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Basic information

Entry
Database: EMDB / ID: EMD-27058
TitleStructures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy
Map data
Sample
  • Virus: Zika virus
    • Protein or peptide: Ankyrin repeat family A protein 2,Envelope E protein
    • Protein or peptide: Membrane M protein
    • Protein or peptide: A11 heavy chain
    • Protein or peptide: A11 light chain
KeywordsZIKV / scFv antibody / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


low-density lipoprotein particle receptor binding / regulation of protein-containing complex assembly / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / histone deacetylase binding / double-stranded RNA binding / viral capsid / regulation of gene expression / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...low-density lipoprotein particle receptor binding / regulation of protein-containing complex assembly / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / histone deacetylase binding / double-stranded RNA binding / viral capsid / regulation of gene expression / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / cytoskeleton / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / 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 / ubiquitin protein ligase binding / host cell nucleus / virion attachment to host cell / protein kinase binding / structural molecule activity / virion membrane / protein-containing complex / proteolysis / extracellular region / ATP binding / membrane / nucleus / metal ion binding / cytosol
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 / Ankyrin repeat / DEAD box, Flavivirus / Flavivirus DEAD domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / 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 / Ankyrin repeat family A protein 2
Similarity search - Component
Biological speciesZika virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu W / Zhang XK / Gong DY / Dai XH / Sharma A / Zhang TH / Rey F / Zhou ZH
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583, DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1S10RR23057, 1S10OD018111, and 1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 and DMR-1548924 United States
CitationJournal: To Be Published
Title: Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy
Authors: Liu W / Zhang XK / Gong DY / Dai XH / Sharma A / Zhang TH / Rey F / Zhou ZH
History
DepositionMay 21, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27058.png

Downloads & links

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Map

FileDownload / File: emd_27058.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-12.100265 - 15.246743
Average (Standard dev.)0.000000000003768 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 265.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27058_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27058_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_27058_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Zika virus

EntireName: Zika virus
Components
  • Virus: Zika virus
    • Protein or peptide: Ankyrin repeat family A protein 2,Envelope E protein
    • Protein or peptide: Membrane M protein
    • Protein or peptide: A11 heavy chain
    • Protein or peptide: A11 light chain

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Supramolecule #1: Zika virus

SupramoleculeName: Zika virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 64320 / Sci species name: Zika virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Ankyrin repeat family A protein 2,Envelope E protein

MacromoleculeName: Ankyrin repeat family A protein 2,Envelope E protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Zika virus
Molecular weightTheoretical: 69.32682 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDTSTNLDIG AQLIVEECPS TYSLTGMPDI KIEHPLDPNS EEGSAQGVAM GMKFILPNRF DMNVCSRFVK SLNEEDSKNI QDQVNSDLE VASVLFKAEC NIHTSPSPGI QVRHVYTPST TKHFSPIKQS TTLTNKIRCI GVSNRDFVEG MSGGTWVDVV L EHGGCVTV ...String:
MDTSTNLDIG AQLIVEECPS TYSLTGMPDI KIEHPLDPNS EEGSAQGVAM GMKFILPNRF DMNVCSRFVK SLNEEDSKNI QDQVNSDLE VASVLFKAEC NIHTSPSPGI QVRHVYTPST TKHFSPIKQS TTLTNKIRCI GVSNRDFVEG MSGGTWVDVV L EHGGCVTV MAQDKPTVDI ELVTTTVSNM AEVRSYCYEA SISDMASDSR CPTQGEAYLD KQSDTQYVCK RTLVDRGWGN GC GLFGKGS LVTCAKFACS KKMTGKSIQP ENLEYRIMLS VHGSQHSGMI VNDTGHETDE NRAKVEITPN SPRAEATLGG FGS LGLDCE PRTGLDFSDL YYLTMNNKHW LVHKEWFHDI PLPWHAGADT GTPHWNNKEA LVEFKDAHAK RQTVVVLGSQ EGAV HTALA GALEAEMDGA KGRLSSGHLK CRLKMDKLRL KGVSYSLCTA AFTFTKIPAE TLHGTVTVEV QYAGTDGPCK VPAQM AVDM QTLTPVGRLI TANPVITEST ENSKMMLELD PPFGDSYIVI GVGEKKITHH WHRSGSTIGK AFEATVRGAK RMAVLG DTA WDFGSVGGAL NSLGKGIHQI FGAAFKSLFG GMSWFSQILI GTLLMWLGLN TKNGSISLMC LALGGVLIFL STAVSA

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Macromolecule #2: Membrane M protein

