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Yorodumi- EMDB-28058: Venezuelan equine encephalitis virus-like particle in complex wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28058 | |||||||||
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Title | Venezuelan equine encephalitis virus-like particle in complex with Fab SKT05, local refinement | |||||||||
Map data | Map obtained using DeepEMHancer | |||||||||
Sample |
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Keywords | Venezuelan equine encephalitis virus / neutralizing antibody / VEEV / VIRUS LIKE PARTICLE-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane Similarity search - Function | |||||||||
Biological species | Venezuelan equine encephalitis virus / Macaca fascicularis (crab-eating macaque) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Tsybovsky Y / Pletnev S / Verardi R / Roederer M / Kwong PD | |||||||||
Funding support | 1 items
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Citation | Journal: Cell / Year: 2023 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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28058.map.gz | 87.6 MB | EMDB map data format | |
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Header (meta data) | emd-28058-v30.xml emd-28058.xml | 24.4 KB 24.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28058_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_28058.png | 88.4 KB | ||
Masks | emd_28058_msk_1.map | 98.9 MB | Mask map | |
Others | emd_28058_additional_1.map.gz emd_28058_additional_2.map.gz emd_28058_half_map_1.map.gz emd_28058_half_map_2.map.gz | 77.1 MB 8.2 MB 77.8 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28058 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28058 | HTTPS FTP |
-Validation report
Summary document | emd_28058_validation.pdf.gz | 968.6 KB | Display | EMDB validaton report |
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Full document | emd_28058_full_validation.pdf.gz | 968.2 KB | Display | |
Data in XML | emd_28058_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | emd_28058_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28058 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28058 | HTTPS FTP |
-Related structure data
Related structure data | 8eeuMC 8decC 8dedC 8deeC 8defC 8deqC 8derC 8dulC 8dunC 8dwoC 8eevC C: citing same article (ref.) M: atomic model generated by this map |
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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_28058.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Map obtained using DeepEMHancer | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.056 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28058_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Map before post-processing
File | emd_28058_additional_1.map | ||||||||||||
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Annotation | Map before post-processing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map obtained using standard post-processing in Relion
File | emd_28058_additional_2.map | ||||||||||||
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Annotation | Map obtained using standard post-processing in Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_28058_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2
File | emd_28058_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex between Venezuelan equine encephalitis virus-like particl...
Entire | Name: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT05 |
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Components |
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-Supramolecule #1: Complex between Venezuelan equine encephalitis virus-like particl...
