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- PDB-1yy8: Crystal structure of the Fab fragment from the monoclonal antibod... -

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Basic information

Entry
Database: PDB / ID: 1yy8
TitleCrystal structure of the Fab fragment from the monoclonal antibody cetuximab/Erbitux/IMC-C225
Components
  • Cetuximab Fab Heavy chain
  • Cetuximab Fab Light chain
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / ANTIBODY DRUG / CANCER
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, S. / Schmitz, K.R. / Jeffrey, P.D. / Wiltzius, J.J.W. / Kussie, P. / Ferguson, K.M.
CitationJournal: Cancer Cell / Year: 2005
Title: Structural basis for inhibition of the epidermal growth factor receptor by cetuximab
Authors: Li, S. / Schmitz, K.R. / Jeffrey, P.D. / Wiltzius, J.J.W. / Kussie, P. / Ferguson, K.M.
History
DepositionFeb 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cetuximab Fab Light chain
B: Cetuximab Fab Heavy chain
C: Cetuximab Fab Light chain
D: Cetuximab Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)94,0264
Polymers94,0264
Non-polymers00
Water6,377354
1
A: Cetuximab Fab Light chain
B: Cetuximab Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0132
Polymers47,0132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-22 kcal/mol
Surface area18880 Å2
MethodPISA
2
C: Cetuximab Fab Light chain
D: Cetuximab Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0132
Polymers47,0132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-21 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.4, 82.0, 211.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Antibody Cetuximab Fab Light chain


Mass: 23287.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: pdHL2 / Cell (production host): mouse myeloma cell line / Production host: Mus musculus (house mouse) / Strain (production host): Sp2/0-Ag15
#2: Antibody Cetuximab Fab Heavy chain


Mass: 23725.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: pdHL2 / Cell (production host): mouse myeloma cell line / Production host: Mus musculus (house mouse) / Strain (production host): Sp2/0-Ag15
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.87 Å3/Da / Density % sol: 56.7 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 73414 / Num. obs: 73414 / % possible obs: 95.6 % / Observed criterion σ(I): 0.5 / Redundancy: 8.6 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 5.5 / % possible all: 0.968

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb ids 1IBG, 1AD9

1ibg

1ad9


Resolution: 2→15 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 3588 -random
Rwork0.2243 ---
all-70346 --
obs-70346 92.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.225 Å20 Å20 Å2
2---10.423 Å20 Å2
3---7.198 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 0 354 6958
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0119
X-RAY DIFFRACTIONc_angle_d1.764
X-RAY DIFFRACTIONc_mcbond_it2.6892.5
X-RAY DIFFRACTIONc_mcangle_it3.4583
X-RAY DIFFRACTIONc_scbond_it4.093.5
X-RAY DIFFRACTIONc_scangle_it5.1294

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