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- PDB-1upn: COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR... -

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Entry
Database: PDB / ID: 1upn
TitleCOMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A
Components
  • COMPLEMENT DECAY-ACCELERATING FACTOR
  • ECHOVIRUS 11 COAT PROTEIN VP1
  • ECHOVIRUS 11 COAT PROTEIN VP2
  • ECHOVIRUS 11 COAT PROTEIN VP3
  • ECHOVIRUS 11 COAT PROTEIN VP4
KeywordsVIRUS/RECEPTOR / COMPLEX (VIRUS COAT-IMMUNE PROTEIN) / ECHOVIRUS / PICORNAVIRUS / CD55 / DAF / VIRUS-RECEPTOR COMPLEX / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / 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 ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / 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 / COPI-mediated anterograde transport / complement activation, classical pathway / side of membrane / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / secretory granule membrane / T=pseudo3 icosahedral viral capsid / Regulation of Complement cascade / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / positive regulation of T cell cytokine production / nucleoside-triphosphate phosphatase / channel activity / virus receptor activity / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / induction by virus of host autophagy / membrane raft / RNA-directed RNA polymerase / Golgi membrane / viral RNA genome replication / cysteine-type endopeptidase activity / innate immune response / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / lipid binding / DNA-templated transcription / Neutrophil degranulation / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane
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/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein ...: / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / 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) / 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
Complement decay-accelerating factor / Genome polyprotein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN ECHOVIRUS 11
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 16 Å
AuthorsBhella, D. / Goodfellow, I.G. / Roversi, P. / Pettigrew, D. / Chaudry, Y. / Evans, D.J. / Lea, S.M.
CitationJournal: J Biol Chem / Year: 2004
Title: The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55).
Authors: David Bhella / Ian G Goodfellow / Pietro Roversi / David Pettigrew / Yasmin Chaudhry / David J Evans / Susan M Lea /
Abstract: Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three- ...Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF(34) and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses.
History
DepositionOct 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 7, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 19, 2017Group: Other
Revision 1.4Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id / _em_software.name
Revision 1.5Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list
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 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
  • EMDB-1057
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  • Simplified surface model + fitted atomic model
  • EMDB-1058
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  • Superimposition on EM map
  • EMDB-1057
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Assembly

Deposited unit
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR


Theoretical massNumber of molelcules
Total (without water)109,3375
Polymers109,3375
Non-polymers00
Water00
1
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR
x 60


Theoretical massNumber of molelcules
Total (without water)6,560,198300
Polymers6,560,198300
Non-polymers00
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: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR
x 5


  • icosahedral pentamer
  • 547 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)546,68325
Polymers546,68325
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR
x 6


  • icosahedral 23 hexamer
  • 656 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)656,02030
Polymers656,02030
Non-polymers00
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

#1: Protein ECHOVIRUS 11 COAT PROTEIN VP1


Mass: 32786.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ECHOVIRUS 11 / Strain: GREGORY / References: UniProt: Q8JKE8
#2: Protein ECHOVIRUS 11 COAT PROTEIN VP2


Mass: 29048.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ECHOVIRUS 11 / Strain: GREGORY / References: UniProt: Q8JKE8
#3: Protein ECHOVIRUS 11 COAT PROTEIN VP3


Mass: 25897.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ECHOVIRUS 11 / Strain: GREGORY / References: UniProt: Q8JKE8
#4: Protein ECHOVIRUS 11 COAT PROTEIN VP4


Mass: 7509.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRUCTURE OF ECHOVIRUS TYPE 11 FITTED INTO CRYO-EM ELECTRON DENSITY FOR ECHOVIRUS TYPE 12. THE EM DENSITY HAS BEEN DEPOSITED IN THE EMDB, WITH ACCESSION CODE 1057
Source: (natural) HUMAN ECHOVIRUS 11 / Strain: GREGORY / References: UniProt: Q8JKE8
#5: Protein COMPLEMENT DECAY-ACCELERATING FACTOR / CD55


Mass: 14094.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08174
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE ...THE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE STRUCTURE WAS FITTED IS THAT OF EV12

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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: ECHOVIRUS TYPE 12 / Type: VIRUS
Buffer solutionName: AMMONIUM MOLYBDATE / pH: 7.4 / Details: AMMONIUM MOLYBDATE
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: Ammonium Molybdate
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE
Crystal grow
*PLUS
Method: electron microscopy / Details: electron microscopy

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Electron microscopy imaging

MicroscopyModel: JEOL 2000EXII / Date: Jul 15, 2002 / Details: PARTICLES SELECTED WITH X3D
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 30000 X / Calibrated magnification: 29200 X / Nominal defocus max: 2000 nm / Nominal defocus min: 300 nm / Cs: 3.4 mm
Specimen holderTemperature: 108 K
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 16
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: MRC IMAGE PROCESSING PACKAGE / Category: 3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: POLAR FOURIER TRANSFORM / Resolution: 16 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 903
Details: MAP BROUGHT TO P23 CRYSTAL WITH UNIT CELL DIMENSIONS OF 599.375 599.375 599.375 90.00 90.00 90.00. MODEL FOR EV11 DOCKED ONTO EV12 EM DENSITY. 0.5 A GAP BETWEEN CD55 DOMAIN 3 AND DOMAIN 4 ...Details: MAP BROUGHT TO P23 CRYSTAL WITH UNIT CELL DIMENSIONS OF 599.375 599.375 599.375 90.00 90.00 90.00. MODEL FOR EV11 DOCKED ONTO EV12 EM DENSITY. 0.5 A GAP BETWEEN CD55 DOMAIN 3 AND DOMAIN 4 WAS INTRODUCED BY RIGID-BODY REFINEMENT OF DOMAIN 4 KEEPING 3 FIXED
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient / Details: REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 1UPN

Accession code: 1UPN / Source name: PDB / Type: experimental model
RefinementHighest resolution: 16 Å
Refinement stepCycle: LAST / Highest resolution: 16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7463 0 0 0 7463

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