[English] 日本語
Yorodumi
- PDB-9vfr: Structure of mature Coxsackievirus A6 virion complexed with its r... -

+
Open data


ID or keywords:

Loading...

-
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 / cell communication / negative regulation of axon regeneration / negative regulation of ossification / regulation of canonical Wnt signaling pathway / limb development / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus ...Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / cell communication / negative regulation of axon regeneration / negative regulation of ossification / regulation of canonical Wnt signaling pathway / limb development / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / TCF dependent signaling in response to WNT / symbiont genome entry into host cell via pore formation in plasma membrane / 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 / ribonucleoside triphosphate phosphatase activity / 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 / RNA-directed RNA polymerase activity / neuronal cell body / apoptotic process / symbiont entry into host cell / DNA-templated transcription / 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 / Spermadhesin, CUB domain superfamily / CUB domain profile. / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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: Nat Commun / Year: 2025
Title: Molecular mechanisms of receptor recognition and antibody neutralization of coxsackievirus A6.
Authors: Xianliang Ke / Xue Li / Zeyu Liu / Kexin Liu / Weichi Liu / Xingyu Yan / Bo Shu / Chao Zhang /
Abstract: Coxsackievirus A6 (CVA6), a major cause of hand, foot, and mouth disease, lacks approved vaccines or drugs. KRM1 is its only known receptor, but its precise role remains unclear. This study ...Coxsackievirus A6 (CVA6), a major cause of hand, foot, and mouth disease, lacks approved vaccines or drugs. KRM1 is its only known receptor, but its precise role remains unclear. This study investigates CVA6's entry mechanism and antibody neutralization. Cryo-EM shows CVA6 clinical strain HeB primarily exists as mature virions. KRM1 binding within the canyon triggers conversion to uncoating intermediate, defining KRM1 as an uncoating receptor for CVA6. However, KRM1 knockout reduces CVA6 infectivity without affecting attachment. Conversely, disrupting heparan sulfate proteoglycan (HSPG) impairs both viral attachment and infectivity, and CVA6 virions bind heparin directly. These results support a two-receptor entry model for CVA6: HSPG mediates viral attachment, while KRM1 induces uncoating. Additionally, we develop two CVA6-specific protective antibodies (1F4 and 3H7), targeting a new antigenic site near the three-fold axis of the viral capsid. These antibodies sterically block KRM1 binding and function post-attachment, consistent with KRM1's role. The findings elucidate CVA6 entry and offer a basis for antibody interventions.
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
Revision 1.1Jun 10, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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))

-
Components

-
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

-
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

-
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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more