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SCR1 of DAF from 1ojv fitted into cryoEM density

by single particle (icosahedral) reconstruction, at 14 A resolution

Movie

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1412, Image by Jmol

#3: With PDB-2qzd, PDB-2qzh, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-1412 (with PDB-2qzd, PDB-2qzh), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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
AuthorsHafenstein, S., Bowman, V.D., Chipman, P.R., Bator Kelly, C.M., Lin, F., Medof, M.E., Rossmann, M.G.
DateDeposition: 2007-08-16, Release: 2007-10-30
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1412, Image by Jmol

#3: With PDB-2qzd, PDB-2qzh, Image by Jmol

#4: Superimposing with EM 3D map: EMDB-1412 (with PDB-2qzd, PDB-2qzh), Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1412

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Article
Citation - primary
ArticleJ. Virol., Vol. 81, Issue 23, Page 12927-35, Year 2007
TitleInteraction of decay-accelerating factor with coxsackievirus B3.
AuthorsSusan Hafenstein, Valorie D Bowman, Paul R Chipman, Carol M Bator Kelly, Feng Lin, M Edward Medof, Michael G Rossmann
Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
KeywordsAntigens, CD55 (chemistry), Cryoelectron Microscopy, Enterovirus B, Human (chemistry), Models, Molecular, Protein Binding, Receptors, Virus (chemistry), Virus Attachment
LinksDOI: 10.1128/JVI.00931-07, PubMed: 17804498, PMC: PMC2169128
Components
ID 1 : CD55 antigen
Image
DescriptionComplement decay-accelerating factor
Typepolypeptide(L)
FragmentSCR1 domain
Formula weight6884.752 Da
Number of molecules1
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: human, Homo, ID:9606, Homo sapiens
Host: Escherichia, ID:562, Escherichia coli

LinksUniProt: P08174, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Detailsone DAF binds each binding site, one per each protomer
Namecoxsackievirus B3, RD strain, complexed with decay-accelerating factor
Entity assembly
Assembly-ID1
GO-IDGO:0005887
InterPro-IDIPR:000436
NameComplement decay-accelerating factor
Buffer
Name50mM MES
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH6.0
Sample concentration2 mg/ml
Sample support
Detailsquantifoils
Vitrification
Detailsblot before plunging
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI/PHILIPS CM300FEG/T
Date2004-08-06
Electron gun
Electron sourceTUNGSTEN HAIRPIN
Accelerating voltage300 kV
Electron dose24 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
CsNominal: 2.0 mm
Nominal defocusMax: 4.6 nm, Min: 1.0 nm
Specimen holder
Tilt angleMin: 0 degrees
Temperature93 Kelvin
Detector
TypeKodak SO-163 film
Processing
2D projection selection
Software nameEMPFT, EM3DR
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
Resolution14 A
3D fitting
Software nameEMPFT, EM3DR
3D fitting list
3D Fitting ID1
PDB entry ID1ojv
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms479
Protein atoms479
Download
PDB format
Allpdb2qzf.ent.gz
pdb2qzf.ent (uncompressed file)
Header onlypdb2qzf.ent.gz
mmCIF format
mmCIF2qzf.cif.gz
XML format
All2qzf.xml.gz
No-atom2qzf-noatom.xml.gz
Ext-atom2qzf-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.7 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.4 MB
.webm (WebM/VP8 format), 2.3 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.5 MB