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- PDB-1jew: CRYO-EM STRUCTURE OF COXSACKIEVIRUS B3(M STRAIN) WITH ITS CELLULA... -

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Entry
Database: PDB / ID: 1jew
TitleCRYO-EM STRUCTURE OF COXSACKIEVIRUS B3(M STRAIN) WITH ITS CELLULAR RECEPTOR, COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR (CAR).
Components
  • COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
  • COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1
  • COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2
  • COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3
  • COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4
KeywordsVirus/Receptor / COXSACKIEVIRUS B3 / CVB3 / CAR / CRYO-EM STRUCTURE / Icosahedral virus / Virus-Receptor COMPLEX
Function / homology
Function and homology information


cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell-bundle of His cell adhesion involved in cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport ...cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell-bundle of His cell adhesion involved in cell communication / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport / cardiac muscle fiber development / negative regulation of cardiac muscle cell proliferation / cell-cell junction organization / connexin binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / suppression by virus of host translation initiation factor activity / suppression by virus of host MDA-5 activity / intercalated disc / suppression by virus of host RIG-I activity / bicellular tight junction / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / actin cytoskeleton reorganization / picornain 3C / suppression by virus of host MAVS activity / T=pseudo3 icosahedral viral capsid / acrosomal vesicle / mitochondrion organization / filopodium / host cell cytoplasmic vesicle membrane / cell adhesion molecule binding / PDZ domain binding / RNA-protein covalent cross-linking / neutrophil chemotaxis / adherens junction / neuromuscular junction / positive stranded viral RNA replication / beta-catenin binding / integral to membrane of host cell / pore formation by virus in membrane of host cell / virus receptor activity / cell body / endocytosis involved in viral entry into host cell / protein complex oligomerization / cell junction / cell-cell junction / growth cone / nucleoside-triphosphate phosphatase / integrin binding / defense response to virus / ion channel activity / suppression by virus of host gene expression / regulation of immune response / heart development / leukocyte migration / basolateral plasma membrane / induction by virus of host autophagy / DNA replication / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / virion attachment to host cell / neuron projection / membrane raft / host cell nucleus / signaling receptor binding / structural molecule activity / integral component of plasma membrane / protein-containing complex / RNA binding / extracellular space / membrane / extracellular region / nucleoplasm / ATP binding / identical protein binding / plasma membrane / metal ion binding / cytoplasm
Immunoglobulin V-set domain / RNA-directed RNA polymerase, catalytic domain / Helicase, superfamily 3, single-stranded RNA virus / Immunoglobulin-like fold / Immunoglobulin / AAA+ ATPase domain / Peptidase S1, PA clan / Immunoglobulin-like domain / Immunoglobulin subtype / P-loop containing nucleoside triphosphate hydrolase ...Immunoglobulin V-set domain / RNA-directed RNA polymerase, catalytic domain / Helicase, superfamily 3, single-stranded RNA virus / Immunoglobulin-like fold / Immunoglobulin / AAA+ ATPase domain / Peptidase S1, PA clan / Immunoglobulin-like domain / Immunoglobulin subtype / P-loop containing nucleoside triphosphate hydrolase / Immunoglobulin subtype 2 / Peptidase C3, picornavirus core protein 2A / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Picornavirus 2B protein / Poliovirus 3A protein-like / Immunoglobulin V-set domain / Viral coat protein subunit / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein (VP4) / picornavirus capsid protein / Picornavirales 3C/3C-like protease domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus/Calicivirus coat protein / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein VP4 / Immunoglobulin-like domain superfamily
Coxsackievirus and adenovirus receptor / Genome polyprotein
Biological speciesHomo sapiens (human)
Coxsackievirus B3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 22 Å
AuthorsRossmann, M.G. / He, Y.
Citation
Journal: Nat Struct Biol / Year: 2001
Title: Interaction of coxsackievirus B3 with the full length coxsackievirus-adenovirus receptor.
Authors: Y He / P R Chipman / J Howitt / C M Bator / M A Whitt / T S Baker / R J Kuhn / C W Anderson / P Freimuth / M G Rossmann /
Abstract: Group B coxsackieviruses (CVB) utilize the coxsackievirus-adenovirus receptor (CAR) to recognize host cells. CAR is a membrane protein with two Ig-like extracellular domains (D1 and D2), a ...Group B coxsackieviruses (CVB) utilize the coxsackievirus-adenovirus receptor (CAR) to recognize host cells. CAR is a membrane protein with two Ig-like extracellular domains (D1 and D2), a transmembrane domain and a cytoplasmic domain. The three-dimensional structure of coxsackievirus B3 (CVB3) in complex with full length human CAR and also with the D1D2 fragment of CAR were determined to approximately 22 A resolution using cryo-electron microscopy (cryo-EM). Pairs of transmembrane domains of CAR associate with each other in a detergent cloud that mimics a cellular plasma membrane. This is the first view of a virus-receptor interaction at this resolution that includes the transmembrane and cytoplasmic portion of the receptor. CAR binds with the distal end of domain D1 in the canyon of CVB3, similar to how other receptor molecules bind to entero- and rhinoviruses. The previously described interface of CAR with the adenovirus knob protein utilizes a side surface of D1.
#1: Journal: Science / Year: 1997
Title: ISOLATION OF A COMMON RECEPTOR FOR COXSACKIE B VIRUSES AND ADENOVIRUSES 2 AND 5
Authors: Bergelson, J.M. / Cunningham, J.A. / Droguett, G. / Kurt-Jones, E.A. / Krithivas, A. / Hong, J.S. / Horwitz, M.S. / Crowell, R.L. / Finberg, R.W.
#2: Journal: Science / Year: 1999
Title: STRUCTURAL ANALYSIS OF THE MECHANISM OF ADENOVIRUS BINDING TO ITS HUMAN CELLULAR RECEPTOR CAR
Authors: Bewley, M.C. / Springer, K. / Zhang, Y.B. / Freimuth, P. / Flanagan, J.M.
#3: Journal: Structure / Year: 1995
Title: THE STRUCTURE OF COXSACKIEVIRUS B3 AT 3.5A RESOLUTION
Authors: Muckelbauer, J.K. / Kremer, M. / Minor, I. / Diana, G. / Dutko, F.J. / Groarke, J. / Pevear, D.C. / Rossman, M.G.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Mar 31, 2021Group: Database references / Source and taxonomy
Category: em_entity_assembly_naturalsource / em_entity_assembly_recombinant ...em_entity_assembly_naturalsource / em_entity_assembly_recombinant / entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Remark 999SEQUENCE THE COXSACKIEVIRUS B3 USED IN THE EM EXPERIMENT IS M STRAIN, WHICH MIGHT BE DIFFERENT ...SEQUENCE THE COXSACKIEVIRUS B3 USED IN THE EM EXPERIMENT IS M STRAIN, WHICH MIGHT BE DIFFERENT SLIGHTLY WITH OTHER ISOLATES GIVING ARISE TO THE CONFLICTS.

