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- PDB-5e8d: Crystal structure of human epiregulin in complex with the Fab fra... -

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Basic information

Entry
Database: PDB / ID: 5e8d
TitleCrystal structure of human epiregulin in complex with the Fab fragment of murine monoclonal antibody 9E5
Components
  • (anti-human epiregulin antibody 9E5 Fab ...) x 2
  • Proepiregulin
KeywordsIMMUNE SYSTEM / Antibody / Immunoglobulin / Monoclonal antibody / Epidermal growth factor / Cancer
Function / homology
Function and homology information


luteinizing hormone signaling pathway / ovarian cumulus expansion / ovulation / ERBB4-ERBB4 signaling pathway / negative regulation of smooth muscle cell differentiation / ERBB2-ERBB4 signaling pathway / primary follicle stage / female meiotic nuclear division / PI3K events in ERBB4 signaling / oocyte maturation ...luteinizing hormone signaling pathway / ovarian cumulus expansion / ovulation / ERBB4-ERBB4 signaling pathway / negative regulation of smooth muscle cell differentiation / ERBB2-ERBB4 signaling pathway / primary follicle stage / female meiotic nuclear division / PI3K events in ERBB4 signaling / oocyte maturation / positive regulation of innate immune response / mRNA transcription / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / ERBB2-EGFR signaling pathway / epidermal growth factor receptor binding / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / Signaling by ERBB4 / ERBB2 Regulates Cell Motility / positive regulation of cell division / PI3K events in ERBB2 signaling / keratinocyte proliferation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / SHC1 events in ERBB4 signaling / anatomical structure morphogenesis / positive regulation of protein kinase activity / GAB1 signalosome / Nuclear signaling by ERBB4 / positive regulation of phosphorylation / keratinocyte differentiation / Signaling by ERBB2 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / positive regulation of mitotic nuclear division / positive regulation of DNA replication / positive regulation of cytokine production / EGFR downregulation / clathrin-coated endocytic vesicle membrane / animal organ morphogenesis / positive regulation of smooth muscle cell proliferation / Signaling by ERBB2 TMD/JMD mutants / growth factor activity / wound healing / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / response to peptide hormone / Downregulation of ERBB2 signaling / positive regulation of interleukin-6 production / cytokine-mediated signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of fibroblast proliferation / negative regulation of epithelial cell proliferation / Cargo recognition for clathrin-mediated endocytosis / cell-cell signaling / PIP3 activates AKT signaling / Clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / Extra-nuclear estrogen signaling / receptor ligand activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / 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
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKado, Y. / Mizohata, E. / Nagatoishi, S. / Iijima, M. / Shinoda, K. / Miyafusa, T. / Nakayama, T. / Yoshizumi, T. / Sugiyama, A. / Kawamura, T. ...Kado, Y. / Mizohata, E. / Nagatoishi, S. / Iijima, M. / Shinoda, K. / Miyafusa, T. / Nakayama, T. / Yoshizumi, T. / Sugiyama, A. / Kawamura, T. / Lee, Y.H. / Matsumura, H. / Doi, H. / Fujitani, H. / Kodama, T. / Shibasaki, Y. / Tsumoto, K. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Cabinet Office, Government of Japan and the Japan Society for the Promotion of Science Japan
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES
Authors: Kado, Y. / Mizohata, E. / Nagatoishi, S. / Iijima, M. / Shinoda, K. / Miyafusa, T. / Nakayama, T. / Yoshizumi, T. / Sugiyama, A. / Kawamura, T. / Lee, Y.H. / Matsumura, H. / Doi, H. / ...Authors: Kado, Y. / Mizohata, E. / Nagatoishi, S. / Iijima, M. / Shinoda, K. / Miyafusa, T. / Nakayama, T. / Yoshizumi, T. / Sugiyama, A. / Kawamura, T. / Lee, Y.H. / Matsumura, H. / Doi, H. / Fujitani, H. / Kodama, T. / Shibasaki, Y. / Tsumoto, K. / Inoue, T.
History
DepositionOct 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Feb 17, 2016Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proepiregulin
H: anti-human epiregulin antibody 9E5 Fab heavy chain
L: anti-human epiregulin antibody 9E5 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6086
Polymers55,3893
Non-polymers2203
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-31 kcal/mol
Surface area21350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.602, 100.291, 187.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11H-402-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Proepiregulin


Mass: 8254.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EREG / Production host: Escherichia coli (E. coli) / References: UniProt: O14944

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Antibody , 2 types, 2 molecules HL

#2: Antibody anti-human epiregulin antibody 9E5 Fab heavy chain


Mass: 23528.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody anti-human epiregulin antibody 9E5 Fab light chain


Mass: 23606.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 3 types, 40 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 2-(N-morphilino)ethansulfonic acid monohydrate, PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 22299 / % possible obs: 97.3 % / Redundancy: 4.5 % / Net I/σ(I): 28.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→14.908 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0.25 / Phase error: 26.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 1130 5.14 %
Rwork0.1897 --
obs0.1934 22005 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→14.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3610 0 13 37 3660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093713
X-RAY DIFFRACTIONf_angle_d1.3295035
X-RAY DIFFRACTIONf_dihedral_angle_d15.0281335
X-RAY DIFFRACTIONf_chiral_restr0.048562
X-RAY DIFFRACTIONf_plane_restr0.007641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61320.35421360.29512451X-RAY DIFFRACTION93
2.6132-2.75020.32521490.26412491X-RAY DIFFRACTION94
2.7502-2.92130.29531380.23172559X-RAY DIFFRACTION96
2.9213-3.14490.27691560.21142570X-RAY DIFFRACTION97
3.1449-3.45780.30641380.19762632X-RAY DIFFRACTION98
3.4578-3.950.27181350.18572661X-RAY DIFFRACTION99
3.95-4.94620.24721410.16222705X-RAY DIFFRACTION99
4.9462-14.90840.22281370.17442806X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -14.6805 Å / Origin y: -12.6538 Å / Origin z: 27.0353 Å
111213212223313233
T0.5194 Å20.1928 Å2-0.0183 Å2-0.6438 Å2-0.0053 Å2--0.4633 Å2
L0.8629 °2-0.2966 °2-0.2364 °2-2.8106 °2-0.4385 °2--0.9352 °2
S-0.1775 Å °-0.3697 Å °-0.2143 Å °0.5717 Å °0.1751 Å °0.0243 Å °0.1305 Å °0.3282 Å °-0.0024 Å °
Refinement TLS groupSelection details: all

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