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- PDB-9ua5: RABV G binding with CTB011 Fab and CTB012 Fab -

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Basic information

Entry
Database: PDB / ID: 9ua5
TitleRABV G binding with CTB011 Fab and CTB012 Fab
Components
  • CTB011 Fab Heavy chain
  • CTB011 Fab light chain
  • CTB012 Fab heavy chain
  • CTB012 Fab light chain
  • Glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / RABV / G protein / Neutralizing antibody / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsCao, L. / Zhang, C.
Funding support1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Glycoprotein
G: CTB011 Fab Heavy chain
K: CTB011 Fab light chain
D: CTB012 Fab light chain
H: CTB012 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)94,5705
Polymers94,5705
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glycoprotein


Mass: 44823.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyssavirus rabies / Production host: Homo sapiens (human) / References: UniProt: R9W5Z3
#2: Antibody CTB011 Fab Heavy chain


Mass: 13165.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody CTB011 Fab light chain


Mass: 11526.706 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody CTB012 Fab light chain


Mass: 12123.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#5: Antibody CTB012 Fab heavy chain


Mass: 12930.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RABV G binding with CTB 011 Fab CTB012 Fab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Lyssavirus rabies11292
31Mus musculus (house mouse)10090
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI SPIRIT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 359068 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036200
ELECTRON MICROSCOPYf_angle_d0.7378401
ELECTRON MICROSCOPYf_dihedral_angle_d6.603866
ELECTRON MICROSCOPYf_chiral_restr0.047915
ELECTRON MICROSCOPYf_plane_restr0.0051070

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