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- PDB-2otw: Crystal structure of Fv polyglutamine complex -

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Basic information

Entry
Database: PDB / ID: 2otw
TitleCrystal structure of Fv polyglutamine complex
Components
  • Fv heavy chain variable domain VH
  • Fv light chain avriable domain VL
  • poly-Gln peptide antigen
KeywordsIMMUNE SYSTEM / Antibody / polyglutamine / complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsLi, P.
CitationJournal: To be Published
Title: Implications of the structure of a poly-Gln/anti-poly-Gln complex for disease progression and therapy
Authors: Li, P.
History
DepositionFeb 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fv light chain avriable domain VL
B: Fv heavy chain variable domain VH
C: Fv light chain avriable domain VL
D: Fv heavy chain variable domain VH
E: poly-Gln peptide antigen
F: poly-Gln peptide antigen


Theoretical massNumber of molelcules
Total (without water)54,4106
Polymers54,4106
Non-polymers00
Water5,224290
1
A: Fv light chain avriable domain VL
B: Fv heavy chain variable domain VH
E: poly-Gln peptide antigen


Theoretical massNumber of molelcules
Total (without water)27,2053
Polymers27,2053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fv light chain avriable domain VL
D: Fv heavy chain variable domain VH
F: poly-Gln peptide antigen


Theoretical massNumber of molelcules
Total (without water)27,2053
Polymers27,2053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.290, 78.724, 49.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsEach antibody/antigen complex contains VH, VL and Peptide

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Components

#1: Antibody Fv light chain avriable domain VL


Mass: 12460.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: VL / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Antibody Fv heavy chain variable domain VH


Mass: 13330.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: VH / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Protein/peptide poly-Gln peptide antigen


Mass: 1413.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: 0.1 M sodium citrate, 0.2 M NH4Ac, 27.5% PEG400, pH 6.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006 / Details: Si (111) crystal
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 28033 / Num. obs: 27313 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.052 / Rsym value: 5.2 / Net I/σ(I): 22.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2243 / Rsym value: 22.1 / % possible all: 81.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2GSG

2gsg


Resolution: 2.35→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2709 -random
Rwork0.226 ---
all0.226 28033 --
obs0.226 27245 97.2 %-
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 0 290 4110
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_bond_d0.006

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