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Yorodumi- EMDB-0932: Cryo-EM structure of immature Zika virus in complex with human an... -
+Open data
-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 | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | immature Zika virus / human antibody / virus | ||||||||||||
Function / homology | Function and homology information response to herbicide / photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 / Homo sapiens (human) / Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | ||||||||||||
Authors | Tan TY / Fibriansah G | ||||||||||||
Funding support | Singapore, 3 items
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Citation | Journal: Nat Commun / Year: 2020 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0932.map.gz | 214.6 MB | EMDB map data format | |
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Header (meta data) | emd-0932-v30.xml emd-0932.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
Images | emd_0932.png | 266.6 KB | ||
Filedesc metadata | emd-0932.cif.gz | 6.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0932 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0932 | HTTPS FTP |
-Validation report
Summary document | emd_0932_validation.pdf.gz | 655.2 KB | Display | EMDB validaton report |
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Full document | emd_0932_full_validation.pdf.gz | 654.8 KB | Display | |
Data in XML | emd_0932_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_0932_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0932 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0932 | HTTPS FTP |
-Related structure data
Related structure data | 6lntMC 0933C 0934C 6lnuC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0932.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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: 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: Homo sapiens (human) |
-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: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 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: Homo sapiens (human) |
-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: Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013) 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: Photosystem q(B) protein |
-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: Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013) 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: Photosystem q(B) protein |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 13.34486 KDa |
Recombinant expression | Organism: Human gammaherpesvirus 4 (Epstein-Barr virus) |
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: Homo sapiens (human) |
Molecular weight | Theoretical: 11.376559 KDa |
Recombinant expression | Organism: Human gammaherpesvirus 4 (Epstein-Barr virus) |
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: Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013) 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: Photosystem q(B) protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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. |
-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: FIELD EMISSION GUN |
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 |
-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: |