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- PDB-11ls: Human Monoclonal Antibody RVC68 in complex with rabies virus glyc... -

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Basic information

Entry
Database: PDB / ID: 11ls
TitleHuman Monoclonal Antibody RVC68 in complex with rabies virus glycoprotein
Components
  • (Monoclonal Antibody RVA122 ...) x 2
  • (Monoclonal Antibody RVC68 ...) x 2
  • Glycoprotein
KeywordsVIRAL PROTEIN / Rabies / Rabies virus glycoprotein / antibody
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 speciesHomo sapiens (human)
Lyssavirus rabies
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 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
DepositionMar 3, 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
E: Monoclonal Antibody RVA122 Heavy Chain
A: Glycoprotein
D: Monoclonal Antibody RVA122 Light Chain
H: Monoclonal Antibody RVC68 Heavy Chain
L: Monoclonal Antibody RVC68 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,5227
Polymers155,0805
Non-polymers4422
Water00
1


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

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Components

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Antibody , 4 types, 4 molecules EDHL

#1: Antibody Monoclonal Antibody RVA122 Heavy Chain


Mass: 28196.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody Monoclonal Antibody RVA122 Light Chain


Mass: 23449.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)
#4: Antibody Monoclonal Antibody RVC68 Heavy Chain


Mass: 27968.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)
#5: Antibody Monoclonal Antibody RVC68 Light Chain


Mass: 23260.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)

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Protein / Sugars , 2 types, 3 molecules A

#2: Protein Glycoprotein


Mass: 52204.164 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: P08667
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
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 RVC68 Fabs
Type: COMPLEX / Entity ID: #1-#5 / 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 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
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 897063 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 142.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00246668
ELECTRON MICROSCOPYf_angle_d0.60019055
ELECTRON MICROSCOPYf_chiral_restr0.04531002
ELECTRON MICROSCOPYf_plane_restr0.0061143
ELECTRON MICROSCOPYf_dihedral_angle_d5.1023946

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