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- PDB-3g5y: Antibodies Specifically Targeting a Locally Misfolded Region of T... -

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Basic information

Entry
Database: PDB / ID: 3g5y
TitleAntibodies Specifically Targeting a Locally Misfolded Region of Tumor Associated EGFR
Components
  • 175 heavy chain
  • 175 light chain
  • EGFR peptide
KeywordsIMMUNE SYSTEM / antibody
Function / homology
Function and homology information


positive regulation of protein kinase C activity / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / response to hydroxyisoflavone / diterpenoid metabolic process / positive regulation of prolactin secretion / Shc-EGFR complex / Inhibition of Signaling by Overexpressed EGFR / ovulation cycle / EGFR interacts with phospholipase C-gamma ...positive regulation of protein kinase C activity / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / response to hydroxyisoflavone / diterpenoid metabolic process / positive regulation of prolactin secretion / Shc-EGFR complex / Inhibition of Signaling by Overexpressed EGFR / ovulation cycle / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / tongue development / response to UV-A / PLCG1 events in ERBB2 signaling / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / Signaling by EGFR / response to cobalamin / intracellular vesicle / negative regulation of epidermal growth factor receptor signaling pathway / eyelid development in camera-type eye / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / hepatocyte growth factor receptor activity / platelet-derived growth factor beta-receptor activity / placental growth factor receptor activity / brain-derived neurotrophic factor receptor activity / boss receptor activity / platelet-derived growth factor alpha-receptor activity / epidermal growth factor receptor activity / protein tyrosine kinase activator activity / Respiratory syncytial virus (RSV) attachment and entry / macrophage colony-stimulating factor receptor activity / positive regulation of bone resorption / protein tyrosine kinase collagen receptor activity / stem cell factor receptor activity / Signaling by ERBB4 / PI3K events in ERBB2 signaling / negative regulation of mitotic cell cycle / insulin-like growth factor receptor activity / transmembrane-ephrin receptor activity / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / GPI-linked ephrin receptor activity / vascular endothelial growth factor receptor activity / peptidyl-tyrosine autophosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hair follicle development / MAP kinase kinase kinase activity / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / embryonic placenta development / fibroblast growth factor receptor activity / insulin receptor activity / salivary gland morphogenesis / positive regulation of vasoconstriction / Signaling by ERBB2 / positive regulation of glial cell proliferation / GRB2 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / SHC1 events in EGFR signaling / transmembrane receptor protein tyrosine kinase activity / EGFR Transactivation by Gastrin / cellular response to dexamethasone stimulus / GRB2 events in ERBB2 signaling / positive regulation of synaptic transmission, glutamatergic / SHC1 events in ERBB2 signaling / ossification / basal plasma membrane / positive regulation of DNA repair / cellular response to epidermal growth factor stimulus / positive regulation of epithelial cell proliferation / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / neuron projection morphogenesis / Signal transduction by L1 / positive regulation of smooth muscle cell proliferation / positive regulation of protein localization to plasma membrane / liver regeneration / astrocyte activation / cellular response to amino acid stimulus / NOTCH3 Activation and Transmission of Signal to the Nucleus / cellular response to estradiol stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / lung development / EGFR downregulation / synaptic membrane / peptidyl-tyrosine phosphorylation / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII
Similarity search - Function
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Epidermal growth factor receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsGarrett, T.P.J. / Burgess, A.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Antibodies specifically targeting a locally misfolded region of tumor associated EGFR
Authors: Garrett, T.P.J. / Burgess, A.W. / Gan, H.K. / Luwor, R.B. / Cartwright, G. / Walker, F. / Orchard, S.G. / Clayton, A.H.A. / Nice, E.C. / Rothacker, J. / Catimel, B. / Cavenee, W.K. / Old, L. ...Authors: Garrett, T.P.J. / Burgess, A.W. / Gan, H.K. / Luwor, R.B. / Cartwright, G. / Walker, F. / Orchard, S.G. / Clayton, A.H.A. / Nice, E.C. / Rothacker, J. / Catimel, B. / Cavenee, W.K. / Old, L.J. / Stockert, E. / Ritter, G. / Adams, T.E. / Hoyne, P.A. / Wittrup, D. / Chao, G. / Cochran, J.R. / Luo, C. / Lou, M. / Huyton, T. / Xu, Y. / Fairlie, W.D. / Yao, S. / Scott, A.M. / Johns, T.G.
History
DepositionFeb 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 12, 2011Group: Structure summary
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 175 light chain
B: 175 heavy chain
E: EGFR peptide


Theoretical massNumber of molelcules
Total (without water)48,4253
Polymers48,4253
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-28 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.176, 69.267, 71.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody 175 light chain


Mass: 23259.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma cell / Production host: Mus musculus (house mouse)
#2: Antibody 175 heavy chain


Mass: 23371.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma cell / Production host: Mus musculus (house mouse)
#3: Protein/peptide EGFR peptide


Mass: 1793.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis / References: UniProt: P00533*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.15M Na formate, 15% PEG1500, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.59→14.18 Å / Num. obs: 43879 / % possible obs: 78.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.086
Reflection shellResolution: 1.59→1.65 Å / Rmerge(I) obs: 0.3 / % possible all: 11.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→14.18 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.046 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25049 2222 5.1 %RANDOM
Rwork0.19577 ---
obs0.19851 41619 78.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.282 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2---0.38 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.59→14.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 0 247 3614
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.016
X-RAY DIFFRACTIONr_angle_refined_deg1.591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.062
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.179
X-RAY DIFFRACTIONr_chiral_restr0.105
X-RAY DIFFRACTIONr_gen_planes_refined0.007
X-RAY DIFFRACTIONr_nbd_refined0.192
X-RAY DIFFRACTIONr_nbtor_refined0.298
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.19
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.153
X-RAY DIFFRACTIONr_mcbond_it0.901
X-RAY DIFFRACTIONr_mcangle_it
LS refinement shellResolution: 1.594→1.635 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 21 -
Rwork0.369 342 -
obs--8.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.049-0.3011-0.82040.26730.24781.625-0.04670.0242-0.0413-0.0184-0.01210.0488-0.05730.15280.0588-0.0512-0.0261-0.00260.01960.0181-0.0196-3.764717.7298-7.4805
20.6332-0.06190.230.10940.01470.62-0.00350.0397-0.00420.03130.016-0.0130.04040.019-0.01260.01260.0029-0.012-0.03470.0044-0.0008-20.38248.8249-40.4247
30.39770.01410.16610.3467-0.07930.88970.00050.0075-0.015-0.0147-0.01320.0118-0.02970.03670.0127-0.01440.0044-0.0086-0.0106-0.005-0.0061-24.337116.8628-0.802
40.5127-0.54150.01191.61060.17390.0997-0.0492-0.0266-0.01750.04810.02750.0195-0.0018-0.02470.02170.03260.01230.0064-0.03420.0037-0.0176-27.66580.1487-28.9301
511.56723.9633-1.95923.50680.19930.68460.1803-0.74090.2270.1071-0.36170.0397-0.23280.25180.1814-0.018-0.0607-0.05050.09390.0449-0.0607-6.021622.36311.5518
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 106
2X-RAY DIFFRACTION2A110 - 213
3X-RAY DIFFRACTION3B1 - 114
4X-RAY DIFFRACTION4B120 - 216
5X-RAY DIFFRACTION5E287 - 302

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