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Structure visualization

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  • 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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Assembly

Deposited unit
R: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
1: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1
2: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2
3: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3
4: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4


Theoretical massNumber of molelcules
Total (without water)107,1945
Polymers107,1945
Non-polymers00
Water0
1
R: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
1: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1
2: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2
3: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3
4: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4
x 60


Theoretical massNumber of molelcules
Total (without water)6,431,617300
Polymers6,431,617300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
R: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
1: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1
2: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2
3: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3
4: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4
x 5


  • icosahedral pentamer
  • 536 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)535,96825
Polymers535,96825
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
R: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
1: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1
2: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2
3: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3
4: COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4
x 6


  • icosahedral 23 hexamer
  • 643 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)643,16230
Polymers643,16230
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR / COXSACKIEVIRUS B-ADENOVIRUS RECEPTOR / HCAR / CVB3 BINDING PROTEIN / Coordinate model: Cα atoms only


Mass: 13358.203 Da / Num. of mol.: 1 / Fragment: Residues 21-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAR / Cell line (production host): A9 CELLS / Production host: Mus musculus (house mouse) / References: UniProt: P78310
#2: Protein COXSACKIEVIRUS CAPSID, COAT PROTEIN VP1 / P1D / Coordinate model: Cα atoms only


Mass: 31380.068 Da / Num. of mol.: 1 / Fragment: Residues 571-851
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 (strain Woodruff) / Genus: Enterovirus / Species: Human enterovirus B / Strain: Woodruff / Description: COXSACKIEVIRUS B3 / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: Q66282
#3: Protein COXSACKIEVIRUS CAPSID, COAT PROTEIN VP2 / P1B / Coordinate model: Cα atoms only


