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- EMDB-26397: Rabies virus glycoprotein pre-fusion trimer in complex with neutr... -

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Basic information

Entry
Database: EMDB / ID: EMD-26397
TitleRabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122
Map dataRabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122
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
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsRabies virus glycoprotein / antibodies / viral fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / membrane
Similarity search - Function
: / Rhabdovirus glycoprotein G PH domain / : / Rhabdovirus spike glycoprotein G central domain / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein fusion domain
Similarity search - Domain/homology
Biological speciesRabies virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 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, 3 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
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-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26397.png

Downloads & links

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Map

FileDownload / File: emd_26397.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.01872543 - 0.060040914
Average (Standard dev.)0.0000012833739 (±0.0020830133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26397_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 for rabies virus glycoprotein pre-fusion...

Fileemd_26397_half_map_1.map
AnnotationHalf map 1 for rabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for rabies virus glycoprotein pre-fusion...

Fileemd_26397_half_map_2.map
AnnotationHalf map 2 for rabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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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: #1-#3

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Macromolecule #1: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rabies virus / Strain: Pasteur vaccins / PV
Molecular weightTheoretical: 49.273547 KDa
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

UniProtKB: Glycoprotein

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Macromolecule #2: RVA122 Fab Light Chain

MacromoleculeName: RVA122 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.44983 KDa
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

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Macromolecule #3: RVA122 Fab Heavy Chain

MacromoleculeName: RVA122 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.196096 KDa
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

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

Details: PBS pH 7.4 with 0.09mM LMNG
GridModel: C-flat-2/1
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 223093
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 1 / Software - Name: RELION
FSC plot (resolution estimation)

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