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- PDB-2qzd: Fitted structure of SCR4 of DAF into cryoEM density -

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Basic information

Entry
Database: PDB / ID: 2qzd
TitleFitted structure of SCR4 of DAF into cryoEM density
ComponentsComplement decay-accelerating factor
KeywordsIMMUNE SYSTEM / SCR4 of DAF from 1ojv fitted into cryoEM density / Blood group antigen / Complement pathway / Glycoprotein / GPI-anchor / Immune response / Innate immunity / Lipoprotein / Membrane / Sushi
Function / homology
Function and homology information


negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / 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) / ficolin-1-rich granule membrane / side of membrane ...negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / 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) / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / complement activation, classical pathway / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / Regulation of Complement cascade / positive regulation of T cell cytokine production / virus receptor activity / positive regulation of cytosolic calcium ion concentration / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / cell surface / extracellular exosome / extracellular region / 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/SCR/CCP superfamily / Sushi/CCP/SCR domain profile.
Similarity search - Domain/homology
Complement decay-accelerating factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14 Å
AuthorsHafenstein, S. / Bowman, V.D. / Chipman, P.R. / Bator Kelly, C.M. / Lin, F. / Medof, M.E. / Rossmann, M.G.
CitationJournal: J Virol / Year: 2007
Title: Interaction of decay-accelerating factor with coxsackievirus B3.
Authors: Susan Hafenstein / Valorie D Bowman / Paul R Chipman / Carol M Bator Kelly / Feng Lin / M Edward Medof / Michael G Rossmann /
Abstract: Many entero-, parecho-, and rhinoviruses use immunoglobulin (Ig)-like receptors that bind into the viral canyon and are required to initiate viral uncoating during infection. However, some of these ...Many entero-, parecho-, and rhinoviruses use immunoglobulin (Ig)-like receptors that bind into the viral canyon and are required to initiate viral uncoating during infection. However, some of these viruses use an alternative or additional receptor that binds outside the canyon. Both the coxsackievirus-adenovirus receptor (CAR), an Ig-like molecule that binds into the viral canyon, and decay-accelerating factor (DAF) have been identified as cellular receptors for coxsackievirus B3 (CVB3). A cryoelectron microscopy reconstruction of a variant of CVB3 complexed with DAF shows full occupancy of the DAF receptor in each of 60 binding sites. The DAF molecule bridges the canyon, blocking the CAR binding site and causing the two receptors to compete with one another. The binding site of DAF on CVB3 differs from the binding site of DAF on the surface of echoviruses, suggesting independent evolutionary processes.
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2012Group: Refinement description
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id

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Structure visualization

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Assembly

Deposited unit
A: Complement decay-accelerating factor


Theoretical massNumber of molelcules
Total (without water)7,2751
Polymers7,2751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Complement decay-accelerating factor / CD55 antigen


Mass: 7274.988 Da / Num. of mol.: 1 / Fragment: SCR4 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD55, CR, DAF / Production host: Escherichia coli (E. coli) / References: UniProt: P08174

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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

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 / pH: 6 / Details: 50mM MES
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

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Aug 6, 2004
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Nominal defocus max: 4.6 nm / Nominal defocus min: 1 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle min: 0 °
Image recordingElectron dose: 24 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EM3DR3D reconstruction
2EMPFT3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 14 Å / Num. of particles: 2269 / Symmetry type: POINT
Atomic model buildingPDB-ID: 1OJV

1ojv

Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms507 0 0 0 507

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