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- PDB-3iyp: The Interaction of Decay-accelerating Factor with Echovirus 7 -

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Basic information

Entry
Database: PDB / ID: 3iyp
TitleThe Interaction of Decay-accelerating Factor with Echovirus 7
Components
  • (PolyproteinProteolysis) x 3
  • Capsid proteinCapsid
  • Complement decay-accelerating factor
KeywordsVIRUS / RECEPTOR / COMPLEX / ECHOVIRUS / DAF / icosahedral virus
Function / homology
Function and homology information


negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane ...negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / complement activation, classical pathway / transport vesicle / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / secretory granule membrane / host cell cytoplasmic vesicle membrane / Regulation of Complement cascade / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / positive regulation of T cell cytokine production / : / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / virus receptor activity / monoatomic ion channel activity / positive regulation of cytosolic calcium ion concentration / host cell cytoplasm / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont entry into host cell / membrane raft / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / Golgi membrane / innate immune response / DNA-templated transcription / lipid binding / Neutrophil degranulation / structural molecule activity / virion attachment to host cell / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain ...Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Picornavirus coat protein VP4 superfamily / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
LAURIC ACID / Complement decay-accelerating factor / Genome polyprotein / Capsid protein VP0 / Genome polyprotein
Similarity search - Component
Biological speciesHuman echovirus 7
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsPlevka, P. / Hafenstein, S. / Zhang, Y. / Harris, K.G. / Cifuente, J.O. / Bowman, V.D. / Chipman, P.R. / Lin, F. / Medof, D.E. / Bator, C.M. / Rossmann, M.G.
CitationJournal: J Virol / Year: 2010
Title: Interaction of decay-accelerating factor with echovirus 7.
Authors: Pavel Plevka / Susan Hafenstein / Katherine G Harris / Javier O Cifuente / Ying Zhang / Valorie D Bowman / Paul R Chipman / Carol M Bator / Feng Lin / M Edward Medof / Michael G Rossmann /
Abstract: Echovirus 7 (EV7) belongs to the Enterovirus genus within the family Picornaviridae. Many picornaviruses use IgG-like receptors that bind in the viral canyon and are required to initiate viral ...Echovirus 7 (EV7) belongs to the Enterovirus genus within the family Picornaviridae. Many picornaviruses use IgG-like receptors that bind in the viral canyon and are required to initiate viral uncoating during infection. However, in addition, some of the enteroviruses use an alternative or additional receptor that binds outside the canyon. Decay-accelerating factor (DAF) has been identified as a cellular receptor for EV7. The crystal structure of EV7 has been determined to 3.1-Å resolution and used to interpret the 7.2-Å-resolution cryo-electron microscopy reconstruction of EV7 complexed with DAF. Each DAF binding site on EV7 is near a 2-fold icosahedral symmetry axis, which differs from the binding site of DAF on the surface of coxsackievirus B3, indicating that there are independent evolutionary processes by which DAF was selected as a picornavirus accessory receptor. This suggests that there is an advantage for these viruses to recognize DAF during the initial process of infection.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 9, 2016Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _entity_src_gen.entity_id / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector_type / _entity_src_gen.plasmid_name / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Jan 31, 2024Group: Source and taxonomy / Category: entity_src_gen

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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
B: Polyprotein
C: Polyprotein
D: Polyprotein
F: Complement decay-accelerating factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,9246
Polymers137,7235
Non-polymers2001
Water0
1
A: Capsid protein
B: Polyprotein
C: Polyprotein
D: Polyprotein
F: Complement decay-accelerating factor
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,275,421360
Polymers8,263,402300
Non-polymers12,01960
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: Capsid protein
B: Polyprotein
C: Polyprotein
D: Polyprotein
F: Complement decay-accelerating factor
hetero molecules
x 5


  • icosahedral pentamer
  • 690 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)689,61830
Polymers688,61725
Non-polymers1,0025
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Polyprotein
C: Polyprotein
D: Polyprotein
F: Complement decay-accelerating factor
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 828 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)827,54236
Polymers826,34030
Non-polymers1,2026
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 ABCDF

#1: Protein Capsid protein / Capsid


Mass: 33313.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human echovirus 7 / References: UniProt: Q9QP24
#2: Protein Polyprotein / Proteolysis


Mass: 26226.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human echovirus 7 / References: UniProt: Q6W9E5
#3: Protein Polyprotein / Proteolysis


Mass: 29072.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human echovirus 7 / References: UniProt: Q6W9E5
#4: Protein Polyprotein / Proteolysis


Mass: 7599.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human echovirus 7 / References: UniProt: Q91QV1
#5: Protein Complement decay-accelerating factor


Mass: 41511.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08174

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2

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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

Component
IDNameTypeDetailsParent-ID
1Human Echovirus 7 in complex with Decay-accelerating Factor (DAF)VIRUSone DAF molecule binds to one asymmetric unit of EV70
3Decay Accelerating Factor1
Molecular weightValue: 6.8 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 0.1 M NaCl, 20mM Tris / pH: 7.2 / Details: 0.1 M NaCl, 20mM Tris
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.1 M NaCl, 20mM Tris
VitrificationCryogen name: ETHANE / Temp: 113 K / Method: Blot for 2 seconds before plunging
Time resolved state: Vitrified 1 hour after mixing DAF with EV7

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Jan 1, 2000
Details: Micrographs were digitized with a Zeiss PHODIS microdensitometer at 7-micron intervals.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3670 nm / Nominal defocus min: 1120 nm / Camera length: 0 mm
Specimen holderSpecimen holder model: OTHER
Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder.
Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2Auto3DEM3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: common lines fourier method / Resolution: 7.2 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 11430 / Symmetry type: POINT
Atomic model building
IDSpaceDetailsProtocolTarget criteria
1REALDETAILS--EV7 capsid protein coordinates were positioned into the cryoEM reconstruction by superimposing icosahedral symmetry elements.
2REALREFINEMENT PROTOCOL--Rigid BodyRIGID BODY FITRcrit
Atomic model building

Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-ID 3D fitting-IDAccession codeInitial refinement model-ID
12X5I

2x5i

12X5I1
21OJY

1ojy

A21OJY2
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms8481 0 14 0 8495

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