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

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Basic information

Entry
Database: PDB / ID: 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
Specimen sourceRattus norvegicus / mammal / ドブネズミ, どぶねずみ /
MethodElectron microscopy (18 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsHafenstein, S. / Bowman, V.D. / Sun, T. / Nelson, C.D. / Palermo, L.M. / Battisti, A.J. / Parrish, C.R. / Rossmann, M.G.
CitationJ. Virol., 2009, 83, 5556-5566

J. Virol., 2009, 83, 5556-5566 StrPapers
Structural comparison of different antibodies interacting with parvovirus capsids.
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

DateDeposition: Apr 9, 2009 / Release: May 12, 2009 / Last modification: May 26, 2009

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Assembly

Deposited unit
A: Fab B, light chain
B: Fab B, heavy chain


Theoretical massNumber of molelcules
Total (without water)23,4172
Polyers23,4172
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)Fab B, light chain


Mass: 11643.164 Da / Num. of mol.: 1 / Fragment: antibody B fragment
Source: (natural) Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /
#2: Polypeptide(L)Fab B, heavy chain


Mass: 11774.089 Da / Num. of mol.: 1
Source: (natural) Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: Fab fragment from MAb B interacting with feline panleukopenia virus (FPV)
Aggregation state: PARTICLE / Number of components: 2
ComponentName: feline panleukopenia virus / Type: VIRUS / Synonym: FPV
Details of the virusEmpty: NO / Enveloped: NO / Virus host category: VERTEBRATES / Virus host species: Felis catus / Virus isolate: STRAIN / Virus type: VIRION
Sample preparationDetails: 10mM Tris / pH: 7.5 / Sample conc.: 1 mg/ml
VitrificationInstrument: plunger / Cryogen name: ETHANE / Temp: 120 K / Method: blot before plunging

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Electron microscopy imaging

EM imagingCamera length: 0 mm
MicroscopyDate: Jun 30, 2004
Electron gunAccelerating voltage: 300 kV / Electron dose: 28.4 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47190 X / Nominal defocus max: 3.7 nm / Nominal defocus min: 1.7 nm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: side mounted nitrogen cooled / Temperature: 93 K / Temperature (max): 83 K / Temperature (min): 83 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: Kodak SO-163 film
EM image scansDetails: scanned at 7 microns and bin averaged to 14 / Number digital images: 56 / Od range: 0.9 / Sampling size: 7 microns / Scanner model: ZEISS SCAI
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Image selectionNumber of particles: 1126
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionMethod: common lines / Software: EMPFT EM3DR / Resolution: 18 A / Resolution method: FSC at 0.5 cutoff / Number of particles: 1126 / CTF correction method: robem
Number of atoms included #LASTProtein: 1648 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1648

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