Mass: 28877.592 Da / Num. of mol.: 1 / Fragment: Residues 70-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 (strain Woodruff) / Genus: Enterovirus / Species: Human enterovirus B / Strain: Woodruff / Description: COXSACKIEVIRUS B3 / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: Q66282
#4: Protein COXSACKIEVIRUS CAPSID, COAT PROTEIN VP3 / P1C / Coordinate model: Cα atoms only


Mass: 26198.684 Da / Num. of mol.: 1 / Fragment: Residues 333-570
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 (strain Woodruff) / Genus: Enterovirus / Species: Human enterovirus B / Strain: Woodruff / Description: COXSACKIEVIRUS B3 / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: Q66282
#5: Protein COXSACKIEVIRUS CAPSID, COAT PROTEIN VP4 / P1A / Coordinate model: Cα atoms only


Mass: 7379.065 Da / Num. of mol.: 1 / Fragment: Residues 2-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 (strain Woodruff) / Genus: Enterovirus / Species: Human enterovirus B / Strain: Woodruff / Description: COXSACKIEVIRUS B3 / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: Q66282

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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: COXSACKIEVIRUS B3(M STRAIN) WITH ITS CELLULAR RECEPTOR
Type: VIRUS
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Coxsackievirus B3 (strain Woodruff)103904
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Mus musculus (house mouse)10090
21Homo sapiens (human)9606
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationDetails: CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, ...Details: CVB3 WAS INCUBATED WITH CAR SAMPLE FOR 1 HOURS AT 25 DEGREES CELSIUS (298 KELVIN) USING A FOUR-FOLD EXCESS OF CAR FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER.
Crystal growTemperature: 298 K / pH: 7.5
Details: WARNING: THIS IS AN CRYO-ELECTRON MICROSCOPY MODEL DEPOSITION. CRYO-EM INFORMATION HAS BEEN INCLUDED IN THE PDB FILE., pH 7.5, ELECTRON MICROSCOPY RECONSTRUCTION, temperature 298K
Crystal grow
*PLUS
Method: electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Jun 1, 2000
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 61000 X / Nominal defocus max: 4600 nm / Nominal defocus min: 1500 nm
Specimen holderTemperature: 120 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: PURDUE PROGRAMS / Category: 3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: COMMON-LINES AND POLAR-FOURIER-TRANSFORM FULLER ET AL. 1996, J.STRUC.BIOL.c 116, 48-55; BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130
Resolution: 22 Å / Resolution method: OTHER / Num. of particles: 635 / Actual pixel size: 2.3 Å
Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST A LOW RESOLUTION DENSITY MAP CALCULATED FROM THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS B3. DENSITIES WERE COMPARED BY ...Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST A LOW RESOLUTION DENSITY MAP CALCULATED FROM THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS B3. DENSITIES WERE COMPARED BY CROSS-CORRELATION WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS CORRELATION WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS 110 ANGSTROMS AND EXTERNAL RADIUS OF 145 ANGSTROMS.
Details: THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 22 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND COMPARING STRUCTURE FACTORS ...Details: THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 22 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND COMPARING STRUCTURE FACTORS OBTAINED FROM SEPARATE RECONSTRUCTIONS (BAKER ET AL. 1991, BIOPHYS.J. 60, 1445-1456). THE EIGENVALUE SPECTRUM GAVE AN INDICATION OF THE RANDOMNESS OF THE DATA THAT WAS INCLUDED IN THE RECONSTRUCTION. THE COMPLETENESS OF THE DATA WAS VERIFIED IN THAT ALL EIGENVALUES EXCEEDED 1.0.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: METHOD--Acta Cryst. D56, 1341 REFINEMENT PROTOCOL--EMFIT DETAILS--THE DIFFERENCE MAP BETWEEN CVB3-CAR COMPLEX AND NATIVE CVB WAS CALCULATED AND THEN FITTED WITH THE N-TERMINAL DOMAIN OF CAR ...Details: METHOD--Acta Cryst. D56, 1341 REFINEMENT PROTOCOL--EMFIT DETAILS--THE DIFFERENCE MAP BETWEEN CVB3-CAR COMPLEX AND NATIVE CVB WAS CALCULATED AND THEN FITTED WITH THE N-TERMINAL DOMAIN OF CAR (1KAC, B-CHAIN). THE AUTOMATIC FITTING WAS DONE USI PROGRAM EMFIT DESCRIBED IN ACTA CRYST. D56, 1341-1349. THE CRYSTAL STRUCTURE OF POLIOVIRUS WAS PLACED INTO THE
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 0 0 938

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