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- PDB-3jcx: Canine Parvovirus complexed with Fab E -

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Basic information

Entry
Database: PDB / ID: 3jcx
TitleCanine Parvovirus complexed with Fab E
Components
  • Capsid protein 2
  • Fab E heavy chain
  • Fab E light chain
KeywordsVIRUS/IMMUNE SYSTEM / parvovirus / antibody / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesCanine parvovirus
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsOrgantini, L.J. / Iketani, S. / Huang, K. / Ashley, R.E. / Makhov, A.M. / Conway, J.F. / Parrish, C.R. / Hafenstein, S.
CitationJournal: J Virol / Year: 2016
Title: Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus.
Authors: Lindsey J Organtini / Hyunwook Lee / Sho Iketani / Kai Huang / Robert E Ashley / Alexander M Makhov / James F Conway / Colin R Parrish / Susan Hafenstein /
Abstract: Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was ...Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM.
IMPORTANCE: Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced ...IMPORTANCE: Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time.
History
DepositionMar 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-6629
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  • Superimposition on EM map
  • EMDB-6629
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein 2
H: Fab E heavy chain
L: Fab E light chain


Theoretical massNumber of molelcules
Total (without water)89,2683
Polymers89,2683
Non-polymers00
Water00
1
A: Capsid protein 2
H: Fab E heavy chain
L: Fab E light chain
x 60


Theoretical massNumber of molelcules
Total (without water)5,356,079180
Polymers5,356,079180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein 2
H: Fab E heavy chain
L: Fab E light chain
x 5


  • icosahedral pentamer
  • 446 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)446,34015
Polymers446,34015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein 2
H: Fab E heavy chain
L: Fab E light chain
x 6


  • icosahedral 23 hexamer
  • 536 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)535,60818
Polymers535,60818
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein 2 / VP2


Mass: 64783.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canine parvovirus / References: UniProt: B2ZG07
#2: Antibody Fab E heavy chain


Mass: 12739.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Strain: B5A8
#3: Antibody Fab E light chain


Mass: 11745.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Strain: B5A8
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

Component
IDNameTypeParent-IDSynonym
1Canine Parvovirus complexed with Fab ECOMPLEX0
2Canine parvovirusVIRUS1COV
3Fab E heavy chain1
4Fab E light chain1
Details of virusEmpty: YES / Enveloped: NO / Host category: CANINES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Canis lupus
Buffer solutionName: PBS / pH: 7.4 / Details: PBS
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Details: Plunged into liquid ethane (FEI VITROBOT MARK II).

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Dec 20, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm
Specimen holderSpecimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 1424

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Processing

EM softwareName: RELION / Category: 3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Single Particle / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47563 / Nominal pixel size: 1.37 Å / Actual pixel size: 1.37 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 0 0 0 6072

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