[English] 日本語
Yorodumi
- EMDB-28060: Venezuelan equine encephalitis virus-like particle in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28060
TitleVenezuelan equine encephalitis virus-like particle in complex with Fab SKT-20, local refinement
Map dataMap obtained by post-processing with DeepEMhancer
Sample
  • Complex: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT20
    • Protein or peptide: Coat protein
    • Protein or peptide: Fab SKT20 heavy chain
    • Protein or peptide: Fab SKT20 light chain
KeywordsVenezuelan 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
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesVenezuelan equine encephalitis virus / Macaca fascicularis (crab-eating macaque)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsTsybovsky Y / Pletnev S / Verardi R / Roederer M / Kwong PD
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionSep 7, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28060.png

Downloads & links

-
Map

FileDownload / File: emd_28060.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap obtained by post-processing with DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 240 pix.
= 295.56 Å		1.23 Å/pix.
x 240 pix.
= 295.56 Å		1.23 Å/pix.
x 240 pix.
= 295.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2315 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.05313566 - 2.0696874
Average (Standard dev.)0.0026540665 (±0.034443643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 295.56 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_28060_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map before post-processing

Fileemd_28060_additional_1.map
AnnotationMap before post-processing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map obtained using standard post-processing in Relion

Fileemd_28060_additional_2.map
AnnotationMap obtained using standard post-processing in Relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 1

Fileemd_28060_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 2

Fileemd_28060_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex between Venezuelan equine encephalitis virus-like particl...

EntireName: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT20
Components
  • Complex: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT20
    • Protein or peptide: Coat protein
    • Protein or peptide: Fab SKT20 heavy chain
    • Protein or peptide: Fab SKT20 light chain

-
Supramolecule #1: Complex between Venezuelan equine encephalitis virus-like particl...

SupramoleculeName: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT20
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The map was obtained after symmetry expansion and signal subtraction. Post-processing was performed with DeepEMhancer.
Source (natural)Organism: Venezuelan equine encephalitis virus
Molecular weightTheoretical: 33 MDa

-
Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Venezuelan equine encephalitis virus
Molecular weightTheoretical: 138.662531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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 SKT20 heavy chain

MacromoleculeName: Fab SKT20 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 25.421338 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQVQESGPG LVKPSETLSL TCAVSSGSIN DDSYYWTWIR QSPGKGLEWL GFIHGGTGKS FYNPSLESRV TISKDTSRNQ FSLTLSSVS AADTAVYYCA RSHFCSNTFC YGWFDVWGPG IRVTVSSAST KGPSVFPLAP SSRSTSESTA ALGCLVKDYF P EPVTVSWN ...String:
QVQVQESGPG LVKPSETLSL TCAVSSGSIN DDSYYWTWIR QSPGKGLEWL GFIHGGTGKS FYNPSLESRV TISKDTSRNQ FSLTLSSVS AADTAVYYCA RSHFCSNTFC YGWFDVWGPG IRVTVSSAST KGPSVFPLAP SSRSTSESTA ALGCLVKDYF P EPVTVSWN SGSLTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYV CNVNHKPSNT KVDKRVEIKT CGGLEVLFQ

-
Macromolecule #3: Fab SKT20 light chain

MacromoleculeName: Fab SKT20 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 23.754445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVVMTQTPLS LPITPGEPAS ISCRSSQSLL HSNGNTYLHW YLQKPGQSPQ LLIYGGSNRA SGVPDRFSGS GSGTDFTLKI SKVEAEDVG VYYCVQAIAF PWTFGQGTKV EIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV ...String:
DVVMTQTPLS LPITPGEPAS ISCRSSQSLL HSNGNTYLHW YLQKPGQSPQ LLIYGGSNRA SGVPDRFSGS GSGTDFTLKI SKVEAEDVG VYYCVQAIAF PWTFGQGTKV EIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV TEQDSKDNTY SLSSTLTLSS TEYQSHKVYA CEVTHQGLSS PVTKSFNRGE C

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 47.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 680160
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 28235
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-8eev:
Venezuelan equine encephalitis virus-like particle in complex with Fab SKT-20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more