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- EMDB-20443: Rhinovirus C15 complexed with domain I of receptor CDHR3 -

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Basic information

Entry
Database: EMDB / ID: EMD-20443
TitleRhinovirus C15 complexed with domain I of receptor CDHR3
Map dataRhinovirus C15 complexed with domain I of receptor CDHR3, postprocessed in Relion
Sample
  • Complex: Complex of rhinovirus C15 with domain I from human CDHR3
    • Complex: domain I from human CDHR3
      • Protein or peptide: Cadherin-related family member 3
    • Virus: Rhinovirus C
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP4
  • Ligand: CALCIUM ION
Keywordsreceptor / cadherin / VIRUS-CELL ADHESION complex
Function / homology
Function and homology information


calcium-dependent cell-cell adhesion / cell-cell adhesion mediated by cadherin / adherens junction organization / catenin complex / cell-cell junction assembly / homophilic cell-cell adhesion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus ...calcium-dependent cell-cell adhesion / cell-cell adhesion mediated by cadherin / adherens junction organization / catenin complex / cell-cell junction assembly / homophilic cell-cell adhesion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / adherens junction / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / beta-catenin binding / host cell cytoplasmic vesicle membrane / cell morphogenesis / cell migration / nucleoside-triphosphate phosphatase / channel activity / virus receptor activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / cadherin binding / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / calcium ion binding / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / plasma membrane
Similarity search - Function
Cadherin / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like ...Cadherin / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Cadherin-related family member 3
Similarity search - Component
Biological speciesHomo sapiens (human) / Rhinovirus C
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSun Y / Watters K
Funding support United States, 1 items
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, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseMar 11, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3.5
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  • Surface view with fitted model
  • Atomic models: PDB-6ppo
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ppo
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20443.png

Downloads & links

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Map

FileDownload / File: emd_20443.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRhinovirus C15 complexed with domain I of receptor CDHR3, postprocessed in Relion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 576 pix.
= 498.24 Å		0.87 Å/pix.
x 576 pix.
= 498.24 Å		0.87 Å/pix.
x 576 pix.
= 498.24 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.865 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-12.061631999999999 - 16.926497999999999
Average (Standard dev.)0.052700795 (±0.96914995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 498.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8650.8650.865
M x/y/z576576576
origin x/y/z0.0000.0000.000
length x/y/z498.240498.240498.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS576576576
D min/max/mean-12.06216.9260.053

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Supplemental data

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Mask #1

Fileemd_20443_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Rhinovirus C15 complexed with domain I of receptor CDHR3, half map 1

Fileemd_20443_half_map_1.map
AnnotationRhinovirus C15 complexed with domain I of receptor CDHR3, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Rhinovirus C15 complexed with domain I of receptor CDHR3, half map 2

Fileemd_20443_half_map_2.map
AnnotationRhinovirus C15 complexed with domain I of receptor CDHR3, half map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of rhinovirus C15 with domain I from human CDHR3

EntireName: Complex of rhinovirus C15 with domain I from human CDHR3
Components
  • Complex: Complex of rhinovirus C15 with domain I from human CDHR3
    • Complex: domain I from human CDHR3
      • Protein or peptide: Cadherin-related family member 3
    • Virus: Rhinovirus C
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP4
  • Ligand: CALCIUM ION

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Supramolecule #1: Complex of rhinovirus C15 with domain I from human CDHR3

SupramoleculeName: Complex of rhinovirus C15 with domain I from human CDHR3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Molecular weightTheoretical: 6 MDa

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Supramolecule #3: domain I from human CDHR3

SupramoleculeName: domain I from human CDHR3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Rhinovirus C

