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- PDB-5kn5: TGFalpha/Epiregulin complex with neutralizing antibody LY3016859 -

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Basic information

Entry
Database: PDB / ID: 5kn5
TitleTGFalpha/Epiregulin complex with neutralizing antibody LY3016859
Components
  • (Epiregulin Antibody LY3016859 Fab ...) x 2
  • Protransforming growth factor alpha
KeywordsIMMUNE SYSTEM / TGFalpha Epiregulin Antibody Fab
Function / homology
Function and homology information


hepatocyte proliferation / Cargo concentration in the ER / COPII-mediated vesicle transport / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / ERBB2-EGFR signaling pathway / epidermal growth factor receptor binding / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of cell division ...hepatocyte proliferation / Cargo concentration in the ER / COPII-mediated vesicle transport / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / ERBB2-EGFR signaling pathway / epidermal growth factor receptor binding / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of cell division / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / mammary gland alveolus development / GAB1 signalosome / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / positive regulation of epithelial cell proliferation / EGFR downregulation / growth factor activity / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / epidermal growth factor receptor signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / Clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / basolateral plasma membrane / angiogenesis / Estrogen-dependent gene expression / positive regulation of MAPK cascade / Extra-nuclear estrogen signaling / receptor ligand activity / intracellular signal transduction / positive regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Laminin / Laminin / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protransforming growth factor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAtwell, S. / Boyles, J.S. / Clawson, D.K. / Druzina, Z. / Josef, G.H. / Weichert, K. / Witcher, D.R.
CitationJournal: Protein Sci. / Year: 2016
Title: Structural basis of selectivity and neutralizing activity of a TGF alpha /epiregulin specific antibody.
Authors: Boyles, J.S. / Atwell, S. / Druzina, Z. / Heuer, J.G. / Witcher, D.R.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epiregulin Antibody LY3016859 Fab Heavy Chain
B: Epiregulin Antibody LY3016859 Fab Light Chain
C: Protransforming growth factor alpha
D: Epiregulin Antibody LY3016859 Fab Heavy Chain
E: Epiregulin Antibody LY3016859 Fab Light Chain
F: Protransforming growth factor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3618
Polymers103,1996
Non-polymers1612
Water2,702150
1
A: Epiregulin Antibody LY3016859 Fab Heavy Chain
B: Epiregulin Antibody LY3016859 Fab Light Chain
C: Protransforming growth factor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7615
Polymers51,6003
Non-polymers1612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-37 kcal/mol
Surface area21210 Å2
MethodPISA
2
D: Epiregulin Antibody LY3016859 Fab Heavy Chain
E: Epiregulin Antibody LY3016859 Fab Light Chain
F: Protransforming growth factor alpha


Theoretical massNumber of molelcules
Total (without water)51,6003
Polymers51,6003
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-48 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.249, 164.346, 64.972
Angle α, β, γ (deg.)90.000, 104.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Protransforming growth factor alpha


Mass: 4489.060 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01135

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Antibody , 2 types, 4 molecules ADBE

#1: Antibody Epiregulin Antibody LY3016859 Fab Heavy Chain


Mass: 23403.330 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Epiregulin Antibody LY3016859 Fab Light Chain


Mass: 23707.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 152 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.17 Å3/Da / Density % sol: 61.22 % / Description: thin plate
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100mM MES pH 6, 14% PEG 3350, 200mM Sodium Sulfate / PH range: 5.8-7.2

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 18, 2011
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.8→24.995 Å / Num. all: 31162 / Num. obs: 31162 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rpim(I) all: 0.077 / Rrim(I) all: 0.149 / Rsym value: 0.106 / Net I/av σ(I): 6.949 / Net I/σ(I): 9.6 / Num. measured all: 117046
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.8-2.953.80.6121.3199.9
2.95-3.133.80.3682.1199.8
3.13-3.353.80.2263.4199.7
3.35-3.613.70.1415.5198.3
3.61-3.963.60.1057.3194.8
3.96-4.433.80.06710.8198.4
4.43-5.113.80.05612.5198.5
5.11-6.263.80.05412.6199.2
6.26-8.853.80.04315.9199.4
8.85-24.9953.60.02821191.8

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→24.995 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.263 1017 -
Rwork0.2064 --
obs-30050 98.5 %
Displacement parametersBiso max: 146.6 Å2 / Biso mean: 48.3199 Å2 / Biso min: 11.87 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7128 0 6 150 7284

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