[English] 日本語
Yorodumi
- EMDB-26398: Rabies virus glycoprotein trimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26398
TitleRabies virus glycoprotein trimer
Map dataRABVG pre-fusion trimer with no interacting fusion loops
Sample
  • Complex: Rabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122
    • Protein or peptide: Glycoprotein
    • Protein or peptide: RVA122 Fab Light Chain
    • Protein or peptide: RVA122 Fab Heavy Chain
KeywordsRabies virus glycoprotein / antibodies / viral fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesRabies virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.92 Å
AuthorsCallaway HM / Zyla D / Larrous F / Dias de Melo G / Hastie KM / Avalos RD / Agarwal A / Bouhry H / Corti D / Saphire EO
Funding support United States, Switzerland, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5F32AI147531-03 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5T32AI07244-36 United States
Swiss National Science FoundationP2EZP3_195680 Switzerland
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)U24GM129547 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structure of the rabies virus glycoprotein trimer bound to a prefusion-specific neutralizing antibody.
Authors: Heather M Callaway / Dawid Zyla / Florence Larrous / Guilherme Dias de Melo / Kathryn M Hastie / Ruben Diaz Avalos / Alyssa Agarwal / Davide Corti / Hervé Bourhy / Erica Ollmann Saphire /
Abstract: Rabies infection is nearly 100% lethal if untreated and kills more than 50,000 people annually, many of them children. Existing rabies vaccines target the rabies virus glycoprotein (RABV-G) but ...Rabies infection is nearly 100% lethal if untreated and kills more than 50,000 people annually, many of them children. Existing rabies vaccines target the rabies virus glycoprotein (RABV-G) but generate short-lived immune responses, likely because the protein is heterogeneous under physiological conditions. Here, we report the 3.39 Å cryo-electron microscopy structure of trimeric, prefusion RABV-G complexed with RVA122, a potently neutralizing human antibody. RVA122 binds to a quaternary epitope at the top of RABV-G, bridging domains and stabilizing RABV-G protomers in a prefusion state. RABV-G trimerization involves side-to-side interactions between the central α helix and adjacent loops, rather than contacts between central helices, and interactions among the fusion loops at the glycoprotein base. These results provide a basis from which to develop improved rabies vaccines based on RABV-G stabilized in the prefusion conformation.
History
DepositionMar 10, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26398.png

Downloads & links

-
Map

FileDownload / File: emd_26398.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRABVG pre-fusion trimer with no interacting fusion loops
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.68 Å/pix.
x 110 pix.
= 294.4 Å		2.68 Å/pix.
x 110 pix.
= 294.4 Å		2.68 Å/pix.
x 110 pix.
= 294.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.67636 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.0603725 - 2.2158403
Average (Standard dev.)-0.0055611404 (±0.144224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110110110
Spacing110110110
CellA=B=C: 294.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Map Half 1

Fileemd_26398_half_map_1.map
AnnotationMap Half 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Hap Half 2

Fileemd_26398_half_map_2.map
AnnotationHap Half 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Rabies virus glycoprotein pre-fusion trimer in complex with neutr...

EntireName: Rabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122
Components
  • Complex: Rabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122
    • Protein or peptide: Glycoprotein
    • Protein or peptide: RVA122 Fab Light Chain
    • Protein or peptide: RVA122 Fab Heavy Chain

-
Supramolecule #1: Rabies virus glycoprotein pre-fusion trimer in complex with neutr...

SupramoleculeName: Rabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Reconstruction with no interacting fusion loops

-
Macromolecule #1: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabies virus / Strain: PV
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVPQALLFVP LLVFPLCFGK FPIYTIPDKL GPWSPIDIHH LSCPNNLVVE DEGCTNLSGF SYMELKVGYI SAIKMNGFTC TGVVTEAET YTNFVGYVTT TFKRKHFRPT PDACRAAYNW KMAGDPRYEE SLHNPYPDYH WLRTVKTTKE SLVIISPSVA D LDPYDRSL ...String:
MVPQALLFVP LLVFPLCFGK FPIYTIPDKL GPWSPIDIHH LSCPNNLVVE DEGCTNLSGF SYMELKVGYI SAIKMNGFTC TGVVTEAET YTNFVGYVTT TFKRKHFRPT PDACRAAYNW KMAGDPRYEE SLHNPYPDYH WLRTVKTTKE SLVIISPSVA D LDPYDRSL HSRVFPGGNC SGVAVSSTYC STNHDYTIWM PENPRLGMSC DIFTNSRGKR ASKGSETCGF VDERGLYKSL KG ACKLKLC GVLGLRLMDG TWVAMQTSNE TKWCPPGQLV NLHDFRSDEI EHLVVEELVK KREECLDALE SIMTTKSVSF RRL SHLRKL VPGFGKAYTI FNKTLMEADA HYKSVRTWNE IIPSKGCLRV GGRCHPHVNG VFFNGIILGP DGNVLIPEMQ SSLL QQHME LLVSSVIPLM HPLADPSTVF KNGDEAEDFV EVHL

-
Macromolecule #2: RVA122 Fab Light Chain

MacromoleculeName: RVA122 Fab Light Chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: QSVLTQSPSA SDTPGQRVTI SCSGSSSNIG SNYVYWYQQF PGTAPKLLIY KSDKRPSGVP DRFSGSTSGT SASLAISGLR SEDEADYYC AAWDNRLSGW LFGGGTKLTV LGTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
QSVLTQSPSA SDTPGQRVTI SCSGSSSNIG SNYVYWYQQF PGTAPKLLIY KSDKRPSGVP DRFSGSTSGT SASLAISGLR SEDEADYYC AAWDNRLSGW LFGGGTKLTV LGTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLRSPV TKSFNRGEC

-
Macromolecule #3: RVA122 Fab Heavy Chain

MacromoleculeName: RVA122 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: QVHLQESGPG LVKPSETLSL TCTVSGDSMN NFYWGWIRQP AGKGLEWIGY IYYSGTTNYN PSLKSRVTIS IDTSKNQFSL KVNSVTAAD TAVYYCARDS GDYVSYYYYG MDVWGPGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QVHLQESGPG LVKPSETLSL TCTVSGDSMN NFYWGWIRQP AGKGLEWIGY IYYSGTTNYN PSLKSRVTIS IDTSKNQFSL KVNSVTAAD TAVYYCARDS GDYVSYYYYG MDVWGPGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDL EVDDDDKAGW SH PQFEKGG GSGGGSGGGS WSHPQFEK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
80.0 g/LNaClSodium chlorideSodium chloride
0.2 g/LKClPotassium chloride
1.44 g/LNa2HPO4Sodium phosphate dibasic
0.24 g/LKH2PO4Potassium phosphate monobasic
0.03 mMLauryl Maltose Neopentyl Glycol

Details: PBS pH 7.4 with 0.03mM LMNG
GridModel: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 26.74 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 103739
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10144

+
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