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- EMDB-63979: RABV G binding with CTB011 Fab and CTB012 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-63979
TitleRABV G binding with CTB011 Fab and CTB012 Fab
Map data
Sample
  • Complex: RABV G binding with CTB 011 Fab CTB012 Fab
    • Protein or peptide: Glycoprotein
    • Protein or peptide: CTB011 Fab Heavy chain
    • Protein or peptide: CTB011 Fab light chain
    • Protein or peptide: CTB012 Fab light chain
    • Protein or peptide: CTB012 Fab heavy chain
KeywordsRABV / G protein / Neutralizing antibody / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 speciesLyssavirus rabies / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsCao L / Zhang C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Emerg Microbes Infect / Year: 2025
Title: Structural basis for broad neutralization of rabies virus by an antibody cocktail SYN023.
Authors: Lei Cao / Jiagui Qu / Chuziyue Zhang / Ruihong Chen / Jinyue Wang / Christine Fehlner-Gardiner / Michael Niezgoda / Panayampalli Subbian Satheshkumar / Xiangxi Wang / Eric Tsao /
History
DepositionMar 31, 2025-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63979.png

Downloads & links

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Map

FileDownload / File: emd_63979.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46
Minimum - Maximum-0.6927848 - 1.3931949
Average (Standard dev.)0.000060714185 (±0.04304184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63979_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63979_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RABV G binding with CTB 011 Fab CTB012 Fab

EntireName: RABV G binding with CTB 011 Fab CTB012 Fab
Components
  • Complex: RABV G binding with CTB 011 Fab CTB012 Fab
    • Protein or peptide: Glycoprotein
    • Protein or peptide: CTB011 Fab Heavy chain
    • Protein or peptide: CTB011 Fab light chain
    • Protein or peptide: CTB012 Fab light chain
    • Protein or peptide: CTB012 Fab heavy chain

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Supramolecule #1: RABV G binding with CTB 011 Fab CTB012 Fab

SupramoleculeName: RABV G binding with CTB 011 Fab CTB012 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Lyssavirus rabies

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Macromolecule #1: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lyssavirus rabies
Molecular weightTheoretical: 44.823402 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KFPIYTIPDK LGPWSPIDIH HLSCPNNLVV EDEGCTNLSG FSYMELKVGY ISAIKMNGFT CTGVVTEAET YTNFVGYVTT TFKRKHFRP TPDACRAAYN WKMAGDPRYE ESLHNPYPDY HWLRTVKTTK ESLVIISPSV ADLDPYDRSL HSPVFPGGNC S GVAVSSTY ...String:
KFPIYTIPDK LGPWSPIDIH HLSCPNNLVV EDEGCTNLSG FSYMELKVGY ISAIKMNGFT CTGVVTEAET YTNFVGYVTT TFKRKHFRP TPDACRAAYN WKMAGDPRYE ESLHNPYPDY HWLRTVKTTK ESLVIISPSV ADLDPYDRSL HSPVFPGGNC S GVAVSSTY CSTNHDYTIW MPENPRLGMS CDIFTNSRGK RASKGSETCG FVDERGLYKS LKGACKLKLC GVLGLRLMDG TW VAMQTSN ETKWCPPGQL VNLHDFRSDE IEHLVVEELV KKREECLDAL ESIMTTKSVS FRRLSHLRKL VPGFGKAYTI FNK TLMEAD AHYKSVRTWN EIIPSKGCLR VGGRCHPHVN GVFFNGIILG PDGNVLIPEM QSSLLQQHME LLVSSVIPLM HPL

UniProtKB: Glycoprotein

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Macromolecule #2: CTB011 Fab Heavy chain

MacromoleculeName: CTB011 Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.165745 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGASVKV SCKASGYSFT DYIMLWVRQA PGQRLEWIGD IYPYYGSTSY NLKFKGKATL TVDTSASTAY MELSSLRSE DTAVYYCARQ GGDGNYVLFD YWGQGTLVTV

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Macromolecule #3: CTB011 Fab light chain

MacromoleculeName: CTB011 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.526706 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCKASQNVG TTVAWYQQKP GKAPKALIYS ASYRYSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QYNSYPFTFG QGTKLEI

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Macromolecule #4: CTB012 Fab light chain

MacromoleculeName: CTB012 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.123598 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPLS LPVTPGEPAS ISCKSTKSLL NSDGFTYLDW YLQKPGQSPQ LLIYLVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCFQSNYL PFTFGGGTKV EI

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Macromolecule #5: CTB012 Fab heavy chain

MacromoleculeName: CTB012 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.930525 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVQPGGSLIL SCAASGFTFS GFAMSWVRQA PGKGLEWVAT ISSGGTYTYS PDSVMGRFTI SRDNAKNSLY LQMNSLRAE DTAVYYCARR LRRNYYSMDY WGQGTMVTV

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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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8a1e

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 359068
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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