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- PDB-9vfr: Structure of mature Coxsackievirus A6 virion complexed with its r... -

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Basic information

Entry
Database: PDB / ID: 9vfr
TitleStructure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1
Components
  • (Genome polyprotein) x 4
  • Kremen protein 1
KeywordsVIRUS / coxsackievirus A6 / KRM1 / receptor
Function / homology
Function and homology information


Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / negative regulation of axon regeneration / cell communication / negative regulation of ossification / limb development / regulation of canonical Wnt signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / TCF dependent signaling in response to WNT / picornain 2A ...Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / negative regulation of axon regeneration / cell communication / negative regulation of ossification / limb development / regulation of canonical Wnt signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / TCF dependent signaling in response to WNT / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / negative regulation of canonical Wnt signaling pathway / host cell cytoplasmic vesicle membrane / virion component / Wnt signaling pathway / viral capsid / transmembrane signaling receptor activity / host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / neuronal cell body / RNA-directed RNA polymerase activity / apoptotic process / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / signal transduction / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / plasma membrane
Similarity search - Function
Kremen / : / Protein of unknown function DUF3724, picornavirus / Protein of unknown function (DUF3724) / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. ...Kremen / : / Protein of unknown function DUF3724, picornavirus / Protein of unknown function (DUF3724) / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Picornavirus coat protein VP4 superfamily / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
MYRISTIC ACID / STEARIC ACID / Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein / Kremen protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Coxsackievirus A6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsKe, X. / Li, X. / Liu, Z. / Liu, K. / Yan, X. / Shu, B. / Zhang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1
Authors: Ke, X. / Li, X. / Liu, Z. / Liu, K. / Yan, X. / Shu, B. / Zhang, C.
History
DepositionJun 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Genome polyprotein
G: Kremen protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,2199
Polymers128,2635
Non-polymers9554
Water00
1
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Genome polyprotein
G: Kremen protein 1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,753,122540
Polymers7,695,806300
Non-polymers57,316240
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: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Genome polyprotein
G: Kremen protein 1
hetero molecules
x 5


  • icosahedral pentamer
  • 646 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)646,09445
Polymers641,31725
Non-polymers4,77620
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Genome polyprotein
G: Kremen protein 1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 775 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)775,31254
Polymers769,58130
Non-polymers5,73224
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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Protein , 5 types, 5 molecules ABCDG

#1: Protein Genome polyprotein / VP1


Mass: 33568.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / References: UniProt: A0A222NWY2
#2: Protein Genome polyprotein / VP2


Mass: 28138.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6
References: UniProt: A0A7D0TR32, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein Genome polyprotein / VP3


Mass: 26324.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6
References: UniProt: A0A4P2SK07, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein Genome polyprotein / VP4


Mass: 7503.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A6 / References: UniProt: E3VJS6
#5: Protein Kremen protein 1 / Dickkopf receptor / Kringle domain-containing transmembrane protein 1 / Kringle-containing protein ...Dickkopf receptor / Kringle domain-containing transmembrane protein 1 / Kringle-containing protein marking the eye and the nose


Mass: 32728.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KREMEN1, KREMEN, KRM1 / Production host: Homo sapiens (human) / References: UniProt: Q96MU8

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Sugars , 1 types, 2 molecules

#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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

ComponentName: coxsackievirus A6 complexed with KRM1 protein / Type: COMPLEX
Details: Purified Coxsackievirus A6 (CV-A6) virions were combined with KRM1 proteins at a 1:120 molar ratio (virus:protein) in PBS (pH 7.4). The binding reaction was carried out at room temperature ...Details: Purified Coxsackievirus A6 (CV-A6) virions were combined with KRM1 proteins at a 1:120 molar ratio (virus:protein) in PBS (pH 7.4). The binding reaction was carried out at room temperature for 35 minutes to allow complex formation. Immediately following incubation, samples were rapidly vitrified for cryo-EM analysis by plunge-freezing in liquid ethane.
Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 273 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 2.7 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5004

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
4cryoSPARC4.5.3CTF correction
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 184763
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19306 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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