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- PDB-2qzf: SCR1 of DAF from 1ojv fitted into cryoEM density -

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Basic information

Entry
Database: PDB / ID: 2qzf
TitleSCR1 of DAF from 1ojv fitted into cryoEM density
DescriptorComplement decay-accelerating factor
KeywordsIMMUNE SYSTEM / SCR1 of DAF from structure 1ojv fitted into cryoEM density / Blood group antigen / Complement pathway / Glycoprotein / GPI-anchor / Immune response / Innate immunity / Lipoprotein / Membrane / Sushi / Immune system
Specimen sourceHomo sapiens / human
MethodElectron microscopy (14 Å resolution / Particle / Single particle)
AuthorsHafenstein, S. / Bowman, V.D. / Chipman, P.R. / Bator Kelly, C.M. / Lin, F. / Medof, M.E. / Rossmann, M.G.
CitationJ. Virol., 2007, 81, 12927-12935

J. Virol., 2007, 81, 12927-12935 StrPapers
Interaction of decay-accelerating factor with coxsackievirus B3.
Susan Hafenstein / Valorie D Bowman / Paul R Chipman / Carol M Bator Kelly / Feng Lin / M Edward Medof / Michael G Rossmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 16, 2007 / Release: Oct 30, 2007
RevisionDateData content typeGroupProviderType
1.0Oct 30, 2007Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2May 30, 2012Structure modelRefinement description

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Assembly

Deposited unit
A: Complement decay-accelerating factor


Theoretical massNumber of molelcules
Total (without water)6,8851
Polyers6,8851
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)Complement decay-accelerating factor / CD55 antigen


Mass: 6884.702 Da / Num. of mol.: 1 / Fragment: SCR1 domain / 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

Component
IDNameTypeDetailsParent ID
1coxsackievirus B3, RD strain, complexed with decay-accelerating factorVIRUSone DAF binds each binding site, one per each protomer0
2Complement decay-accelerating factor1
Buffer solutionName: 50mM MES / Details: 50mM MES / pH: 6
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: quantifoils
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: blot before plunging

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Aug 6, 2004
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 / Nominal defocus max: 4.6 nm / Nominal defocus min: 1 nm / Cs: 2 mm
Specimen holderTemperature: 93 kelvins / Tilt angle min: 0 deg.
Image recordingElectron dose: 24 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EM3DRRECONSTRUCTION
2EMPFTRECONSTRUCTION
SymmetryPoint symmetry: I
3D reconstructionResolution: 14 Å / Number of particles: 2269 / Symmetry type: POINT
Atomic model buildingPDB-ID: 1OJV
Number of atoms included #LASTProtein: 479 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 479

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