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- EMDB-0932: Cryo-EM structure of immature Zika virus in complex with human an... -
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Basic information
Entry | Database: EMDB / ID: EMD-0932 | ||||||||||||
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Title | Cryo-EM structure of immature Zika virus in complex with human antibody DV62.5 Fab | ||||||||||||
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![]() | immature Zika virus / human antibody / virus | ||||||||||||
Function / homology | ![]() 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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase ...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 / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / 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 / viral envelope / lipid binding / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | ||||||||||||
![]() | Tan TY / Fibriansah G | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Capsid protein structure in Zika virus reveals the flavivirus assembly process. Authors: Ter Yong Tan / Guntur Fibriansah / Victor A Kostyuchenko / Thiam-Seng Ng / Xin-Xiang Lim / Shuijun Zhang / Xin-Ni Lim / Jiaqi Wang / Jian Shi / Marc C Morais / Davide Corti / Shee-Mei Lok / ![]() ![]() ![]() Abstract: Structures of flavivirus (dengue virus and Zika virus) particles are known to near-atomic resolution and show detailed structure and arrangement of their surface proteins (E and prM in immature virus ...Structures of flavivirus (dengue virus and Zika virus) particles are known to near-atomic resolution and show detailed structure and arrangement of their surface proteins (E and prM in immature virus or M in mature virus). By contrast, the arrangement of the capsid proteins:RNA complex, which forms the core of the particle, is poorly understood, likely due to inherent dynamics. Here, we stabilize immature Zika virus via an antibody that binds across the E and prM proteins, resulting in a subnanometer resolution structure of capsid proteins within the virus particle. Fitting of the capsid protein into densities shows the presence of a helix previously thought to be removed via proteolysis. This structure illuminates capsid protein quaternary organization, including its orientation relative to the lipid membrane and the genomic RNA, and its interactions with the transmembrane regions of the surface proteins. Results show the capsid protein plays a central role in the flavivirus assembly process. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 214.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.4 KB 19.4 KB | Display Display | ![]() |
Images | ![]() | 266.6 KB | ||
Filedesc metadata | ![]() | 6.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 655.2 KB | Display | ![]() |
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Full document | ![]() | 654.8 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 8.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lntMC ![]() 0933C ![]() 0934C ![]() 6lnuC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.69 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Entire | Name: ![]() |
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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: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: The virus was isolated from Zika patient. The immature Zika virus was grown in Aedes Albopictus clone C6/36 cell. The anti-prM antibody DV62.5 was generated from EBV-immortalized PBMC that ...Details: The virus was isolated from Zika patient. The immature Zika virus was grown in Aedes Albopictus clone C6/36 cell. The anti-prM antibody DV62.5 was generated from EBV-immortalized PBMC that was obtained from dengue patient. Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: ![]() |
-Supramolecule #2: Zika virus
Supramolecule | Name: Zika virus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #5 |
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Source (natural) | Organism: ![]() Strain: D3/SG/05K863DK1/2005 |
-Supramolecule #3: anti-prM antibody DV62.5
Supramolecule | Name: anti-prM antibody DV62.5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Envelope protein
Macromolecule | Name: Envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: flavivirin |
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Source (natural) | Organism: ![]() Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013 |
Molecular weight | Theoretical: 54.444051 KDa |
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 #2: pre-membrane protein
Macromolecule | Name: pre-membrane protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: flavivirin |
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Source (natural) | Organism: ![]() Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013 |
Molecular weight | Theoretical: 18.561266 KDa |
Sequence | String: RGSAYYMYLD RNDAGEAISF PTTLGMNKCY IQIMDLGHMC DATMSYECPM LDEGVEPDDV DCWCNTTSTW VVYGTCHHKK GEARRSRRA VTLPSHSTRK LQTRSQTWLE SREYTKHLIR VENWIFRNPG FALAAAAIAW LLGSSTSQKV IYLVMILLIA P AYS UniProtKB: Genome polyprotein |
-Macromolecule #3: Fab DV62.5 heavy-chain variable region
Macromolecule | Name: Fab DV62.5 heavy-chain variable region / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.34486 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVQLVQSGAE VKKPGASLKV SCKASGYTFT SYGLSWVRQA PGQGLEWMGW ITPYNGNTKY TQKLQGRVTM TTDTSTSTVY MELRSLRSD DTAVYYCARD SGTYAFYFDY WGQGTLVTVS S |
-Macromolecule #4: Fab DV62.5 light-chain variable region
Macromolecule | Name: Fab DV62.5 light-chain variable region / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.376559 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: SYELTQPLSV SVALGQTASI TCGGNNIGSK NVHWYQQKPG QAPVLVIYKY VNRPSGIPER FSGSNSGNTA TLTISRAQAG DEADYYCQV WDSSTYVFGT GTKVTVL |
-Macromolecule #5: capsid protein
Macromolecule | Name: capsid protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: flavivirin |
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Source (natural) | Organism: ![]() Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013 |
Molecular weight | Theoretical: 12.747635 KDa |
Sequence | String: KKSGGFRIVN MLKRGVARVS PFGGLKRLPA GLLLGHGPIR MVLAILAFLR FTAIKPSLGL INRWGSVGKK EAMEIIKKFK KDLAAMLRI INARKEKKRR GADTSVGIVG LLLTTAMA UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 / Details: 10 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA, pH 8 |
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Vitrification | Cryogen name: ETHANE |
Details | Immature Zika virus-Fab DV62.5 complex sample was prepared by mixing purified immature Zika virus with Fab DV62.5 at an E protein-Fab DV62.5 ratio of 1:1.1 and then the mixture was incubated at 37deg C for 30 min prior to sample blotting onto the grid. |
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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: 18.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 47000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 19295 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: FLEXIBLE FIT | ||||||||
Output model | ![]() PDB-6lnt: |