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- PDB-6psf: Rhinovirus C15 complexed with domains I and II of receptor CDHR3 -

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Basic information

Entry
Database: PDB / ID: 6psf
TitleRhinovirus C15 complexed with domains I and II of receptor CDHR3
Components
  • Cadherin-related family member 3
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
  • Capsid protein VP4
KeywordsVIRUS/CELL ADHESION / receptor / cadherin / VIRUS-CELL ADHESION complex
Function / homology
Function and homology information


cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / synaptic cleft / axon terminus / picornain 2A ...cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / synaptic cleft / axon terminus / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / adherens junction / host cell cytoplasmic vesicle membrane / cell morphogenesis / endocytosis involved in viral entry into host cell / beta-catenin binding / nucleoside-triphosphate phosphatase / channel activity / cell migration / virus receptor activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / cadherin binding / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / calcium ion binding / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Cadherin / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein / Poliovirus 3A protein-like ...Cadherin / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Cadherin-related family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Rhinovirus C
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSun, Y. / Watters, K. / Klose, T. / Palmenberg, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Cryo-EM structure of rhinovirus C15a bound to its cadherin-related protein 3 receptor.
Authors: Yingyuan Sun / Kelly Watters / Marchel G Hill / Qianglin Fang / Yue Liu / Richard J Kuhn / Thomas Klose / Michael G Rossmann / Ann C Palmenberg /
Abstract: Infection by (RV-C), a species of Picornaviridae , is strongly associated with childhood asthma exacerbations. Cellular binding and entry by all RV-C, which trigger these episodes, is mediated by ...Infection by (RV-C), a species of Picornaviridae , is strongly associated with childhood asthma exacerbations. Cellular binding and entry by all RV-C, which trigger these episodes, is mediated by the first extracellular domain (EC1) of cadherin-related protein 3 (CDHR3), a surface cadherin-like protein expressed primarily on the apical surfaces of ciliated airway epithelial cells. Although recombinant EC1 is a potent inhibitor of viral infection, there is no molecular description of this protein or its binding site on RV-C. Here we present cryo-electron microscopy (EM) data resolving the EC1 and EC1+2 domains of human CDHR3 complexed with viral isolate C15a. Structure-suggested residues contributing to required interfaces on both EC1 and C15a were probed and identified by mutagenesis studies with four different RV-C genotypes. In contrast to most other rhinoviruses, which bind intercellular adhesion molecule 1 receptors via a capsid protein VP1-specific fivefold canyon feature, the CDHR3 EC1 contacts C15a, and presumably all RV-Cs, in a unique cohesive footprint near the threefold vertex, encompassing residues primarily from viral protein VP3, but also from VP1 and VP2. The EC1+2 footprint on C15a is similar to that of EC1 alone but shows that steric hindrance imposed by EC2 would likely prevent multiprotein binding by the native receptor at any singular threefold vertex. Definition of the molecular interface between the RV-Cs and their receptors provides new avenues that can be explored for potential antiviral therapies.
History
DepositionJul 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / 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_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
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP3
C: Capsid protein VP2
D: Capsid protein VP4
U: Cadherin-related family member 3


Theoretical massNumber of molelcules
Total (without water)120,5775
Polymers120,5775
Non-polymers00
Water00
1
A: Capsid protein VP1
B: Capsid protein VP3
C: Capsid protein VP2
D: Capsid protein VP4
U: Cadherin-related family member 3
x 60


Theoretical massNumber of molelcules
Total (without water)7,234,599300
Polymers7,234,599300
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 VP1
B: Capsid protein VP3
C: Capsid protein VP2
D: Capsid protein VP4
U: Cadherin-related family member 3
x 5


  • icosahedral pentamer
  • 603 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)602,88325
Polymers602,88325
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP3
C: Capsid protein VP2
D: Capsid protein VP4
U: Cadherin-related family member 3
x 6


  • icosahedral 23 hexamer
  • 723 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)723,46030
Polymers723,46030
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 VP1


Mass: 31802.623 Da / Num. of mol.: 1 / Fragment: UNP residues 568-846 / Source method: isolated from a natural source / Source: (natural) Rhinovirus C
References: UniProt: E5D8F2, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein Capsid protein VP3


Mass: 25965.037 Da / Num. of mol.: 1 / Fragment: UNP residues 333-567 / Source method: isolated from a natural source / Source: (natural) Rhinovirus C
References: UniProt: E5D8F2, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein Capsid protein VP2


Mass: 29090.658 Da / Num. of mol.: 1 / Fragment: UNP residues 68-332 / Source method: isolated from a natural source / Source: (natural) Rhinovirus C
References: UniProt: E5D8F2, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein Capsid protein VP4


Mass: 7174.758 Da / Num. of mol.: 1 / Fragment: UNP residues 2-67 / Source method: isolated from a natural source / Source: (natural) Rhinovirus C
References: UniProt: E5D8F2, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#5: Protein Cadherin-related family member 3 / CDHR3 / Cadherin-like protein 28


Mass: 26543.570 Da / Num. of mol.: 1
Fragment: extracellular cadherin-like domains 1-2 (UNP residues 20-237)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDHR3, CDH28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZTQ4

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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
IDNameTypeEntity IDParent-IDSource
1Complex of rhinovirus C15 with domain I and domain II (EC1-2) from human CDHR3COMPLEXall0MULTIPLE SOURCES
2Rhinovirus CVIRUS#1-#41NATURAL
3domain I and domain II (EC1-2) from human CDHR3COMPLEX#51RECOMBINANT
Molecular weightValue: 6 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Rhinovirus C463676
23Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Recombinantly expressed EC1-2 was incubated with RV-C viruses overnight at 4 degrees C.
Specimen supportDetails: unspecified
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: NITROGEN / Humidity: 80 % / Chamber temperature: 298 K
Details: 3 second blotting time. Instrument placed in BSL2 hood.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 32 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2452
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansSampling size: 0.865 µm / Width: 3838 / Height: 3710 / Movie frames/image: 60 / Used frames/image: 1-60

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9Cootmodel refinement
10PHENIXmodel refinement
11JALIGNinitial Euler assignment
12JALIGNfinal Euler assignment
13RELION1.4classification
14J3DR3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 22981
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9607 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 100 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 5K0U

5k0u


Pdb chain-ID: A / Accession code: 5K0U / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01425220
ELECTRON MICROSCOPYf_angle_d0.741579360
ELECTRON MICROSCOPYf_dihedral_angle_d16.69252300
ELECTRON MICROSCOPYf_chiral_restr0.05264440
ELECTRON MICROSCOPYf_plane_restr0.00574640

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