MacromoleculeName: Membrane M protein / type: protein_or_peptide / ID: 2
Details: Model includes only small envelope protein M UNP residues 216-290
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Zika virus
Molecular weightTheoretical: 379.600719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKNPKKKSGG FRIVNMLKRG VARVSPFGGL KRLPAGLLLG HGPIRMVLAI LAFLRFTAIK PSLGLINRWG SVGKKEAMEI IKKFKKDLA AMLRIINARK EKKRRGADTS VGIVGLLLTT AMAAEVTRRG SAYYMYLDRN DAGEAISFPT TLGMNKCYIQ I MDLGHMCD ...String:
MKNPKKKSGG FRIVNMLKRG VARVSPFGGL KRLPAGLLLG HGPIRMVLAI LAFLRFTAIK PSLGLINRWG SVGKKEAMEI IKKFKKDLA AMLRIINARK EKKRRGADTS VGIVGLLLTT AMAAEVTRRG SAYYMYLDRN DAGEAISFPT TLGMNKCYIQ I MDLGHMCD ATMSYECPML DEGVEPDDVD CWCNTTSTWV VYGTCHHKKG EARRSRRAVT LPSHSTRKLQ TRSQTWLESR EY TKHLIRV ENWIFRNPGF ALAAAAIAWL LGSSTSQKVI YLVMILLIAP AYSIRCIGVS NRDFVEGMSG GTWVDVVLEH GGC VTVMAQ DKPTVDIELV TTTVSNMAEV RSYCYEASIS DMASDSRCPT QGEAYLDKQS DTQYVCKRTL VDRGWGNGCG LFGK GSLVT CAKFACSKKM TGKSIQPENL EYRIMLSVHG SQHSGMIVND TGHETDENRA KVEITPNSPR AEATLGGFGS LGLDC EPRT GLDFSDLYYL TMNNKHWLVH KEWFHDIPLP WHAGADTGTP HWNNKEALVE FKDAHAKRQT VVVLGSQEGA VHTALA GAL EAEMDGAKGR LSSGHLKCRL KMDKLRLKGV SYSLCTAAFT FTKIPAETLH GTVTVEVQYA GTDGPCKVPA QMAVDMQ TL TPVGRLITAN PVITESTENS KMMLELDPPF GDSYIVIGVG EKKITHHWHR SGSTIGKAFE ATVRGAKRMA VLGDTAWD F GSVGGALNSL GKGIHQIFGA AFKSLFGGMS WFSQILIGTL LMWLGLNTKN GSISLMCLAL GGVLIFLSTA VSADVGCSV DFSKKETRCG TGVFVYNDVE AWRDRYKYHP DSPRRLAAAV KQAWEDGICG ISSVSRMENI MWRSVEGELN AILEENGVQL TVVVGSVKN PMWRGPQRLP VPVNELPHGW KAWGKSYFVR AAKTNNSFVV DGDTLKECPL KHRAWNSFLV EDHGFGVFHT S VWLKVRED YSLECDPAVI GTAVKGKEAV HSDLGYWIES EKNDTWRLKR AHLIEMKTCE WPKSHTLWTD GIEESDLIIP KS LAGPLSH HNTREGYRTQ MKGPWHSEEL EIRFEECPGT KVHVEETCGT RGPSLRSTTA SGRVIEEWCC RECTMPPLSF RAK DGCWYG MEIRPRKEPE SNLVRSMVTA GSTDHMDHFS LGVLVILLMV QEGLKKRMTT KIIISTSMAV LVAMILGGFS MSDL AKLAI LMGATFAEMN TGGDVAHLAL IAAFKVRPAL LVSFIFRANW TPRESMLLAL ASCLLQTAIS ALEGDLMVLI NGFAL AWLA IRAMVVPRTD NITLAILAAL TPLARGTLLV AWRAGLATCG GFMLLSLKGK GSVKKNLPFV MALGLTAVRL VDPINV VGL LLLTRSGKRS WPPSEVLTAV GLICALAGGF AKADIEMAGP MAAVGLLIVS YVVSGKSVDM YIERAGDITW EKDAEVT GN SPRLDVALDE SGDFSLVEDD GPPMREIILK VVLMTICGMN PIAIPFAAGA WYVYVKTGKR SGALWDVPAP KEVKKGET T DGVYRVMTRR LLGSTQVGVG VMQEGVFHTM WHVTKGSALR SGEGRLDPYW GDVKQDLVSY CGPWKLDAAW DGHSEVQLL AVPPGERARN IQTLPGIFKT KDGDIGAVAL DYPAGTSGSP ILDKCGRVIG LYGNGVVIKN GSYVSAITQG RREEETPVEC FEPSMLKKK QLTVLDLHPG AGKTRRVLPE IVREAIKTRL RTVILAPTRV VAAEMEEALR GLPVRYMTTA VNVTHSGTEI V DLMCHATF TSRLLQPIRV PNYNLYIMDE AHFTDPSSIA ARGYISTRVE MGEAAAIFMT ATPPGTRDAF PDSNSPIMDT EV EVPERAW SSGFDWVTDH SGKTVWFVPS VRNGNEIAAC LTKAGKRVIQ LSRKTFETEF QKTKHQEWDF