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- PDB-38pm: Australian bat lyssavirus glycoprotein PH domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 38pm
TitleAustralian bat lyssavirus glycoprotein PH domain in complex with broadly neutralizing human antibodies A6 and RVC20
Components
  • Antibody A6 heavy chain
  • Antibody A6 light chain
  • Antibody RVC20 heavy chain
  • Antibody RVC20 light chain
  • Glycoprotein
KeywordsVIRAL PROTEIN / ABVL / PHD / antibody / neutralizing
Function / homology: / Rhabdovirus glycoprotein G PH domain / : / Rhabdovirus spike glycoprotein G central domain / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein fusion domain / viral envelope / virion membrane / Glycoprotein
Function and homology information
Biological speciesHomo sapiens (human)
Lyssavirus australis
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXu, K. / Xu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UH2AI171611 United States
CitationJournal: Emerg Microbes Infect / Year: 2026
Title: Peripheral human mAb therapy yields modulation of neuroinflammation and long-term functional recovery from lyssavirus infection.
Authors: Celeste Huaman / Yan Xu / Nathaniel M Lott / Elise M Santorella / Madeline Rader / Allison M Strazzella / Caitlyn Clouse / Jocelyn M King / Mattie Melnyk / Junping Hong / Lianying Yan / ...Authors: Celeste Huaman / Yan Xu / Nathaniel M Lott / Elise M Santorella / Madeline Rader / Allison M Strazzella / Caitlyn Clouse / Jocelyn M King / Mattie Melnyk / Junping Hong / Lianying Yan / Adrian C Paskey / Andrea E Luquette / Francisco Malagon / Regina Z Cer / Kimberly A Bishop-Lilly / Daniel P Perl / Christopher C Broder / Kai Xu / Brian C Schaefer /
Abstract: Rabies is a fatal encephalitis caused by viruses in the lyssavirus genus. We previously demonstrated that intraperitoneal administration of a single dose of neutralizing human monoclonal antibody ...Rabies is a fatal encephalitis caused by viruses in the lyssavirus genus. We previously demonstrated that intraperitoneal administration of a single dose of neutralizing human monoclonal antibody (mAb) F11 can protect mice from fatal lyssavirus infection, post-central nervous system (CNS) invasion. However, the molecular basis of F11 neutralization remains unknown. Here, we use structural and functional analyses to define neutralizing activity of F11 and the related mAb, A6. Cryo-electron microscopy (EM) and negative-stain EM reveal that both mAbs bind Domain III of the glycoprotein G, recognizing a prefusion-specific epitope distinct from previously characterized antibodies including RVC20. Binding stabilizes the prefusion state, blocking membrane fusion. We furthermore found that a single dose of either A6 or RVC20 protected animals from mortality induced by Australian bat lyssavirus (ABLV), while promoting substantial long-term functional recovery. Moreover, A6 similarly protected animals from mortality following infection with a currently circulating wild isolate of rabies virus (RABV). Transcriptomics analysis of brain RNA and protein-based analysis of brain tissue homogenates demonstrated that therapy with A6 broadly reduced expression of neuroinflammatory mediators during the acute phase of infection. Interestingly, infection of animals with a non-lethal attenuated mutant of ABLV resulted in similar neuroinflammation. Thus, a robust neuroinflammatory response to ABLV does not predict mortality. Overall, peripheral therapy with A6 and similar neutralizing mAbs promotes survival and long-term functional recovery from CNS-resident lyssavirus infection in a manner that includes suppression of the G pre- to postfusion transition and modulation of neuroinflammation.
History
DepositionSep 11, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody RVC20 heavy chain
B: Antibody RVC20 light chain
H: Antibody A6 heavy chain
L: Antibody A6 light chain
G: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)61,1685
Polymers61,1685
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: Antibody Antibody RVC20 heavy chain


Mass: 13627.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody RVC20 light chain


Mass: 11523.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Antibody A6 heavy chain


Mass: 14091.765 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Antibody A6 light chain


Mass: 11441.696 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Protein Glycoprotein


Mass: 10483.997 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyssavirus australis / Production host: Homo sapiens (human) / References: UniProt: Q9QSP1
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: Lyssavirus australis / Type: VIRUS / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Lyssavirus australis
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.2 / Details: 5mM HEPES buffer pH7.2, 150nM NaCl
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 1mg/ml in HBS buffer, purfied from HEK293 recombinant expression and purified with NiNTA resin via Hisx6 tag
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 273 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 8000 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 30000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3particle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
13cryoSPARC33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 195885 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034349
ELECTRON MICROSCOPYf_angle_d0.5495886
ELECTRON MICROSCOPYf_dihedral_angle_d13.7331556
ELECTRON MICROSCOPYf_chiral_restr0.041637
ELECTRON MICROSCOPYf_plane_restr0.004748

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