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- PDB-7bzt: Cryo-EM structure of mature Coxsackievirus A10 in complex with KR... -

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Basic information

Entry
Database: PDB / ID: 7bzt
TitleCryo-EM structure of mature Coxsackievirus A10 in complex with KRM1 at pH 7.4
Components
  • (Capsid protein ...Capsid) x 4
  • KRM1
KeywordsVIRUS / Picornavirus / Coxsackievirus A10 / pH 7.4 / mature particle / KRM1 / complex
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 / 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 / negative regulation of axon regeneration / cell communication / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / TCF dependent signaling in response to WNT / host cell cytoplasmic vesicle membrane / negative regulation of canonical Wnt signaling pathway / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / Wnt signaling pathway / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / neuronal cell body / DNA-templated transcription / apoptotic process / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Kremen / 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 ...Kremen / 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 / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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
SPHINGOSINE / Genome polyprotein / Genome polyprotein / Kremen protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Coxsackievirus A10
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsCui, Y. / Peng, R. / Song, H. / Tong, Z. / Gao, G.F. / Qi, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Molecular basis of Coxsackievirus A10 entry using the two-in-one attachment and uncoating receptor KRM1.
Authors: Yingzi Cui / Ruchao Peng / Hao Song / Zhou Tong / Xiao Qu / Sheng Liu / Xin Zhao / Yan Chai / Peiyi Wang / George F Gao / Jianxun Qi /
Abstract: KREMEN1 (KRM1) has been identified as a functional receptor for Coxsackievirus A10 (CV-A10), a causative agent of hand-foot-and-mouth disease (HFMD), which poses a great threat to infants globally. ...KREMEN1 (KRM1) has been identified as a functional receptor for Coxsackievirus A10 (CV-A10), a causative agent of hand-foot-and-mouth disease (HFMD), which poses a great threat to infants globally. However, the underlying mechanisms for the viral entry process are not well understood. Here we determined the atomic structures of different forms of CV-A10 viral particles and its complex with KRM1 in both neutral and acidic conditions. These structures reveal that KRM1 selectively binds to the mature viral particle above the canyon of the viral protein 1 (VP1) subunit and contacts across two adjacent asymmetry units. The key residues for receptor binding are conserved among most KRM1-dependent enteroviruses, suggesting a uniform mechanism for receptor binding. Moreover, the binding of KRM1 induces the release of pocket factor, a process accelerated under acidic conditions. Further biochemical studies confirmed that receptor binding at acidic pH enabled CV-A10 virion uncoating in vitro. Taken together, these findings provide high-resolution snapshots of CV-A10 entry and identify KRM1 as a two-in-one receptor for enterovirus infection.
History
DepositionApr 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Aug 19, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: KRM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,1019
Polymers136,1385
Non-polymers9634
Water0
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: KRM1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,226,078540
Polymers8,168,291300
Non-polymers57,787240
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: KRM1
hetero molecules
x 5


  • icosahedral pentamer
  • 686 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)685,50745
Polymers680,69125
Non-polymers4,81620
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: KRM1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 823 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)822,60854
Polymers816,82930
Non-polymers5,77924
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: KRM1
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 8.23 MDa, 300 polymers
Theoretical massNumber of molelcules
Total (without water)8,226,078540
Polymers8,168,291300
Non-polymers57,787240
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60

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Components

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Capsid protein ... , 4 types, 4 molecules ABCD

#1: Protein Capsid protein VP1 /


Mass: 33204.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10 / References: UniProt: A0A0C5AWF6*PLUS
#2: Protein Capsid protein VP2 /


Mass: 27783.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10 / References: UniProt: G0YPI2
#3: Protein Capsid protein VP3 /


Mass: 26187.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10 / References: UniProt: G0YPI2
#4: Protein Capsid protein VP4 /


Mass: 7464.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A10 / References: UniProt: G0YPI2

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Protein / Non-polymers / Sugars , 3 types, 5 molecules E

#5: Protein KRM1


Mass: 41499.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q96MU8*PLUS
#6: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Feature type: SUBJECT OF INVESTIGATION
#7: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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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Details

Has ligand of interestY
Sequence detailsThe genome sequence of chain A have been deposit in GenBank: MT263729

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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 A10 / Type: VIRUS / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Coxsackievirus A10
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1140GATAN K2 SUMMIT (4k x 4k)
2140GATAN K2 SUMMIT (4k x 4k)
3140GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28084 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038831
ELECTRON MICROSCOPYf_angle_d0.58712056
ELECTRON MICROSCOPYf_dihedral_angle_d22.3233144
ELECTRON MICROSCOPYf_chiral_restr0.151320
ELECTRON MICROSCOPYf_plane_restr0.0051569

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