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- EMDB-20001: Structure of canine parvovirus in complex with transferrin recept... -

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Basic information

Entry
Database: EMDB / ID: EMD-20001
TitleStructure of canine parvovirus in complex with transferrin receptor type-1
Map dataIcosahedral 3D map of CPV incubated with TfR
Sample
  • Virus: Canine parvovirus 2
    • Protein or peptide: Capsid protein VP1
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
Similarity search - Function
Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesCPV-2 (virus) / Canine parvovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLee H / Hafenstein S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Transferrin receptor binds virus capsid with dynamic motion.
Authors: Hyunwook Lee / Heather M Callaway / Javier O Cifuente / Carol M Bator / Colin R Parrish / Susan L Hafenstein /
Abstract: Canine parvovirus (CPV) is an important pathogen causing severe diseases in dogs, including acute hemorrhagic enteritis, myocarditis, and cerebellar disease. Cross-species transmission of CPV occurs ...Canine parvovirus (CPV) is an important pathogen causing severe diseases in dogs, including acute hemorrhagic enteritis, myocarditis, and cerebellar disease. Cross-species transmission of CPV occurs as a result of mutations on the viral capsid surface that alter the species-specific binding to the host receptor, transferrin receptor type-1 (TfR). The interaction between CPV and TfR has been extensively studied, and previous analyses have suggested that the CPV-TfR complex is asymmetric. To enhance the understanding of the underlying molecular mechanisms, we determined the CPV-TfR interaction using cryo-electron microscopy to solve the icosahedral (3.0-Å resolution) and asymmetric (5.0-Å resolution) complex structures. Structural analyses revealed conformational variations of the TfR molecules relative to the binding site, which translated into dynamic molecular interactions between CPV and TfR. The precise footprint of the receptor on the virus capsid was identified, along with the identity of the amino acid residues in the virus-receptor interface. Our "rock-and-roll" model provides an explanation for previous findings and gives insights into species jumping and the variation in host ranges associated with new pandemics in dogs.
History
DepositionMar 18, 2019-
Header (metadata) releaseApr 10, 2019-
Map releaseSep 18, 2019-
UpdateDec 4, 2019-
Current statusDec 4, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6oas
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6oas
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20001.png

Downloads & links

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Map

FileDownload / File: emd_20001.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral 3D map of CPV incubated with TfR
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.13256781 - 0.22821085
Average (Standard dev.)0.00010531477 (±0.011799409)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 444.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z444.000444.000444.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-0.1330.2280.000

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Supplemental data

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Sample components

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Entire : Canine parvovirus 2

EntireName: Canine parvovirus 2
Components
  • Virus: Canine parvovirus 2
    • Protein or peptide: Capsid protein VP1

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Supramolecule #1: Canine parvovirus 2

SupramoleculeName: Canine parvovirus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 246878 / Sci species name: Canine parvovirus 2 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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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
Source (natural)Organism: CPV-2 (virus)
Molecular weightTheoretical: 61.562367 KDa
SequenceString: GVGISTGTFN NQTEFKFLEN GWVEITANSS RLVHLNMPES ENYRRVVVNN MDKTAVNGNM ALDDIHAQIV TPWSLVDANA WGVWFNPGD WQLIVNTMSE LHLVSFEQEI FNVVLKTVSE SATQPPTKVY NNDLTASLMV ALDSNNTMPF TPAAMRSETL G FYPWKPTI ...String:
GVGISTGTFN NQTEFKFLEN GWVEITANSS RLVHLNMPES ENYRRVVVNN MDKTAVNGNM ALDDIHAQIV TPWSLVDANA WGVWFNPGD WQLIVNTMSE LHLVSFEQEI FNVVLKTVSE SATQPPTKVY NNDLTASLMV ALDSNNTMPF TPAAMRSETL G FYPWKPTI PTPWRYYFQW DRTLIPSHTG TSGTPTNIYH GTDPDDVQFY TIENSVPVHL LRTGDEFATG TFFFDCKPCR LT HTWQTNR ALGLPPFLNS LPQSEGATNF GDIGVQQDKR RGVTQMGNTN YITEATIMRP AEVGYSAPYY SFEASTQGPF KTP IAAGRG GAQTDENQAA DGNPRYAFGR QHGQKTTTTG ETPERFTYIA HQDTGRYPEG DWIQNINFNL PVTNDNVLLP TDPI GGKTG INYTNIFNTY GPLTALNNVP PVYPNGQIWD KEFDTDLKPR LHVNAPFVCQ NNCPGQLFVK VAPNLTNEYD PDASA NMSR IVTYSDFWWK GKLVFKAKLR ASHTWNPIQQ MSINVDNQFN YVPSNIGGMK IVYEKSQLAP RKLY

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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

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 150.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 132120

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