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

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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
DescriptorCOMPLEMENT DECAY-ACCELERATING FACTOR
(ECHOVIRUS 11 COAT PROTEIN ...) x 4
KeywordsVIRUS/RECEPTOR / COMPLEX (VIRUS COAT-IMMUNE PROTEIN) / ECHOVIRUS / PICORNAVIRUS / CD55 / DAF / VIRUS-RECEPTOR COMPLEX / ICOSAHEDRAL VIRUS
Specimen sourceHomo sapiens / human
HUMAN ECHOVIRUS 11 / virus
MethodElectron microscopy (16 Å resolution / Particle / Single particle)
AuthorsBhella, D. / Goodfellow, I.G. / Roversi, P. / Pettigrew, D. / Chaudry, Y. / Evans, D.J. / Lea, S.M.
CitationJ. Biol. Chem., 2004, 279, 8325-8332

J. Biol. Chem., 2004, 279, 8325-8332 Yorodumi Papers
The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55).
David Bhella / Ian G Goodfellow / Pietro Roversi / David Pettigrew / Yasmin Chaudhry / David J Evans / Susan M Lea

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 8, 2003 / Release: Jan 7, 2004
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 7, 2004Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Apr 19, 2017Structure modelOther
1.4Aug 30, 2017Structure modelData collection / Refinement descriptionem_3d_fitting / em_software_em_3d_fitting.target_criteria / _em_software.image_processing_id / _em_software.name
Remark 700 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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  • 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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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
Polyers109,3375
Non-polymers00
Water0
#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
Polyers6,560,198300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#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
Polyers546,68325
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#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
Polyers656,02030
Non-polymers00
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

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Components

#1: Polypeptide(L)ECHOVIRUS 11 COAT PROTEIN VP1


Mass: 32786.668 Da / Num. of mol.: 1 / Source: (natural) HUMAN ECHOVIRUS 11 / virus / References: UniProt: Q8JKE8

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)ECHOVIRUS 11 COAT PROTEIN VP2


Mass: 29048.549 Da / Num. of mol.: 1 / Source: (natural) HUMAN ECHOVIRUS 11 / virus / References: UniProt: Q8JKE8

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)ECHOVIRUS 11 COAT PROTEIN VP3


Mass: 25897.391 Da / Num. of mol.: 1 / Source: (natural) HUMAN ECHOVIRUS 11 / virus / References: UniProt: Q8JKE8

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)ECHOVIRUS 11 COAT PROTEIN VP4


Mass: 7509.299 Da / Num. of mol.: 1
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 / virus / References: UniProt: Q8JKE8

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)COMPLEMENT DECAY-ACCELERATING FACTOR / CD55


Mass: 14094.727 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P08174

Cellular component

Molecular function

Biological process

  • CD4-positive, alpha-beta T cell cytokine production (GO: 0035743)
  • complement activation, classical pathway (GO: 0006958)
  • ER to Golgi vesicle-mediated transport (GO: 0006888)
  • innate immune response (GO: 0045087)
  • negative regulation of complement activation (GO: 0045916)
  • neutrophil degranulation (GO: 0043312)
  • positive regulation of CD4-positive, alpha-beta T cell activation (GO: 2000516)
  • positive regulation of CD4-positive, alpha-beta T cell proliferation (GO: 2000563)
  • positive regulation of cytosolic calcium ion concentration (GO: 0007204)
  • regulation of complement activation (GO: 0030449)
  • regulation of lipopolysaccharide-mediated signaling pathway (GO: 0031664)
  • respiratory burst (GO: 0045730)
Sequence detailsTHE 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 / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: ECHOVIRUS TYPE 12 / Type: VIRUS
Buffer solutionName: AMMONIUM MOLYBDATE / Details: AMMONIUM MOLYBDATE / pH: 7.4
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
Temp unit: unknown / Method: electron microscopy / Details: electron microscopy

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Electron microscopy imaging

MicroscopyMicroscope model: 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 / Calibrated magnification: 29200 / Nominal defocus max: 2000 nm / Nominal defocus min: 300 nm / Cs: 3.4 mm
Specimen holderTemperature: 108 kelvins
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 16
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: MRC IMAGE PROCESSING PACKAGE / Category: RECONSTRUCTION
SymmetryPoint symmetry: I
3D reconstructionMethod: POLAR FOURIER TRANSFORM / Resolution: 16 Å / Resolution method: FSC 0.5 CUT-OFF / Number 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 WAS INTRODUCED BY RIGID-BODY REFINEMENT OF DOMAIN 4 KEEPING 3 FIXED
Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--X-RAY / Ref protocol: OTHER / Ref space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 1UPN
Least-squares processHighest resolution: 16 Å
Refine hist #LASTHighest resolution: 16 Å
Number of atoms included #LASTProtein: 7463 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7463

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