PDB-3iy1: Variable domains of the WAM of Fab B fitted into the cr...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3iy1
Title	Variable domains of the WAM of Fab B fitted into the cryoEM reconstruction of the virus-Fab B complex
Descriptor	Fab B
Keywords	IMMUNE SYSTEM, cryoEM, neutralizing antibody, parvovirus, canine, feline, fab footprint
Authors	Hafenstein, S., Bowman, V.D., Sun, T., Nelson, C.D., Palermo, L.M., Battisti, A.J., Parrish, C.R., Rossmann, M.G.
Date	Deposition: 2009-04-09, Release: 2009-05-12
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-5106, Made by Jmol #3: Superimposing with EM 3D map: EMDB-5106, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-5106 CiteFit EMDB-5105 Cite EMDB-5107 Cite EMDB-5108 Cite EMDB-5109 Cite EMDB-5110 Cite EMDB-5111 Cite EMDB-5112 Cite PDB-3iy0 Cite PDB-3iy2 Cite PDB-3iy3 Cite PDB-3iy4 Cite PDB-3iy5 Cite PDB-3iy6 Cite PDB-3iy7 Cite Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3iy4 PDB-3iy2 PDB-3iy3 PDB-3iy6 PDB-3iy7 PDB-3iy5 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

Components
ID 1 : Fab B, light chain
Image
Description	Fab B, light chain
Type	polymer
Fragment	antibody B fragment
Formula weight	11643.164 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:10116 Organism scientific: Rattus norvegicus
Links	Sequence view
ID 2 : Fab B, heavy chain
Image
Description	Fab B, heavy chain
Type	polymer
Formula weight	11774.089 Da
Number of molecules	1
Source	Method: Isolated from a natural source NCBI taxonomy: ID:10116 Organism scientific: Rattus norvegicus
Links	Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	Fab fragment from MAb B interacting with feline panleukopenia virus (FPV)
Num components	2
Entity assembly
Name	feline panleukopenia virus
Synonym	FPV
Type	VIRUS
Virus entity
Empty	NO
Enveloped	NO
Ictvdb id	00.050.1.01.007.00.007
Virus host category	VERTEBRATES
Virus host species	Felis catus
Virus isolate	STRAIN
Virus type	VIRION
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
Details	10mM Tris
Entity assembly id	1
pH	7.5
Sample concentration	1 mg/ml
Vitrification
Cryogen name	ETHANE
Instrument	plunger
Method	blot before plunging
Temp	120 Kelvin

Electron Microscopy
Imaging
Date	2004-06-30
Electron gun
Accelerating voltage	300 kV
Electron dose	28.4 e/A**2
Illumination mode	FLOOD BEAM
Lens
Mode	BRIGHT FIELD
Magnification	calibrated: 47190 X, nominal: 45000 X
Detector distance	0.0
Nominal defocus	max: 3.7 nm, min: 1.7 nm
Specimen holder
Specimen holder	model: GATAN LIQUID NITROGEN, type: side mounted nitrogen cooled
Tilt angle	min: 0.0 degrees, max: 0.0 degrees
Temperature	93 Kelvin
Recording temperature	maximum: 83, minimum: 83
Detector
Type	Kodak SO-163 film
Image scans
Details	scanned at 7 microns and bin averaged to 14
Number digital images	56
Od range	0.9
Sampling size	7
Scanner model	ZEISS SCAI