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Variable domains of the WAM of Fab B fitted into the cryoEM reconstruction of the virus-Fab B complex

by single particle (icosahedral) reconstruction, at 18 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-5106, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-5106, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3iy1
TitleVariable domains of the WAM of Fab B fitted into the cryoEM reconstruction of the virus-Fab B complex
DescriptorFab B
KeywordsIMMUNE SYSTEM, cryoEM, neutralizing antibody, parvovirus, canine, feline, fab footprint
AuthorsHafenstein, S., Bowman, V.D., Sun, T., Nelson, C.D., Palermo, L.M., Battisti, A.J., Parrish, C.R., Rossmann, M.G.
DateDeposition: 2009-04-09, Release: 2009-05-12
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-5106, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-5106, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-5106

CiteFit

Cite: data citing same article

Fit: target map of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - primary
ArticleJ. Virol., Vol. 83, Issue 11, Page 5556-66, Year 2009
TitleStructural comparison of different antibodies interacting with parvovirus capsids.
AuthorsSusan Hafenstein, Valorie D Bowman, Tao Sun, Christian D S Nelson, Laura M Palermo, Paul R Chipman, Anthony J Battisti, Colin R Parrish, Michael G Rossmann
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2054, USA.
KeywordsAmino Acid Sequence, Antibodies, Monoclonal (chemistry), Antibody Specificity, Antigens (chemistry), Capsid (chemistry), Computational Biology, Conserved Sequence, Cryoelectron Microscopy, Crystallography, X-Ray, Immunoglobulin Fab Fragments (chemistry), Models, Molecular, Molecular Sequence Data, Parvovirus (chemistry), Protein Binding, Protein Structure, Quaternary, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein
LinksDOI: 10.1128/JVI.02532-08, PubMed: 19321620, PMC: PMC2681957
Components
ID 1 : Fab B, light chain
Image
DescriptionFab B, light chain
Typepolypeptide(L)
Fragmentantibody B fragment
Formula weight11643.164 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:10116
Organism scientific: Rattus norvegicus

LinksSequence view
ID 2 : Fab B, heavy chain
Image
DescriptionFab B, heavy chain
Typepolypeptide(L)
Formula weight11774.089 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:10116
Organism scientific: Rattus norvegicus
LinksSequence view
Sample
Assembly
Aggregation statePARTICLE
NameFab fragment from MAb B interacting with feline panleukopenia virus (FPV)
Num components2
Entity assembly
Assembly-ID1
Namefeline panleukopenia virus
SynonymFPV
TypeVIRUS
Virus entity
EmptyNO
EnvelopedNO
Ictvdb id00.050.1.01.007.00.007
Virus host categoryVERTEBRATES
Virus host speciesFelis catus
Virus isolateSTRAIN
Virus typeVIRION
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
Details10mM Tris
pH7.5
Sample concentration1 mg/ml
Vitrification
Cryogen nameETHANE
Instrumentplunger
Methodblot before plunging
Temp120 Kelvin
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
Date2004-06-30
Electron gun
Accelerating voltage300 kV
Electron dose28.4 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 47190 X, Nominal: 45000 X
Detector distance0.0
Nominal defocusMax: 3.7 nm, Min: 1.7 nm
Specimen holder
Specimen holderModel: GATAN LIQUID NITROGEN, Type: side mounted nitrogen cooled
Tilt angleMin: 0.0 degrees, Max: 0.0 degrees
Temperature93 Kelvin
Recording temperatureMaximum: 83, Minimum: 83
Detector
TypeKodak SO-163 film
Image scans
Detailsscanned at 7 microns and bin averaged to 14
Number digital images56
Od range0.9
Sampling size7
Scanner modelZEISS SCAI
Processing
2D projection selection
Number of particles1126
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
CTF correction methodrobem
Methodcommon lines
Number of particles1126
Resolution18 A
Resolution methodFSC at 0.5 cutoff
SoftwareEMPFT EM3DR
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms1648
Protein atoms1648
Download
PDB format
Allpdb3iy1.ent.gz
pdb3iy1.ent (uncompressed file)
Header onlypdb3iy1.ent.gz
mmCIF format
mmCIF3iy1.cif.gz
XML format
All3iy1.xml.gz
No-atom3iy1-noatom.xml.gz
Ext-atom3iy1-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.6 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), 3.5 MB
.webm (WebM/VP8 format), 4.7 MB