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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
Specimen sourceHomo sapiens / human
MethodElectron microscopy (14 A resolution / Single particle / Vitreous ice (cryo EM))
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

DateDeposition: Aug 16, 2007 / Release: Oct 30, 2007 / Last modification: May 30, 2012

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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: 6884.752 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)
  • 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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: coxsackievirus B3, RD strain, complexed with decay-accelerating factor
Aggregation state: PARTICLE
Details: one DAF binds each binding site, one per each protomer
ComponentName: Complement decay-accelerating factor
Buffer solutionName: 50mM MES
Sample preparationpH: 6 / Sample conc.: 2 mg/ml
Specimen supportDetails: quantifoils
VitrificationDetails: 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 / Electron dose: 24 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4.6 nm / Nominal defocus min: 1 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle min: 0 deg.
CameraType: 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

Image selectionSoftware name: EMPFT, EM3DR
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionResolution: 14 A
Atomic model buildingSoftware name: EMPFT, EM3DR
Atomic model buildingPDB-ID: 1ojv
Number of atoms included #LASTProtein: 479 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 479

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