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Open data
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Basic information
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Title | Cryo-EM Structure of Western Equine Encephalitis Virus | |||||||||
![]() | Virus like particle of western equine encephalitis virus | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Pletnev S / Verardi R / Roedeger M / Kwong P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Vaccine elicitation and structural basis for antibody protection against alphaviruses. Authors: Matthew S Sutton / Sergei Pletnev / Victoria Callahan / Sungyoul Ko / Yaroslav Tsybovsky / Tatsiana Bylund / Ryan G Casner / Gabriele Cerutti / Christina L Gardner / Veronica Guirguis / ...Authors: Matthew S Sutton / Sergei Pletnev / Victoria Callahan / Sungyoul Ko / Yaroslav Tsybovsky / Tatsiana Bylund / Ryan G Casner / Gabriele Cerutti / Christina L Gardner / Veronica Guirguis / Raffaello Verardi / Baoshan Zhang / David Ambrozak / Margaret Beddall / Hong Lei / Eun Sung Yang / Tracy Liu / Amy R Henry / Reda Rawi / Arne Schön / Chaim A Schramm / Chen-Hsiang Shen / Wei Shi / Tyler Stephens / Yongping Yang / Maria Burgos Florez / Julie E Ledgerwood / Crystal W Burke / Lawrence Shapiro / Julie M Fox / Peter D Kwong / Mario Roederer / ![]() Abstract: Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine ...Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine encephalitis virus-like particles (VLPs), a regimen that protects against aerosol challenge with all three viruses. Single- and triple-virus-specific antibodies were isolated, and we identified 21 unique binding groups. Cryo-EM structures revealed that broad VLP binding inversely correlated with sequence and conformational variability. One triple-specific antibody, SKT05, bound proximal to the fusion peptide and neutralized all three Env-pseudotyped encephalitic alphaviruses by using different symmetry elements for recognition across VLPs. Neutralization in other assays (e.g., chimeric Sindbis virus) yielded variable results. SKT05 bound backbone atoms of sequence-diverse residues, enabling broad recognition despite sequence variability; accordingly, SKT05 protected mice against Venezuelan equine encephalitis virus, chikungunya virus, and Ross River virus challenges. Thus, a single vaccine-elicited antibody can protect in vivo against a broad range of alphaviruses. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 927.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.4 KB 19.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 22.3 KB | Display | ![]() |
Images | ![]() | 102.7 KB | ||
Masks | ![]() | 1000 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 926.9 MB 926.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8decMC ![]() 8dedC ![]() 8deeC ![]() 8defC ![]() 8deqC ![]() 8derC ![]() 8dulC ![]() 8dunC ![]() 8dwoC ![]() 8eeuC ![]() 8eevC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Annotation | Virus like particle of western equine encephalitis virus | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Virus like particle of western equine encephalitis virus
File | emd_27389_half_map_1.map | ||||||||||||
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Annotation | Virus like particle of western equine encephalitis virus | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Virus like particle of western equine encephalitis virus
File | emd_27389_half_map_2.map | ||||||||||||
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Annotation | Virus like particle of western equine encephalitis virus | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Western equine encephalitis virus
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Western equine encephalitis virus
Supramolecule | Name: Western equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11039 / Sci species name: Western equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes |
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-Macromolecule #1: Spike glycoprotein E1
Macromolecule | Name: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 47.36882 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCR FHTVIPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTAHLDTFVN GVTPGSSRDL K VIAGPISA ...String: FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCR FHTVIPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTAHLDTFVN GVTPGSSRDL K VIAGPISA AFSPFDHKVV IRKGLVYNYD FPEYGAMKPG AFGDIQASSL DATDIVARTD IRLLKPSVKN IHVPYTQAVS GY EMWKNNS GRPLQETAPF GCKIEVEPLR ASNCAYGHIP ISIDIPDAAF VRSSESPTIL EVSCTVADCI YSADFGGSLT LQY KADREG HCPVHSHSTT AVLKEATTHV TAVGSITLHF STSSPQANFI VSLCGKKTTC NAECKPPADH IIGEPHKVDQ EFQA AVSKT SWNWLLALFG GASSLIVVGL IVLVCSSMLI NTRR UniProtKB: Structural polyprotein |
-Macromolecule #2: Spike glycoprotein E2
Macromolecule | Name: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 46.374848 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SITDDFTLTS PYLGFCPYCR HSAPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSFD HDHDIKEDSM DKIAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVHGKL VKCHVYDHLK E TSAGYITM ...String: SITDDFTLTS PYLGFCPYCR HSAPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSFD HDHDIKEDSM DKIAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVHGKL VKCHVYDHLK E TSAGYITM HRPGPHAYKS YLEEASGEVY IKPPSGKNVT YECKCGDYST GIVSTRTKMN GCTKAKQCIA YKSDQTKWVF NS PDLIRHT DHSVQGKLHI PFRLTPTVCP VPLAHTPTVT KWFKGITLHL TATRPTLLTT RKLGLRADAT AEWITGTTSR NFS VGREGL EYVWGNHEPV RVWAQESAPG DPHGWPHEII IHYYHRHPVY TVIVLCGVAL AILVGTASSA ACIAKARRDC LTPY ALAPN ATVPTALAVL CCI UniProtKB: Structural polyprotein |
-Macromolecule #3: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 29.11473 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MFPYPQLNFP PVYPTNPMAY RDPNPPRCRW RPFRPPLAAQ IEDLRRSIAN LTFKQRSPNP PPGPPPKKKK SAPKPKPTQP KKKKQQAKK TKRKPKPGKR QRMCMKLESD KTFPIMLNGQ VNGYACVVGG RLMKPLHVEG KIDNEQLAAV KLKKASMYDL E YGDVPQNM ...String: MFPYPQLNFP PVYPTNPMAY RDPNPPRCRW RPFRPPLAAQ IEDLRRSIAN LTFKQRSPNP PPGPPPKKKK SAPKPKPTQP KKKKQQAKK TKRKPKPGKR QRMCMKLESD KTFPIMLNGQ VNGYACVVGG RLMKPLHVEG KIDNEQLAAV KLKKASMYDL E YGDVPQNM KSDTLQYTSD KPPGFYNWHH GAVQYENGRF TVPRGVGGKG DSGRPILDNR GRVVAIVLGG ANEGTRTALS VV TWNQKGV TIKDTPEGSE PW UniProtKB: Structural polyprotein |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 2937 / Average electron dose: 43.5 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | ![]() PDB-8dec: |