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- PDB-2osl: Crystal structure of Rituximab Fab in complex with an epitope peptide -

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Basic information

Entry
Database: PDB / ID: 2osl
TitleCrystal structure of Rituximab Fab in complex with an epitope peptide
Components
  • B-lymphocyte antigen CD20
  • heavy chain of the Rituximab Fab fragment,heavy chain of the Rituximab Fab fragment
  • light chain of the Rituximab Fab fragment,light chain of the Rituximab Fab fragment
KeywordsIMMUNE SYSTEM / Fab-peptide complex / Rituximab / chimeric antibody
Function / homology
Function and homology information


store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation ...store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation / response to bacterium / protein tetramerization / B cell receptor signaling pathway / 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
CD20-like family / Membrane-spanning 4-domains subfamily A / 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: 2.6 Å
AuthorsDu, J. / Zhong, C. / Ding, J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural basis for recognition of CD20 by therapeutic antibody Rituximab
Authors: Du, J. / Wang, H. / Zhong, C. / Peng, B. / Zhang, M. / Li, B. / Huo, S. / Guo, Y. / Ding, J.
History
DepositionFeb 6, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 15, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num
Revision 1.5Jun 17, 2020Group: Data collection / Source and taxonomy / Category: entity_src_gen / struct_biol
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.6Oct 25, 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 1.7Apr 10, 2024Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_genus
Remark 999SEQUENCE Sequence database references for chain L, B and chain H, A do not currently exist.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: light chain of the Rituximab Fab fragment,light chain of the Rituximab Fab fragment
H: heavy chain of the Rituximab Fab fragment,heavy chain of the Rituximab Fab fragment
B: light chain of the Rituximab Fab fragment,light chain of the Rituximab Fab fragment
A: heavy chain of the Rituximab Fab fragment,heavy chain of the Rituximab Fab fragment
P: B-lymphocyte antigen CD20
Q: B-lymphocyte antigen CD20


Theoretical massNumber of molelcules
Total (without water)99,3286
Polymers99,3286
Non-polymers00
Water3,819212
1
L: light chain of the Rituximab Fab fragment,light chain of the Rituximab Fab fragment
H: heavy chain of the Rituximab Fab fragment,heavy chain of the Rituximab Fab fragment
P: B-lymphocyte antigen CD20


Theoretical massNumber of molelcules
Total (without water)49,6643
Polymers49,6643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: light chain of the Rituximab Fab fragment,light chain of the Rituximab Fab fragment
A: heavy chain of the Rituximab Fab fragment,heavy chain of the Rituximab Fab fragment
Q: B-lymphocyte antigen CD20


Theoretical massNumber of molelcules
Total (without water)49,6643
Polymers49,6643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.421, 98.809, 107.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsthe Biological Assembly is monomer.

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Components

#1: Antibody light chain of the Rituximab Fab fragment,light chain of the Rituximab Fab fragment


Mass: 23078.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein was produced as a chimeric fab fragment. residues 1-106 is from murine and 107-213 is from human.
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Species: , / Description: The antibody was purchased from Roche. / Production host: synthetic construct (others)
#2: Antibody heavy chain of the Rituximab Fab fragment,heavy chain of the Rituximab Fab fragment


Mass: 23733.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein was produced as a chimeric fab fragment. residues 1-121 is from murine and 122-224 is from human.
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Species: , / Description: The antibody was purchased from Roche. / Production host: synthetic construct (others)
#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.: 2 / Fragment: epitope peptide / Source method: obtained synthetically
Details: the epitope peptide was synthesized at Shanghai Science Peptide Biological Technology
Source: (synth.) Homo sapiens (human) / References: UniProt: P11836
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M calcium acetate, 0.1M sodium cacodylate, 18% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 32638 / Num. obs: 29570 / % possible obs: 90.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 62.749 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Χ2: 0.892 / Net I/σ(I): 7.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2 / Num. unique all: 2958 / Rsym value: 0.434 / Χ2: 0.492 / % possible all: 91.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AD0

1ad0


Resolution: 2.6→43.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1491027.625 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1460 5 %RANDOM
Rwork0.239 ---
all-32153 --
obs-29131 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.903 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 49 Å2
Baniso -1Baniso -2Baniso -3
1-9.91 Å20 Å20 Å2
2---1.32 Å20 Å2
3----8.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6888 0 0 212 7100
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d29
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it3.11.5
X-RAY DIFFRACTIONc_mcangle_it4.922
X-RAY DIFFRACTIONc_scbond_it3.262
X-RAY DIFFRACTIONc_scangle_it5.822.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.428 230 4.8 %
Rwork0.356 4600 -
obs-4830 91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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