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- PDB-3j6n: Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Int... -

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Basic information

Entry
Database: PDB / ID: 3j6n
TitleKinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-particle
ComponentsCoxsackie and adenovirus receptor
KeywordsCELL ADHESION / Coxsackievirus B3 / CVB3 / CAR
Function / homology
Function and homology information


AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport / cell-cell junction organization / connexin binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cardiac muscle cell development / intercalated disc / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / filopodium / mitochondrion organization / PDZ domain binding / adherens junction / Cell surface interactions at the vascular wall / neuromuscular junction / beta-catenin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell junction / cell-cell junction / heart development / cell body / virus receptor activity / growth cone / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / neuron projection / membrane raft / signaling receptor binding / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...: / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Coxsackievirus and adenovirus receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsOrgantini, L.J. / Makhov, A.M. / Conway, J.F. / Hafenstein, S. / Carson, S.D.
CitationJournal: J Virol / Year: 2014
Title: Kinetic and structural analysis of coxsackievirus B3 receptor interactions and formation of the A-particle.
Authors: Lindsey J Organtini / Alexander M Makhov / James F Conway / Susan Hafenstein / Steven D Carson /
Abstract: The coxsackievirus and adenovirus receptor (CAR) has been identified as the cellular receptor for group B coxsackieviruses, including serotype 3 (CVB3). CAR mediates infection by binding to CVB3 and ...The coxsackievirus and adenovirus receptor (CAR) has been identified as the cellular receptor for group B coxsackieviruses, including serotype 3 (CVB3). CAR mediates infection by binding to CVB3 and catalyzing conformational changes in the virus that result in formation of the altered, noninfectious A-particle. Kinetic analyses show that the apparent first-order rate constant for the inactivation of CVB3 by soluble CAR (sCAR) at physiological temperatures varies nonlinearly with sCAR concentration. Cryo-electron microscopy (cryo-EM) reconstruction of the CVB3-CAR complex resulted in a 9.0-Å resolution map that was interpreted with the four available crystal structures of CAR, providing a consensus footprint for the receptor binding site. The analysis of the cryo-EM structure identifies important virus-receptor interactions that are conserved across picornavirus species. These conserved interactions map to variable antigenic sites or structurally conserved regions, suggesting a combination of evolutionary mechanisms for receptor site preservation. The CAR-catalyzed A-particle structure was solved to a 6.6-Å resolution and shows significant rearrangement of internal features and symmetric interactions with the RNA genome.
IMPORTANCE: This report presents new information about receptor use by picornaviruses and highlights the importance of attaining at least an ∼9-Å resolution for the interpretation of cryo-EM ...IMPORTANCE: This report presents new information about receptor use by picornaviruses and highlights the importance of attaining at least an ∼9-Å resolution for the interpretation of cryo-EM complex maps. The analysis of receptor binding elucidates two complementary mechanisms for preservation of the low-affinity (initial) interaction of the receptor and defines the kinetics of receptor-catalyzed conformational change to the A-particle.
History
DepositionMar 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-5927
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  • Superimposition on EM map
  • EMDB-5927
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Structure viewerMolecule:
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Assembly

Deposited unit
K: Coxsackie and adenovirus receptor


Theoretical massNumber of molelcules
Total (without water)23,7311
Polymers23,7311
Non-polymers00
Water00
1
K: Coxsackie and adenovirus receptor
x 60


Theoretical massNumber of molelcules
Total (without water)1,423,85160
Polymers1,423,85160
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
K: Coxsackie and adenovirus receptor
x 5


  • icosahedral pentamer
  • 119 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)118,6545
Polymers118,6545
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
K: Coxsackie and adenovirus receptor
x 6


  • icosahedral 23 hexamer
  • 142 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)142,3856
Polymers142,3856
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 Coxsackie and adenovirus receptor


Mass: 23730.842 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P78310*PLUS
Has protein modificationY
Sequence detailsTHE HUMAN PROTEIN WAS IMAGED, BUT THE PROTEIN SEQUENCE THAT WAS FIT TO THE ELECTRON MICROSCOPY MAP ...THE HUMAN PROTEIN WAS IMAGED, BUT THE PROTEIN SEQUENCE THAT WAS FIT TO THE ELECTRON MICROSCOPY MAP WAS MURINE (UNP P97792 RESIDUES 20-233).

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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
IDNameTypeDetailsParent-ID
1Coxsackievirus B3 complexed with CARCOMPLEXicosahedral virus0
2Human coxsackievirus B3VIRUS1
3Coxsackievirus and adenovirus receptor1
Molecular weightValue: 7 MDa / Experimental value: YES
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 50 mM MES, 100 mM NaCl / pH: 6 / Details: 50 mM MES, 100 mM NaCl
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow-discharged holey carbon Quantifoil electron microscopy grids
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: OTHER / Temp: 95 K / Humidity: 95 %
Details: Plunged into ethane-propane (FEI VITROBOT MARK III)

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Aug 1, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3660 nm / Nominal defocus min: 1980 nm / Cs: 2 mm / Astigmatism: CTFFIND3 / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 96
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Situsmodel fitting
2Auto3DEM3D reconstruction
3EMAN3D reconstruction
CTF correctionDetails: AUTO3DEM
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Common Lines / Resolution: 9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 9302 / Nominal pixel size: 1.25 Å / Actual pixel size: 1.25 Å
Details: (Single particle details: Particles were selected using EMAN) (Single particle--Applied symmetry: I)
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient / Details: REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 3JZ7

3jz7


Pdb chain-ID: K / Accession code: 3JZ7 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 0 0 1627

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