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- EMDB-65032: Structure of mature Coxsackievirus A6 virion complexed with its r... -

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Basic information

Entry
Database: EMDB / ID: EMD-65032
TitleStructure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1
Map data
Sample
  • Complex: coxsackievirus A6 complexed with KRM1 protein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Kremen protein 1
  • Ligand: STEARIC ACID
  • Ligand: MYRISTIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscoxsackievirus A6 / KRM1 / receptor / VIRUS
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
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein / Kremen protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Coxsackievirus A6
Methodsingle 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, 1 items
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, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65032.png

Downloads & links

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Map

FileDownload / File: emd_65032.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 600 pix.
= 570. Å		0.95 Å/pix.
x 600 pix.
= 570. Å		0.95 Å/pix.
x 600 pix.
= 570. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.14393209 - 0.4135689
Average (Standard dev.)0.0032678132 (±0.026814334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 570.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65032_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65032_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : coxsackievirus A6 complexed with KRM1 protein

EntireName: coxsackievirus A6 complexed with KRM1 protein
Components
  • Complex: coxsackievirus A6 complexed with KRM1 protein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Kremen protein 1
  • Ligand: STEARIC ACID
  • Ligand: MYRISTIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: coxsackievirus A6 complexed with KRM1 protein

SupramoleculeName: coxsackievirus A6 complexed with KRM1 protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
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.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A6
Molecular weightTheoretical: 33.568379 KDa
SequenceString: NDPITNAVES AVSALADTTI SRVTAANTAA STHSLGTGRV PALQAAETGA SSNSSDENLI ETRCVMNRNG VNEASVEHFY SRAGLVGVV EVKDSGTSLD GYTVWPIDVM GFVQQRRKLE LSTYMRFDAE FTFVSNLNNS TTPGMLLQYM YVPPGAPKPD S RKSYQWQT ...String:
NDPITNAVES AVSALADTTI SRVTAANTAA STHSLGTGRV PALQAAETGA SSNSSDENLI ETRCVMNRNG VNEASVEHFY SRAGLVGVV EVKDSGTSLD GYTVWPIDVM GFVQQRRKLE LSTYMRFDAE FTFVSNLNNS TTPGMLLQYM YVPPGAPKPD S RKSYQWQT ATNPSVFAKL SDPPPQVSVP FMSPATAYQW FYDGYPTFGE HKQATNLQYG QCPNNMMGHF AIRTVSESTT GK NIHVRVY MRIKHVRAWV PRPLRSQAYM VKNYPTYSQT ITNTATDRAS ITTTDYEGGV PASPQRTS

UniProtKB: Genome polyprotein

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Macromolecule #2: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus A6
Molecular weightTheoretical: 28.138604 KDa
SequenceString: SPSVEACGYS DRVAQLTVGN STITTQEAAN IVLSYGEWPE YCPSTDATAV DKPTRPDVSV NRFYTLSTKS WKTESTGWYW KFPDVLNDT GVFGQNAQFH YLYRSGFCMH VQCNASKFHQ GALLVAAIPE FVIAASSPAT KPNSQGLYPD FAHTNPGKDG Q EFRDPYVL ...String:
SPSVEACGYS DRVAQLTVGN STITTQEAAN IVLSYGEWPE YCPSTDATAV DKPTRPDVSV NRFYTLSTKS WKTESTGWYW KFPDVLNDT GVFGQNAQFH YLYRSGFCMH VQCNASKFHQ GALLVAAIPE FVIAASSPAT KPNSQGLYPD FAHTNPGKDG Q EFRDPYVL DAGIPLSQAL IFPHQWINLR TNNCATIIMP YINALPFDSA LNHSNFGLVV IPISPLKYCN GATTEVPITL TI APLNSEF SGLRQAIKQ

UniProtKB: Genome polyprotein

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Macromolecule #3: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus A6
Molecular weightTheoretical: 26.32476 KDa
SequenceString: GFPTELKPGT NQFLTTDDGT SPPILPGFEP TPLIHIPGEF TSLLDLCQVE TILEVNNTTG TTGVSRLLIP VRAQNNVDQL CASFQVDPG RNGPWQSTMV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LIAYTPPGSA QPTTREAAML GTHIVWDFGL Q SSVTLVIP ...String:
GFPTELKPGT NQFLTTDDGT SPPILPGFEP TPLIHIPGEF TSLLDLCQVE TILEVNNTTG TTGVSRLLIP VRAQNNVDQL CASFQVDPG RNGPWQSTMV GQICRYYTQW SGSLKVTFMF TGSFMATGKM LIAYTPPGSA QPTTREAAML GTHIVWDFGL Q SSVTLVIP WISNTHFRAV KTGGVYDYYA TGIVTIWYQT NFVVPPDTPT EANIIALGAA QKNFTLKLCK DTDEIQQTAE YQ

UniProtKB: Genome polyprotein

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Macromolecule #4: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A6
Molecular weightTheoretical: 7.503163 KDa
SequenceString:
MGAQVSTQKS GSHETRNVAT EGSTINFTNI NYYKDSYAAS ASRQDFAQDP AKFTRPVLDA IREAAAPLQ

UniProtKB: Genome polyprotein

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Macromolecule #5: Kremen protein 1

MacromoleculeName: Kremen protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.728531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PECFTANGAD YRGTQNWTAL QGGKPCLFWN ETFQHPYNTL KYPNGEGGLG EHNYCRNPDG DVSPWCYVAE HEDGVYWKYC EIPACQMPG NLGCYKDHGN PPPLTGTSKT SNKLTIQTCI SFCRSQRFKF AGMESGYACF CGNNPDYWKY GEAASTECNS V CFGDHTQP ...String:
PECFTANGAD YRGTQNWTAL QGGKPCLFWN ETFQHPYNTL KYPNGEGGLG EHNYCRNPDG DVSPWCYVAE HEDGVYWKYC EIPACQMPG NLGCYKDHGN PPPLTGTSKT SNKLTIQTCI SFCRSQRFKF AGMESGYACF CGNNPDYWKY GEAASTECNS V CFGDHTQP CGGDGRIILF DTLVGACGGN YSAMSSVVYS PDFPDTYATG RVCYWTIRVP GASHIHFSFP LFDIRDSADM VE LLDGYTH RVLARFHGRS RPPLSFNVSL DFVILYFFSD RINQAQGFAV LYQAVK

UniProtKB: Kremen protein 1

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Macromolecule #6: STEARIC ACID

MacromoleculeName: STEARIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: STE
Molecular weightTheoretical: 284.477 Da
Chemical component information

ChemComp-STE:
STEARIC ACID

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Macromolecule #7: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 7 / Number of copies: 1 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.4
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 273.0 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5004 / Average exposure time: 2.7 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 184763
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: AB-initio reconstructuction in cryoSPARC (V4.5.3)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 19306
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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