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- PDB-11iw: Mouse monoclonal antibody A2 in complex with rabies virus glycoprotein -

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Basic information

Entry
Database: PDB / ID: 11iw
TitleMouse monoclonal antibody A2 in complex with rabies virus glycoprotein
Components
  • Antibody A2 Heavy Chain
  • Antibody A2 Light Chain
  • Antibody RVA122 Heavy Chain
  • Antibody RVA122 Light Chain
  • Glycoprotein
KeywordsVIRAL PROTEIN/Immune System / Rabies / Rabies virus glycoprotein / antibody / 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
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
Homo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsCallaway, H.M. / Zyla, D. / Hastie, K. / Harkins, S. / Kothalawalage, S. / Samarasinghe, S. / Flynn, A. / Hariharan, C. / Yin, J. / Corti, D. ...Callaway, H.M. / Zyla, D. / Hastie, K. / Harkins, S. / Kothalawalage, S. / Samarasinghe, S. / Flynn, A. / Hariharan, C. / Yin, J. / Corti, D. / Bouhry, H. / Dessain, S. / Saphire, E.O.
Funding support United States, 2items
OrganizationGrant numberCountry
Other private United States
Other private United States
CitationJournal: To Be Published
Title: Antigenic landscape of rabies and related lyssaviruses revealed by cryo-EM
Authors: Callaway, H.M. / Zyla, D. / Hastie, K. / Harkins, S. / Kothalawalage, S. / Samarasinghe, S. / Flynn, A. / Hariharan, C. / Yin, J. / Corti, D. / Bouhry, H. / Dessain, S. / Saphire, E.O.
History
DepositionFeb 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 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: Glycoprotein
D: Antibody RVA122 Light Chain
J: Antibody A2 Light Chain
E: Antibody RVA122 Heavy Chain
I: Antibody RVA122 Heavy Chain
G: Antibody RVA122 Heavy Chain
F: Antibody RVA122 Light Chain
H: Antibody RVA122 Light Chain
B: Glycoprotein
C: Glycoprotein
K: Antibody A2 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)363,19211
Polymers363,19211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Glycoprotein


Mass: 52204.164 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyssavirus rabies / Production host: Homo sapiens (human) / References: UniProt: P08667
#2: Antibody Antibody RVA122 Light Chain


Mass: 23449.830 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody Antibody A2 Light Chain


Mass: 23378.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly)
#4: Antibody Antibody RVA122 Heavy Chain


Mass: 28196.096 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)
#5: Antibody Antibody A2 Heavy Chain


Mass: 28263.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly)
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: Complex of RABV-G pre-fusion trimers with RVA122 and A2 Fabs
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Lyssavirus rabies
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMSodium chlorideNaCl1
227 mMPotassium ChlorideKCl1
3100 mMSodium PhosphateNa2HPO41
418 mMPotassium PhosphateKH2PO41
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19_4092model refinement
3EPUimage acquisition
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 484050 / Symmetry type: POINT
RefinementHighest resolution: 3.01 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315941
ELECTRON MICROSCOPYf_angle_d0.54821645
ELECTRON MICROSCOPYf_dihedral_angle_d5.5052175
ELECTRON MICROSCOPYf_chiral_restr0.0422355
ELECTRON MICROSCOPYf_plane_restr0.0152762

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