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- PDB-6ppo: Rhinovirus C15 complexed with domain I of receptor CDHR3 -

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Basic information

Entry
Database: PDB / ID: 6ppo
TitleRhinovirus C15 complexed with domain I of receptor CDHR3
Components
  • (Capsid protein ...Capsid) x 4
  • Cadherin-related family member 3
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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / synaptic transmission, glutamatergic / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / adherens junction / cell morphogenesis / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / virus receptor activity / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / cadherin binding / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / calcium ion binding / 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 / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like ...Cadherin / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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: 3.2 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 8, 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
  • EMDB-20443
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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6708
Polymers108,5505
Non-polymers1203
Water0
1
A: Capsid protein VP1
B: Capsid protein VP3
C: Capsid protein VP2
D: Capsid protein VP4
U: Cadherin-related family member 3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,520,228480
Polymers6,513,014300
Non-polymers7,214180
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
hetero molecules
x 5


  • icosahedral pentamer
  • 543 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)543,35240
Polymers542,75125
Non-polymers60115
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
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 652 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)652,02348
Polymers651,30130
Non-polymers72118
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

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Capsid protein ... , 4 types, 4 molecules ABCD

#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

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Protein / Non-polymers , 2 types, 4 molecules U

#5: Protein Cadherin-related family member 3 / Cadherin-like protein 28


Mass: 14517.157 Da / Num. of mol.: 1
Fragment: Extracellular cadherin-like domain 1 (UNP residues 20-130)
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
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestN

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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 from human CDHR3COMPLEX#1-#50MULTIPLE SOURCES
2Rhinovirus CVIRUS#1-#41NATURAL
3domain I 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
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: NITROGEN / Humidity: 80 % / Chamber temperature: 298 K / Details: 3s 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 FIELDBright-field microscopy / 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: 1500
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: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9JALIGNinitial Euler assignment
10JALIGNfinal Euler assignment
11RELION1.4classification
12J3DR3D reconstruction
13Cootmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 22000
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14978 / 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

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