SupramoleculeName: Rhinovirus C / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / NCBI-ID: 463676 / Sci species name: Rhinovirus C / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Rhinovirus C
Molecular weightTheoretical: 31.802623 KDa
SequenceString: NNDDPVENFV ESTLKEVLVV PDTKPSGPQH TTKPSILGAM EIGASSNATP ESTIETRYVY NTNTNAEADV EMFLGRSALW GKVTLTRQY AKWEINFQEQ AHIRKKFEFF TYLRFDMEVT IVTNNKGLMQ IMFVPPGIDH PETHDDRKWD SASNPSVFFQ P KSGFPRFT ...String:
NNDDPVENFV ESTLKEVLVV PDTKPSGPQH TTKPSILGAM EIGASSNATP ESTIETRYVY NTNTNAEADV EMFLGRSALW GKVTLTRQY AKWEINFQEQ AHIRKKFEFF TYLRFDMEVT IVTNNKGLMQ IMFVPPGIDH PETHDDRKWD SASNPSVFFQ P KSGFPRFT IPFTGLASAY YMFYDGYDKP KGSDNNEYGI APTNDMGLLC FRTLDNSGGN DVKIYVKPKH ITAWVPRPPR AT QYTHKYS TNYHYKPNSS GPDEHVLKDR HFIKTRPLIS SA

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Rhinovirus C
Molecular weightTheoretical: 25.965037 KDa
SequenceString: GLPTRLPSGS QQFMTTEDEQ SPNILPGFHP SKKIHIPGMI TNVMHMARVD SFIPINNIQG EVGKVSMYYI TVTKKTVTER ILVLPLEMS NTLFATTLLG EVLNYYANWS GSITITFMCV CDAFSTGKFL VAYTPPGGKL PEDRKQAMLG VHIIWDLGLQ S SCTIVVPW ...String:
GLPTRLPSGS QQFMTTEDEQ SPNILPGFHP SKKIHIPGMI TNVMHMARVD SFIPINNIQG EVGKVSMYYI TVTKKTVTER ILVLPLEMS NTLFATTLLG EVLNYYANWS GSITITFMCV CDAFSTGKFL VAYTPPGGKL PEDRKQAMLG VHIIWDLGLQ S SCTIVVPW ISSGFYRRTK ADSFTHGGYV SLWYQTAFVP PVSGGTGSIL ATCSACPDMS VRMLRDSPMM EQKNELQ

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Rhinovirus C
Molecular weightTheoretical: 29.090658 KDa
SequenceString: SPSVEACGYS DRLKQITIGN STITTQDSLH TVLAYGEWPT YLSDIDATSV DKPTHPETSA DRFYTLDSVE WQVGSHGWWW KLPDALKDM GVFGQNMYYH SMGRSGFIIH TQCNATKFHS GALIVAVIPE HQLAYVGGVK VNVGYDHTHP GQSGHQIRGP S QSNDRSGG ...String:
SPSVEACGYS DRLKQITIGN STITTQDSLH TVLAYGEWPT YLSDIDATSV DKPTHPETSA DRFYTLDSVE WQVGSHGWWW KLPDALKDM GVFGQNMYYH SMGRSGFIIH TQCNATKFHS GALIVAVIPE HQLAYVGGVK VNVGYDHTHP GQSGHQIRGP S QSNDRSGG KPDEDPLFNC NGTLLGNITI FPHQIINLRT NNSSTIVVPY INCVPMDNML KHNNLSLVII PLVPLRPGSS GI NSVPITV TIAPYKSEFS GAMEAQRQ

UniProtKB: Genome polyprotein

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Macromolecule #4: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Rhinovirus C
Molecular weightTheoretical: 7.174758 KDa
SequenceString:
GAQVSRQNNG THENGVTASN GSVIKYFNIN YYKDSASSGL SRQDFSQDPS KFTQPLVDTL TNPALM

UniProtKB: Genome polyprotein

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Macromolecule #5: Cadherin-related family member 3

MacromoleculeName: Cadherin-related family member 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.517157 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MASDYKDDDD KLHLILLPAT GNVAENSPPG TSVHKFSVKL SASLSPVIPG FPQIVNSNPL TEAFRVNWLS GTYFEVVTTG MEQLDFETG PNIFDLQIYV KDEVGVTDLQ VLTVQVTDVN EPPGGTKHHH HHH

UniProtKB: Cadherin-related family member 3

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4
GridMaterial: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 20.265 kPa
VitrificationCryogen name: NITROGEN / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3
Details: 3s blotting time. Instrument placed in BSL2 hood..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-60 / Number grids imaged: 1 / Number real images: 1500 / Average exposure time: 12.0 sec. / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 22000
Startup modelType of model: OTHER
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: J3DR / Number images used: 14978
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: JALIGN
Final angle assignmentType: PROJECTION MATCHING / Software - Name: JALIGN
Final 3D classificationNumber classes: 100 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5k0u


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 100
Output model

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

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