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- PDB-2c8i: Complex Of Echovirus Type 12 With Domains 1, 2, 3 and 4 Of Its Re... -

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Entry
Database: PDB / ID: 2c8i
TitleComplex Of Echovirus Type 12 With Domains 1, 2, 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 / PICORNAVIRUS / DAF / VIRUS-RECEPTOR COMPLEX / ANTIGEN / BLOOD GROUP ANTIGEN / COMPLEMENT PATHWAY / GPI-ANCHOR / IMMUNE RESPONSE / INNATE IMMUNITY / LIPOPROTEIN / PLASMA / SUSHI
Specimen sourceHomo sapiens / human
HUMAN ECHOVIRUS 11 / virus
MethodElectron microscopy (14 Å resolution / Particle / Single particle)
AuthorsPettigrew, D.M. / Williams, D.T. / Kerrigan, D. / Evans, D.J. / Lea, S.M. / Bhella, D.
CitationJ. Biol. Chem., 2006, 281, 5169-5177

primary. J. Biol. Chem., 2006, 281, 5169-5177 Yorodumi Papers
Structural and functional insights into the interaction of echoviruses and decay-accelerating factor.
David M Pettigrew / David T Williams / David Kerrigan / David J Evans / Susan M Lea / David Bhella

#1. J.Biol.Chem., 2004, 279, 8325- Yorodumi Papers
Complex of Echovirus Type 12 with Domains 3 and 4 of its Receptor Decay Accelerating Factor (Cd55) by Cryo Electron Microscopy at 16 A
Bhella, D. / Goodfellow, I.G. / Roversi, P. / Pettigrew, D. / Chaudry, Y. / Evans, D.J. / Lea, S.M.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 5, 2005 / Release: Jan 17, 2006
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 17, 2006Structure modelrepositoryInitial release
1.1Aug 30, 2017Structure modelData collectionem_software_em_software.image_processing_id

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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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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)127,9965
Polyers127,9965
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)7,679,740300
Polyers7,679,740300
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
  • 640 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)639,97825
Polyers639,97825
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
  • 768 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)767,97430
Polyers767,97430
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 / Coordinate model: Cα atoms only


Mass: 32447.342 Da / Num. of mol.: 1 / Source: (natural) HUMAN ECHOVIRUS 11 / virus / References: UniProt: P29813

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)ECHOVIRUS 11 COAT PROTEIN VP2 / Coordinate model: Cα atoms only


Mass: 27996.480 Da / Num. of mol.: 1 / Source: (natural) HUMAN ECHOVIRUS 11 / virus / References: UniProt: P29813

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)ECHOVIRUS 11 COAT PROTEIN VP3 / Coordinate model: Cα atoms only


Mass: 25897.391 Da / Num. of mol.: 1 / Source: (natural) HUMAN ECHOVIRUS 11 / virus / References: UniProt: P29813

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)ECHOVIRUS 11 COAT PROTEIN VP4 / Coordinate model: Cα atoms only


Mass: 6620.287 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: P29813

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)COMPLEMENT DECAY-ACCELERATING FACTOR / CD55 / Coordinate model: Cα atoms only


Mass: 35034.164 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)

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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 BOUND TO DECAY ACCELERATING FACTOR / Type: VIRUS / Details: CRYO-NEGATIVE STAIN IMAGES. 96 FOCAL PAIRS.
Buffer solutionName: PHOSPHATE BUFFERED SALINE / Details: PHOSPHATE BUFFERED SALINE / 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: STAINED WITH AMMONIUM MOLYBDATE PH 7.2. VITRIFIED IN LIQUID ETHANE (CRYO-NEGATIVE STAIN)

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 1200 / Date: Sep 1, 2004
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 30000 / Calibrated magnification: 29100 / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm / Cs: 3.4 mm
Specimen holderTemperature: 100 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 192
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategoryImage processing ID
1EM3DR2RECONSTRUCTION1
2PFT2RECONSTRUCTION1
CTF correctionDetails: DEFOCUS PAIR IMAGES OF INDIVIDUAL PARTICLES
SymmetryPoint symmetry: I
3D reconstructionMethod: POLAR FOURIER TRANSFORM METHOD / Resolution: 14 Å / Number of particles: 1501 / Nominal pixel size: 2.18 / Actual pixel size: 2.18
Details: THE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE STRUCTURE WAS FITTED IS THAT OF EV12
Symmetry type: POINT
Atomic model buildingDetails: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--LOCAL CORRELATION
Ref protocol: OTHER / Ref space: REAL / Target criteria: OPTIMAL CORRELATION
Atomic model buildingPDB-ID: 1H8T
Least-squares processHighest resolution: 14 Å
Refine hist #LASTHighest resolution: 14 Å
Number of atoms included #LASTProtein: 1091 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1091

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