VVTTDISEMG ANF KADRVI DSRRCLKPVI LDGERVILAG PMPVTHASAA QRRGRIGRNP NKPGDEYLYG GGCAETDEDH AHWLEARMLL DNIY LQDGL IASLYRPEAD KVAAIEGEFK LRTEQRKTFV ELMKRGDLPV WLAYQVASAG ITYTDRRWCF DGTTNNTIME DSVPA EVWT RHGEKRVLKP RWMDARVCSD HAALKSFKEF AAGKRGAAFG VMEALGTLPG HMTERFQEAI DNLAVLMRAE TGSRPY KAA AAQLPETLET IMLLGLLGTV SLGIFFVLMR NKGIGKMGFG MVTLGASAWL MWLSEIEPAR IACVLIVVFL LLVVLIP EP EKQRSPQDNQ MAIIIMVAVG LLGLITANEL GWLERTKSDL SHLMGRREEG ATIGFSMDID LRPASAWAIY AALTTFIT P AVQHAVTTSY NNYSLMAMAT QAGVLFGMGK GMPFYAWDFG VPLLMMGCYS QLTPLTLIVA IILLVAHYMY LIPGLQAAA ARAAQKRTAA GIMKNPVVDG IVVTDIDTMT IDPQVEKKMG QVLLIAVAVS SAILSRTAWG WGEAGALITA ATSTLWEGSP NKYWNSSTA TSLCNIFRGS YLAGASLIYT VTRNAGLVKR RGGGTGETLG EKWKARLNQM SALEFYSYKK SGITEVCREE A RRALKDGV ATGGHAVSRG SAKLRWLVER GYLQPYGKVI DLGCGRGGWS YYAATIRKVQ EVKGYTKGGP GHEEPVLVQS YG WNIVRLK SGVDVFHMAA EPCDTLLCDI GESSSSPEVE EARTLRVLSM VGDWLEKRPG AFCIKVLCPY TSTMMETLER LQR RYGGGL VRVPLSRNST HEMYWVSGAK SNTIKSVSTT SQLLLGRMDG PRRPVKYEED VNLGSGTRAV VSCAEAPNMK IIGN RIERI RSEHAETWFF DENHPYRTWA YHGSYEAPTQ GSASSLINGV VRLLSKPWDV VTGVTGIAMT DTTPYGQQRV FKEKV DTRV PDPQEGTRQV MSMVSSWLWK ELGKHKRPRV CTKEEFINKV RSNAALGAIF EEEKEWKTAV EAVNDPRFWA LVDKER EHH LRGECQSCVY NMMGKREKKQ GEFGKAKGSR AIWYMWLGAR FLEFEALGFL NEDHWMGREN SGGGVEGLGL QRLGYVL EE MSRIPGGRMY ADDTAGWDTR ISRFDLENEA LITNQMEKGH RALALAIIKY TYQNKVVKVL RPAEKGKTVM DIISRQDQ R GSGQVVTYAL NTFTNLVVQL IRNMEAEEVL EMQDLWLLRR SEKVTNWLQS NGWDRLKRMA VSGDDCVVKP IDDRFAHAL RFLNDMGKVR KDTQEWKPST GWDNWEEVPF CSHHFNKLHL KDGRSIVVPC RHQDELIGRA RVSPGAGWSI RETACLAKSY AQMWQLLYF HRRDLRLMAN AICSSVPVDW VPTGRTTWSI HGKGEWMTTE DMLVVWNRVW IEENDHMEDK TLVTKWTDIP Y LGKREDLW CGSLIGHRPR TTWAENIKNT VNMVRRIIGD EEKYMDYLST QVRYLGEEGS TPGVL

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Macromolecule #3: A11 heavy chain

MacromoleculeName: A11 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.858386 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVRPGGSLRL SCAASGFSYS NHWMHWVRQA PGKGLVWVSR INSDGSTRNY ADFVKGRFTI SRDNAENTLY LEMNSLTAD DTAVYYCVRD GVRFYYDSTG YYPDSFFKYG MDVWGQGTTV TVSS

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Macromolecule #4: A11 light chain

MacromoleculeName: A11 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.633908 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPVSV SGSPGQSITI SCTGTSSNAD TYNLVSWYQQ RPGKAPKLMI YEGTKRPSGV SNRFSASKSA TAASLTISGL QPEDEADYY CCSYATSRTL VFGGGTKLTV VG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 26.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1124970
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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