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- PDB-3g5v: Antibodies Specifically Targeting a Locally Misfolded Region of T... -

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Basic information

Entry
Database: PDB / ID: 3g5v
TitleAntibodies Specifically Targeting a Locally Misfolded Region of Tumor Associated EGFR
Components
  • 806 light chain
  • 808 heavy chain
  • Epidermal Growth Factor Receptor peptide
KeywordsIMMUNE SYSTEM / antibody
Function / homology
Function and homology information


response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity ...response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / regulation of nitric-oxide synthase activity / ERBB2 Activates PTK6 Signaling / morphogenesis of an epithelial fold / intracellular vesicle / Signaling by EGFR / response to cobalamin / negative regulation of epidermal growth factor receptor signaling pathway / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / Signaling by ERBB4 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein insertion into membrane / eyelid development in camera-type eye / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / regulation of JNK cascade / activation of phospholipase C activity / positive regulation of cyclin-dependent protein serine/threonine kinase activity / PI3K events in ERBB2 signaling / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / positive regulation of bone resorption / positive regulation of DNA replication / GAB1 signalosome / positive regulation of nitric oxide mediated signal transduction / salivary gland morphogenesis / regulation of peptidyl-tyrosine phosphorylation / peptidyl-tyrosine autophosphorylation / positive regulation of glial cell proliferation / positive regulation of phosphorylation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / cellular response to cadmium ion / positive regulation of DNA repair / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / neurogenesis / cellular response to dexamethasone stimulus / SHC1 events in ERBB2 signaling / ossification / positive regulation of synaptic transmission, glutamatergic / basal plasma membrane / regulation of ERK1 and ERK2 cascade / neuron projection morphogenesis / positive regulation of superoxide anion generation / Signal transduction by L1 / epithelial cell proliferation / cellular response to estradiol stimulus / liver regeneration / positive regulation of epithelial cell proliferation / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / cellular response to amino acid stimulus / positive regulation of protein localization to plasma membrane / EGFR downregulation / clathrin-coated endocytic vesicle membrane / positive regulation of smooth muscle cell proliferation / lung development / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / positive regulation of MAP kinase activity / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / negative regulation of protein catabolic process / cell-cell adhesion / receptor protein-tyrosine kinase / ruffle membrane / Downregulation of ERBB2 signaling / kinase binding
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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Epidermal growth factor receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsGarrett, T.P.J. / Burgess, A.W. / Huyton, T. / Xu, Y.
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 / Refinement description / Version format compliance
Revision 1.2Oct 12, 2011Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 806 light chain
B: 808 heavy chain
C: Epidermal Growth Factor Receptor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2569
Polymers47,9083
Non-polymers3486
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-28 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.925, 83.161, 72.214
Angle α, β, γ (deg.)90.00, 92.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Epidermal Growth Factor Receptor peptide


Mass: 1793.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis / References: UniProt: P00533*PLUS

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Antibody , 2 types, 2 molecules AB

#1: Antibody 806 light chain


Mass: 23333.547 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 808 heavy chain


Mass: 22780.312 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)

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Non-polymers , 4 types, 205 molecules

#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2M ammonium acetate, 16-18% PEG5000 monomethylether, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 27692 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.066
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.282 / % possible all: 79.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→41.581 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0 / SU B: 13.044 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.36 / ESU R: 0.247 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1389 5 %RANDOM
Rwork0.226 ---
obs0.229 26284 96.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: MASK / Bsol: 49.572 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 63.61 Å2 / Biso mean: 33.822 Å2 / Biso min: 15.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å20.56 Å2
2---0.26 Å20 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.001→41.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3285 0 23 199 3507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223357
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.9484566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4335428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23924.552134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14715514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8021511
X-RAY DIFFRACTIONr_chiral_restr0.0750.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022545
X-RAY DIFFRACTIONr_nbd_refined0.1970.21416
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.215
X-RAY DIFFRACTIONr_mcbond_it0.3111.52206
X-RAY DIFFRACTIONr_mcangle_it0.51923449
X-RAY DIFFRACTIONr_scbond_it0.79631355
X-RAY DIFFRACTIONr_scangle_it1.24.51114
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 73 -
Rwork0.292 1494 -
all-1567 -
obs--76.63 %
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)
12.2386-1.4087-0.05944.19160.84955.578-0.1549-0.1391-0.00980.33240.15910.0355-0.47840.036-0.0042-0.1935-0.05260.0197-0.24290.0027-0.177819.607513.50857.9564
21.08440.9729-1.12275.0017-6.197914.4080.14230.19430.16990.19330.48610.1181-0.3868-1.5761-0.6284-0.16610.02180.0630.15670.0766-0.12748.2119-1.723640.6997
31.87230.17140.72133.57030.93576.84660.1514-0.0526-0.04360.50390.0641-0.05990.8628-0.1784-0.2154-0.0921-0.0662-0.0045-0.28180.012-0.212616.7538-6.96581.2004
41.9868-0.013-1.09597.81380.7959.8353-0.0087-0.1015-0.1413-0.49990.38820.95041.1858-2.8785-0.37950.0476-0.4163-0.12750.96240.2653-0.06660.225-8.101927.7182
56.03119.05950.405916.8496-3.61299.2349-0.55620.66960.1062-0.97040.6148-0.8586-1.12790.9224-0.05870.0228-0.14170.1115-0.0134-0.0303-0.0825.015211.1485-11.4584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2A109 - 212
3X-RAY DIFFRACTION3B1 - 117
4X-RAY DIFFRACTION4B118 - 213
5X-RAY DIFFRACTION5C287 - 302

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