Supramolecule | Name: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT05 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The map was obtained using symmetry expansion and signal subtraction. DeepEMHancer was used for post-processing. |
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Source (natural) | Organism: Venezuelan equine encephalitis virus |
Molecular weight | Theoretical: 33 MDa |
-Macromolecule #1: Coat protein
Macromolecule | Name: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Venezuelan equine encephalitis virus |
Molecular weight | Theoretical: 138.662531 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSAKKPKKEA SQKQKGGGQG KKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTFP IMLEGKINGY ACVVGGKLFR PMHVEGKIDN D VLAALKTK ...String: MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSAKKPKKEA SQKQKGGGQG KKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTFP IMLEGKINGY ACVVGGKLFR PMHVEGKIDN D VLAALKTK KASKYDLEYA DVPQNMRADT FKYTHEKPQG YYSWHHGAVQ YENGRFTVPK GVGAKGDSGR PILDNQGRVV AI VLGGVNE GSRTALSVVM WNEKGVTVKY TPENCEQWSL VTTMCLLANV TFPCAQPPIC YDRKPAETLA MLSVNVDNPG YDE LLEAAV KCPGRKRRST EELFNEYKLT RPYMARCIRC AVGSCHSPIA IEAVKSDGHD GYVRLQTSSQ YGLDSSGNLK GRTM RYDMH GTIKEIPLHQ VSLYTSRPCH IVDGHGYFLL ARCPAGDSIT MEFKKDSVRH SCSVPYEVKF NPVGRELYTH PPEHG VEQA CQVYAHDAQN RGAYVEMHLP GSEVDSSLVS LSGSSVTVTP PDGTSALVEC ECGGTKISET INKTKQFSQC TKKEQC RAY RLQNDKWVYN SDKLPKAAGA TLKGKLHVPF LLADGKCTVP LAPEPMITFG FRSVSLKLHP KNPTYLITRQ LADEPHY TH ELISEPAVRN FTVTEKGWEF VWGNHPPKRF WAQETAPGNP HGLPHEVITH YYHRYPMSTI LGLSICAAIA TVSVAAST W LFCRSRVACL TPYRLTPNAR IPFCLAVLCC ARTARAETTW ESLDHLWNNN QQMFWIQLLI PLAALIVVTR LLRCVCCVV PFLVMAGAAA PAYEHATTMP SQAGISYNTI VNRAGYAPLP ISITPTKIKL IPTVNLEYVT CHYKTGMDSP AIKCCGSQEC TPTYRPDEQ CKVFTGVYPF MWGGAYCFCD TENTQVSKAY VMKSDDCLAD HAEAYKAHTA SVQAFLNITV GEHSIVTTVY V NGETPVNF NGVKITAGPL STAWTPFDRK IVQYAGEIYN YDFPEYGAGQ PGAFGDIQSR TVSSSDLYAN TNLVLQRPKA GA IHVPYTQ APSGFEQWKK DKAPSLKFTA PFGCEIYTNP IRAENCAVGS IPLAFDIPDA LFTRVSETPT LSAAECTLNE CVY SSDFGG IATVKYSASK SGKCAVHVPS GTATLKEAAV ELTEQGSATI HFSTANIHPE FRLQICTSYV TCKGDCHPPK DHIV THPQY HAQTFTAAVS KTAWTWLTSL LGGSAVIIII GLVLATIVAM YVLTNQKHN UniProtKB: Structural polyprotein |
-Macromolecule #2: Fab SKT05 heavy chain
Macromolecule | Name: Fab SKT05 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca fascicularis (crab-eating macaque) |
Molecular weight | Theoretical: 25.517631 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGAG LVQPGGSLRL SCAASGFTFS DSWMSWVRQS PGKGLEWVGR IKGKPDGETA AYAASVKGRF SISRDDSKNT LYLQMNSLK TEDTAVYYCT RDDRTSCRRG VCYAAFHSWG QGVLVTVSSA STKGPSVFPL APSSRSTSES TAALGCLVKD Y FPEPVTVS ...String: EVQLVESGAG LVQPGGSLRL SCAASGFTFS DSWMSWVRQS PGKGLEWVGR IKGKPDGETA AYAASVKGRF SISRDDSKNT LYLQMNSLK TEDTAVYYCT RDDRTSCRRG VCYAAFHSWG QGVLVTVSSA STKGPSVFPL APSSRSTSES TAALGCLVKD Y FPEPVTVS WNSGSLTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YVCNVNHKPS NTKVDKRVEI KTCGGLEVLF Q |
-Macromolecule #3: Fab SKT05 light chain
Macromolecule | Name: Fab SKT05 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Macaca fascicularis (crab-eating macaque) |
Molecular weight | Theoretical: 23.238729 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASAGDRVT LTCRASQAIS FYLAWYQQKP GKAPKRLIYD ASELQGGVPS RFSGSGSGTD FTLSINSLQP EDSATYFCL QYDSPPFTFG PGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String: DIQMTQSPSS LSASAGDRVT LTCRASQAIS FYLAWYQQKP GKAPKRLIYD ASELQGGVPS RFSGSGSGTD FTLSINSLQP EDSATYFCL QYDSPPFTFG PGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRGEC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.8 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: 2.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
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Output model | PDB-8eeu: |