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- EMDB-8184: CryoEM structure of the native empty particle of a human rhinovirus C -

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Basic information

Entry
Database: EMDB / ID: EMD-8184
TitleCryoEM structure of the native empty particle of a human rhinovirus C
Map dataCryoEM structure of the native empty particle of a human rhinovirus C
Sample
  • Virus: Rhinovirus C15a
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP0
Keywordsvirus / jelly roll
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / 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 / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / 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 / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / 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 / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
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 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
Biological speciesRhinovirus C / Rhinovirus C15a
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsLiu Y / Hill MG
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI104317 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Atomic structure of a rhinovirus C, a virus species linked to severe childhood asthma.
Authors: Yue Liu / Marchel G Hill / Thomas Klose / Zhenguo Chen / Kelly Watters / Yury A Bochkov / Wen Jiang / Ann C Palmenberg / Michael G Rossmann /
Abstract: Isolates of rhinovirus C (RV-C), a recently identified Enterovirus (EV) species, are the causative agents of severe respiratory infections among children and are linked to childhood asthma ...Isolates of rhinovirus C (RV-C), a recently identified Enterovirus (EV) species, are the causative agents of severe respiratory infections among children and are linked to childhood asthma exacerbations. The RV-C have been refractory to structure determination because they are difficult to propagate in vitro. Here, we report the cryo-EM atomic structures of the full virion and native empty particle (NEP) of RV-C15a. The virus has 60 "fingers" on the virus outer surface that probably function as dominant immunogens. Because the NEPs also display these fingers, they may have utility as vaccine candidates. A sequence-conserved surface depression adjacent to each finger forms a likely binding site for the sialic acid on its receptor. The RV-C, unlike other EVs, are resistant to capsid-binding antiviral compounds because the hydrophobic pocket in VP1 is filled with multiple bulky residues. These results define potential molecular determinants for designing antiviral therapeutics and vaccines.
History
DepositionMay 16, 2016-
Header (metadata) releaseJun 8, 2016-
Map releaseJul 13, 2016-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 13.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 13.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5jzg
  • Surface level: 13.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5jzg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8184.png

Downloads & links

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Map

FileDownload / File: emd_8184.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of the native empty particle of a human rhinovirus C
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 480 pix.
= 499.2 Å		1.04 Å/pix.
x 480 pix.
= 499.2 Å		1.04 Å/pix.
x 480 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 13.4 / Movie #1: 13.4
Minimum - Maximum-48.974299999999999 - 67.214264
Average (Standard dev.)0.06435112 (±3.4875524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 499.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z499.200499.200499.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-48.97467.2140.064

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Supplemental data

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Sample components

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Entire : Rhinovirus C15a

EntireName: Rhinovirus C15a
Components
  • Virus: Rhinovirus C15a
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP0

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Supramolecule #1: Rhinovirus C15a

SupramoleculeName: Rhinovirus C15a / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The cDNA of RV-C15 isolate was used to produce RNA transcripts in vitro, which were then used for transfection in HeLa WisL cells. The resultant recombinant RV-C15 virus was adapted in HeLa ...Details: The cDNA of RV-C15 isolate was used to produce RNA transcripts in vitro, which were then used for transfection in HeLa WisL cells. The resultant recombinant RV-C15 virus was adapted in HeLa cells expressing the RV-C receptor CDHR3 via multiple passage. The derivative was the RV-C15a virus.
NCBI-ID: 463676 / Sci species name: Rhinovirus C15a / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.8 MDa
Virus shellShell ID: 1 / Name: Capsid (p3) / Diameter: 300.0 Å / T number (triangulation number): 3

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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: Rhinovirus C
Molecular weightTheoretical: 31.802623 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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
Source (natural)Organism: Rhinovirus C
Molecular weightTheoretical: 25.965037 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 VP0

MacromoleculeName: Capsid protein VP0 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinovirus C
Molecular weightTheoretical: 36.247344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GAQVSRQNNG THENGVTASN GSVIKYFNIN YYKDSASSGL SRQDFSQDPS KFTQPLVDTL TNPALMSPSV EACGYSDRLK QITIGNSTI TTQDSLHTVL AYGEWPTYLS DIDATSVDKP THPETSADRF YTLDSVEWQV GSHGWWWKLP DALKDMGVFG Q NMYYHSMG ...String:
GAQVSRQNNG THENGVTASN GSVIKYFNIN YYKDSASSGL SRQDFSQDPS KFTQPLVDTL TNPALMSPSV EACGYSDRLK QITIGNSTI TTQDSLHTVL AYGEWPTYLS DIDATSVDKP THPETSADRF YTLDSVEWQV GSHGWWWKLP DALKDMGVFG Q NMYYHSMG RSGFIIHTQC NATKFHSGAL IVAVIPEHQL AYVGGVKVNV GYDHTHPGQS GHQIRGPSQS NDRSGGKPDE DP LFNCNGT LLGNITIFPH QIINLRTNNS STIVVPYINC VPMDNMLKHN NLSLVIIPLV PLRPGSSGIN SVPITVTIAP YKS EFSGAM EAQRQ

UniProtKB: Genome polyprotein

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
120.0 mMNaClsodium chloride
1.0 mMC10H16N2O8EDTA
GridModel: Ultra thin Lacey carbon / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: LACEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 3-70 / Number grids imaged: 3 / Number real images: 3614 / Average exposure time: 14.0 sec. / Average electron dose: 25.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 0.7000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 14000
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: 24882
Details: A mixed population of empty particles, full particles, and junk
Startup modelType of model: INSILICO MODEL
Details: For each of the half subsets, random orientation was assigned to each of the 150 randomly selected particles. The resulting models were much like a ball in appearance. Refinement was then ...Details: For each of the half subsets, random orientation was assigned to each of the 150 randomly selected particles. The resulting models were much like a ball in appearance. Refinement was then performed by searching for the best orientation and particle center of each particle image relative to the current 3D reconstructions using projection matching. Three of these structures were selected for further refinement using all the available particle images in the half subset. These structures converged to roughly the same reconstruction. One of these structures was randomly chosen to extend the refinement.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 3614
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 6.5 degrees
Software - Name: jspr
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 0.5 degrees
Software - Name: jspr
Final 3D classificationNumber classes: 156 / Software - Name: RELION (ver. 1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-5jzg:
CryoEM structure of the native empty particle of a human rhinovirus C

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