+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33718 | ||||||||||||
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Title | ZIKV_Fab_G9E | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | virus complexed with antibody / VIRUS | ||||||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / double-stranded RNA binding / viral capsid / 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 / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / 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 | ||||||||||||
Biological species | Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 Å | ||||||||||||
Authors | Shu B / Thiam-Seng N / Lok S | ||||||||||||
Funding support | Singapore, 3 items
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Citation | Journal: PLoS Pathog / Year: 2023 Title: Structure and neutralization mechanism of a human antibody targeting a complex Epitope on Zika virus. Authors: Cameron Adams / Derek L Carbaugh / Bo Shu / Thiam-Seng Ng / Izabella N Castillo / Ryan Bhowmik / Bruno Segovia-Chumbez / Ana C Puhl / Stephen Graham / Sean A Diehl / Helen M Lazear / Shee- ...Authors: Cameron Adams / Derek L Carbaugh / Bo Shu / Thiam-Seng Ng / Izabella N Castillo / Ryan Bhowmik / Bruno Segovia-Chumbez / Ana C Puhl / Stephen Graham / Sean A Diehl / Helen M Lazear / Shee-Mei Lok / Aravinda M de Silva / Lakshmanane Premkumar / Abstract: We currently have an incomplete understanding of why only a fraction of human antibodies that bind to flaviviruses block infection of cells. Here we define the footprint of a strongly neutralizing ...We currently have an incomplete understanding of why only a fraction of human antibodies that bind to flaviviruses block infection of cells. Here we define the footprint of a strongly neutralizing human monoclonal antibody (mAb G9E) with Zika virus (ZIKV) by both X-ray crystallography and cryo-electron microscopy. Flavivirus envelope (E) glycoproteins are present as homodimers on the virion surface, and G9E bound to a quaternary structure epitope spanning both E protomers forming a homodimer. As G9E mainly neutralized ZIKV by blocking a step after viral attachment to cells, we tested if the neutralization mechanism of G9E was dependent on the mAb cross-linking E molecules and blocking low-pH triggered conformational changes required for viral membrane fusion. We introduced targeted mutations to the G9E paratope to create recombinant antibodies that bound to the ZIKV envelope without cross-linking E protomers. The G9E paratope mutants that bound to a restricted epitope on one protomer poorly neutralized ZIKV compared to the wild-type mAb, demonstrating that the neutralization mechanism depended on the ability of G9E to cross-link E proteins. In cell-free low pH triggered viral fusion assay, both wild-type G9E, and epitope restricted paratope mutant G9E bound to ZIKV but only the wild-type G9E blocked fusion. We propose that, beyond antibody binding strength, the ability of human antibodies to cross-link E-proteins is a critical determinant of flavivirus neutralization potency. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33718.map.gz | 236.7 MB | EMDB map data format | |
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Header (meta data) | emd-33718-v30.xml emd-33718.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
Images | emd_33718.png | 204.2 KB | ||
Filedesc metadata | emd-33718.cif.gz | 6.3 KB | ||
Others | emd_33718_half_map_1.map.gz emd_33718_half_map_2.map.gz | 268.5 MB 268.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33718 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33718 | HTTPS FTP |
-Validation report
Summary document | emd_33718_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_33718_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_33718_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | emd_33718_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33718 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33718 | HTTPS FTP |
-Related structure data
Related structure data | 7yarMC 8dv6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33718.map.gz / Format: CCP4 / Size: 290.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.71 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33718_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33718_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Entire | Name: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 |
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Components |
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-Supramolecule #1: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Supramolecule | Name: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 |
-Supramolecule #2: Zika virus ZIKV/H.
Supramolecule | Name: Zika virus ZIKV/H. / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: heavy chain, light chain
Supramolecule | Name: heavy chain, light chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: heavy chain
Macromolecule | Name: heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.694539 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: RVHLVESGGG VVQPGRSLRL SCVASGFAFS NYHMHWVRQA PGKGLEWVAI IWDDGSDQYY ADSVKGRFTI SRDNSKNTLF LQMNRLRAE DTALYYCVGG SSAYNGDNGW REAASLDDWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String: RVHLVESGGG VVQPGRSLRL SCVASGFAFS NYHMHWVRQA PGKGLEWVAI IWDDGSDQYY ADSVKGRFTI SRDNSKNTLF LQMNRLRAE DTALYYCVGG SSAYNGDNGW REAASLDDWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSC |
-Macromolecule #2: light chain
Macromolecule | Name: light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.58192 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SALTQPASVS GSPGQSITIF CSGSSNDVGG YNYVSWYQQY PGKVPKLLIY DVNSRPSGVS NRFSGSKSGN TASLTISGLQ AEDEADYYC SSYTSRRTWV FGGGTIVTVL GQPKANPTVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADGSPVK A GVETTKPS ...String: SALTQPASVS GSPGQSITIF CSGSSNDVGG YNYVSWYQQY PGKVPKLLIY DVNSRPSGVS NRFSGSKSGN TASLTISGLQ AEDEADYYC SSYTSRRTWV FGGGTIVTVL GQPKANPTVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADGSPVK A GVETTKPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPT |
-Macromolecule #3: E protein
Macromolecule | Name: E protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: flavivirin |
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Source (natural) | Organism: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013 |
Molecular weight | Theoretical: 54.444051 KDa |
Recombinant expression | Organism: Aedes albopictus C6/36 cell densovirus |
Sequence | String: IRCIGVSNRD FVEGMSGGTW VDVVLEHGGC VTVMAQDKPT VDIELVTTTV SNMAEVRSYC YEASISDMAS DSRCPTQGEA YLDKQSDTQ YVCKRTLVDR GWGNGCGLFG KGSLVTCAKF ACSKKMTGKS IQPENLEYRI MLSVHGSQHS GMIVNDTGHE T DENRAKVE ...String: IRCIGVSNRD FVEGMSGGTW VDVVLEHGGC VTVMAQDKPT VDIELVTTTV SNMAEVRSYC YEASISDMAS DSRCPTQGEA YLDKQSDTQ YVCKRTLVDR GWGNGCGLFG KGSLVTCAKF ACSKKMTGKS IQPENLEYRI MLSVHGSQHS GMIVNDTGHE T DENRAKVE ITPNSPRAEA TLGGFGSLGL DCEPRTGLDF SDLYYLTMNN KHWLVHKEWF HDIPLPWHAG ADTGTPHWNN KE ALVEFKD AHAKRQTVVV LGSQEGAVHT ALAGALEAEM DGAKGRLSSG HLKCRLKMDK LRLKGVSYSL CTAAFTFTKI PAE TLHGTV TVEVQYAGTD GPCKVPAQMA VDMQTLTPVG RLITANPVIT ESTENSKMML ELDPPFGDSY IVIGVGEKKI THHW HRSGS TIGKAFEATV RGAKRMAVLG DTAWDFGSVG GALNSLGKGI HQIFGAAFKS LFGGMSWFSQ ILIGTLLMWL GLNTK NGSI SLMCLALGGV LIFLSTAVSA UniProtKB: Genome polyprotein |
-Macromolecule #4: M protein
Macromolecule | Name: M protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 |
Molecular weight | Theoretical: 8.388786 KDa |
Recombinant expression | Organism: Aedes albopictus C6/36 cell densovirus |
Sequence | String: AVTLPSHSTR KLQTRSQTWL ESREYTKHLI RVENWIFRNP GFALAAAAIA WLLGSSTSQK VIYLVMILLI APAAA UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Sugar embedding | Material: ice |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.7 µm / Nominal defocus min: 3.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4465 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 258 |
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Output model | PDB-7yar: |