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- PDB-3pp3: Epitope characterization and crystal structure of GA101 provide i... -

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Basic information

Entry
Database: PDB / ID: 3pp3
TitleEpitope characterization and crystal structure of GA101 provide insights into the molecular basis for the type I / type II distinction of anti- CD20 antibodies
Components
  • GA101 Fab heavy chain
  • GA101 Fab light chain
KeywordsIMMUNE SYSTEM / antibody Fab-fragment Ig-domain / antibody / CD20
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.508 Å
AuthorsHopfner, K.-P. / Lammens, A.
CitationJournal: Blood / Year: 2011
Title: Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for type I/II distinction of CD20 antibodies.
Authors: Niederfellner, G. / Lammens, A. / Mundigl, O. / Georges, G.J. / Schaefer, W. / Schwaiger, M. / Franke, A. / Wiechmann, K. / Jenewein, S. / Slootstra, J.W. / Timmerman, P. / Brannstrom, A. / ...Authors: Niederfellner, G. / Lammens, A. / Mundigl, O. / Georges, G.J. / Schaefer, W. / Schwaiger, M. / Franke, A. / Wiechmann, K. / Jenewein, S. / Slootstra, J.W. / Timmerman, P. / Brannstrom, A. / Lindstrom, F. / Mossner, E. / Umana, P. / Hopfner, K.P. / Klein, C.
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Sep 6, 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 1.4Nov 6, 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
H: GA101 Fab heavy chain
L: GA101 Fab light chain
I: GA101 Fab heavy chain
K: GA101 Fab light chain


Theoretical massNumber of molelcules
Total (without water)95,8694
Polymers95,8694
Non-polymers00
Water9,494527
1
H: GA101 Fab heavy chain
L: GA101 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,9352
Polymers47,9352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-26 kcal/mol
Surface area20150 Å2
MethodPISA
2
I: GA101 Fab heavy chain
K: GA101 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,9352
Polymers47,9352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-25 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)273.140, 38.038, 90.220
Angle α, β, γ (deg.)90.00, 98.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody GA101 Fab heavy chain


Mass: 23969.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Chinese hamster ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody GA101 Fab light chain


Mass: 23964.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Chinese hamster ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.41 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 24% (w/v) PEG4000, 0.15 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2008
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 32252 / Num. obs: 31465 / % possible obs: 97.6 % / Observed criterion σ(F): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.105 / Rsym value: 0.067 / Net I/σ(I): 12.42
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.277 / % possible all: 93.1

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Processing

Software
NameVersionClassification
Exesdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T04

1t04


Resolution: 2.508→25 Å / SU ML: 0.4 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 1998 6.36 %RANDOM
Rwork0.2059 ---
obs0.21 31432 97.56 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.581 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.1872 Å20 Å22.2572 Å2
2--2.0538 Å20 Å2
3---5.1334 Å2
Refinement stepCycle: LAST / Resolution: 2.508→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6673 0 0 527 7200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036843
X-RAY DIFFRACTIONf_angle_d0.6689305
X-RAY DIFFRACTIONf_dihedral_angle_d13.3732451
X-RAY DIFFRACTIONf_chiral_restr0.0451047
X-RAY DIFFRACTIONf_plane_restr0.0031187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5078-2.57040.39631250.29961850X-RAY DIFFRACTION88
2.5704-2.63990.38071410.29912062X-RAY DIFFRACTION97
2.6399-2.71750.38841410.2852073X-RAY DIFFRACTION96
2.7175-2.80520.3621390.26682055X-RAY DIFFRACTION98
2.8052-2.90530.31081430.25182106X-RAY DIFFRACTION98
2.9053-3.02160.32351410.23252082X-RAY DIFFRACTION99
3.0216-3.15890.26591460.22972145X-RAY DIFFRACTION99
3.1589-3.32530.31241410.21432092X-RAY DIFFRACTION99
3.3253-3.53330.26241450.2062125X-RAY DIFFRACTION99
3.5333-3.80550.25261460.18922161X-RAY DIFFRACTION99
3.8055-4.18750.23971450.16672133X-RAY DIFFRACTION99
4.1875-4.79130.18271450.142144X-RAY DIFFRACTION99
4.7913-6.0280.22161480.17452179X-RAY DIFFRACTION99
6.028-29.46630.22831520.20382227X-RAY DIFFRACTION97

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