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- PDB-3pp4: Epitope characterization and crystal structure of GA101 provide i... -

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Basic information

Entry
Database: PDB / ID: 3pp4
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
  • B-lymphocyte antigen CD20
  • GA101 Fab heavy chain
  • GA101 Fab light chain
KeywordsIMMUNE SYSTEM / antibody Fab fragment Ig-domain / CD20 / cyclic peptide / antibody antigen
Function / homology
Function and homology information


store-operated calcium entry / calcium ion import into cytosol / positive regulation of calcium ion import across plasma membrane / epidermal growth factor receptor binding / B cell activation / humoral immune response / B cell proliferation / immunoglobulin binding / plasma membrane raft / B cell differentiation ...store-operated calcium entry / calcium ion import into cytosol / positive regulation of calcium ion import across plasma membrane / epidermal growth factor receptor binding / B cell activation / humoral immune response / B cell proliferation / immunoglobulin binding / plasma membrane raft / B cell differentiation / B cell receptor signaling pathway / response to bacterium / protein tetramerization / MHC class II protein complex binding / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane
Similarity search - Function
Membrane-spanning 4-domains subfamily A / CD20-like family / CD20-like family / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
B-lymphocyte antigen CD20
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: GA101 Fab heavy chain
L: GA101 Fab light chain
P: B-lymphocyte antigen CD20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8224
Polymers50,7873
Non-polymers351
Water13,673759
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-42 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.050, 85.900, 72.870
Angle α, β, γ (deg.)90.00, 116.34, 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.: 1
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.: 1
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: Protein/peptide B-lymphocyte antigen CD20 / B-lymphocyte surface antigen B1 / Bp35 / Leukocyte surface antigen Leu-16 / Membrane-spanning 4- ...B-lymphocyte surface antigen B1 / Bp35 / Leukocyte surface antigen Leu-16 / Membrane-spanning 4-domains subfamily A member 1


Mass: 2852.051 Da / Num. of mol.: 1 / Fragment: large extracellular loop (UNP residues 163-187) / Source method: obtained synthetically / Details: CD20 / Source: (synth.) Homo sapiens (human) / References: UniProt: P11836
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% (w/v) PEG4000, 4% (v/v) isopropanol, 0.1 M sodium acetate, pH 6.0, 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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2008
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 61332 / Num. obs: 60342 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.055 / Rsym value: 0.043 / Net I/σ(I): 17.9
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.21 / % possible all: 96.8

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Processing

Software
NameVersionClassification
EXESdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PP3

3pp3


Resolution: 1.6→42.95 Å / SU ML: 0.17 / σ(F): 1.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 2000 3.31 %RANDOM
Rwork0.1373 ---
obs0.139 60342 98.57 %-
all-61332 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.508 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1319 Å20 Å22.5823 Å2
2---0.3777 Å2-0 Å2
3----7.3775 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 1 759 4292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043878
X-RAY DIFFRACTIONf_angle_d0.9465354
X-RAY DIFFRACTIONf_dihedral_angle_d15.1921457
X-RAY DIFFRACTIONf_chiral_restr0.06618
X-RAY DIFFRACTIONf_plane_restr0.004687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5994-1.63940.19851380.13544014X-RAY DIFFRACTION95
1.6394-1.68370.20341410.12734129X-RAY DIFFRACTION98
1.6837-1.73320.18641420.11564154X-RAY DIFFRACTION98
1.7332-1.78920.17211420.11124122X-RAY DIFFRACTION98
1.7892-1.85310.1811420.11044168X-RAY DIFFRACTION99
1.8531-1.92730.19871440.11754170X-RAY DIFFRACTION99
1.9273-2.0150.1881420.11974159X-RAY DIFFRACTION99
2.015-2.12130.18141440.12054188X-RAY DIFFRACTION99
2.1213-2.25420.20091440.12424207X-RAY DIFFRACTION99
2.2542-2.42820.19481430.13274163X-RAY DIFFRACTION99
2.4282-2.67250.19031440.13774218X-RAY DIFFRACTION100
2.6725-3.05920.18621450.13974222X-RAY DIFFRACTION100
3.0592-3.85380.16941460.12664249X-RAY DIFFRACTION100
3.8538-42.96550.15851430.14274179X-RAY DIFFRACTION97

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