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Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb 16
by single particle (icosahedral) reconstruction, at 18 A resolution
#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-3iy5, Surface level: 1, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-3iy5, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5110 |
|---|---|
| Title | Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb 16 |
| Map | This is a map of the FAb from neutralizing antibody MAb 16 interacting with FPV |
| Sample | Fab fragment from MAb 15 interacting with feline panleukopenia virus (FPV) |
| Keywords |  parvovirus, antigenic epitope, antibody, Fab, neutralizing |
| Authors | Hafenstein S, Bowman VD, Sun T, Nelson CDS, Palermo LM, Chipman PR, Battisti AJ, Parrish CR, Rossmann MG |
| Date | Deposition: 2009-03-10, Header release: 2009-04-03, Map release: 2009-09-30, Last update: 2011-09-12 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-3iy5, Surface level: 1, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-3iy5, Made by Jmol |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | J. Virol., Vol. 83, Issue 11, Page 5556-66, Year 2009 |
|---|---|
| Title | Structural comparison of different antibodies interacting with parvovirus capsids. |
| Authors | Susan 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. |
| Keywords | Amino 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 |
| Links | DOI: 10.1128/JVI.02532-08, PubMed: 19321620, PMC: PMC2681957 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5110.map ( map file in CCP4 format, 24920 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||
| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
| ||||||||||||||||||||||||
| Unit Cell | A= B= C: 529.92 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 2.88 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is a map of the FAb from neutralizing antibody MAb 16 interacting with FPV | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | Fab fragment from MAb 15 interacting with feline panleukopenia virus (FPV) |
|---|---|
| Number of Components | 2 |
| Component #1: virus - FPV | |
| Scientific name | Feline panleukopenia virus |
| Common Name | FPV |
| Scientific Name of Species | Feline panleukopenia virus |
| Common Name of Species | FPV |
| NCBI taxonomy | 10786 |
| Empty | No |
| Enveloped | No |
| Isolate | STRAIN |
| Class | VIRION |
| Natural Source | NCBI taxonomy: 9685 Host Species: Felis catus Host Category: VERTEBRATES |
| Shell | Id: 1 , Diameter: 280 A, T Number: 1 |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 1 mg/ml |
|---|---|
| Specimen Support Details | quantifoils |
| Specimen State | particle |
| Buffer | Details: 10mM Tris-HCL pH: 7.5 |
| Vitrification | |
| Method | blot before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: plunger |
| Instrument | HOMEMADE PLUNGER |
| Temperature | 120 Kelvin |
| Imaging | |
| Microscope | FEI/PHILIPS CM300FEG/T |
| Date | 03-JUN-2004 |
| Electron Gun | |
| Electron Source | TUNGSTEN HAIRPIN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 37.7 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 45000, Calibrated: 47190 |
| Astigmatism | astigmatism was corrected at 100,000 times magnification |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 400 nm - 4800 nm |
| Specimen Holder | |
| Holder | side mounted nitrogen cooled |
| Model | GATAN LIQUID NITROGEN |
| Temperature | 93 K ( 83 - 83 K) |
| Camera | |
| Detector | Kodak SO-163 film |
| Image Acquisition | |
| Od Range | 0.9 |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 48 |
| Sampling Size | 7 |
| Quant Bit Number | 8 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | common lines |
| Software | EMPFT EM3DR |
| CTF Correction | robem |
| Resolution By Author | 18 A |
| Resolution Method | FSC at 0.5 cutoff |
| Single Particle | |
| Number of Projections | 2084 |
| Applied Symmetry | I (icosahedral) |
| Atomic Model Fitting | |
| Fitted Coordinate | |
| PDB entry ID | |
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