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- PDB-7d85: Crystal structure of anti-ErbB3 Fab ISU104 in complex with human ... -

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Basic information

Entry
Database: PDB / ID: 7d85
TitleCrystal structure of anti-ErbB3 Fab ISU104 in complex with human ErbB3 extracellular domain 3
Components
  • Anti-ErbB3 Fab heavy chain
  • Anti-ErbB3 Fab light chain
  • Receptor tyrosine-protein kinase erbB-3
KeywordsIMMUNE SYSTEM / Transferase/Immune System
Function / homology
Function and homology information


neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade ...neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / ERBB3:ERBB2 complex / GRB7 events in ERBB2 signaling / positive regulation of calcineurin-NFAT signaling cascade / peripheral nervous system development / ErbB-3 class receptor binding / negative regulation of cell adhesion / negative regulation of motor neuron apoptotic process / motor neuron apoptotic process / ERBB2 Activates PTK6 Signaling / ERBB2-ERBB3 signaling pathway / protein tyrosine kinase activator activity / Signaling by ERBB4 / growth factor binding / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / lateral plasma membrane / Schwann cell development / negative regulation of signal transduction / extrinsic apoptotic signaling pathway in absence of ligand / Signaling by ERBB2 / myelination / Downregulation of ERBB2:ERBB3 signaling / SHC1 events in ERBB2 signaling / neurogenesis / basal plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 TMD/JMD mutants / wound healing / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / heart development / regulation of cell population proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / basolateral plasma membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein kinase activity / apical plasma membrane / protein heterodimerization activity / phosphorylation / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / signal transduction / extracellular space / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
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 ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsYoo, Y. / Cho, H.S.
CitationJournal: Mol.Cancer Ther. / Year: 2021
Title: A Novel Therapeutic Anti-ErbB3, ISU104 Exhibits Potent Antitumorigenic Activity by Inhibiting Ligand Binding and ErbB3 Heterodimerization.
Authors: Hong, M. / Yoo, Y. / Kim, M. / Kim, J.Y. / Cha, J.S. / Choi, M.K. / Kim, U. / Kim, K. / Sohn, Y. / Bae, D. / Cho, H.S. / Hong, S.B.
History
DepositionOct 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor tyrosine-protein kinase erbB-3
B: Anti-ErbB3 Fab heavy chain
C: Anti-ErbB3 Fab light chain
D: Receptor tyrosine-protein kinase erbB-3
E: Anti-ErbB3 Fab heavy chain
F: Anti-ErbB3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,36113
Polymers136,8136
Non-polymers1,5487
Water70339
1
A: Receptor tyrosine-protein kinase erbB-3
B: Anti-ErbB3 Fab heavy chain
C: Anti-ErbB3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2917
Polymers68,4073
Non-polymers8854
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-10 kcal/mol
Surface area27320 Å2
MethodPISA
2
D: Receptor tyrosine-protein kinase erbB-3
E: Anti-ErbB3 Fab heavy chain
F: Anti-ErbB3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0706
Polymers68,4073
Non-polymers6643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-14 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.290, 77.780, 93.940
Angle α, β, γ (deg.)90.000, 113.410, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Receptor tyrosine-protein kinase erbB-3 / Proto-oncogene-like protein c-ErbB-3 / Tyrosine kinase-type cell surface receptor HER3


Mass: 21490.555 Da / Num. of mol.: 2 / Fragment: extracellular domain 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB3, HER3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21860, receptor protein-tyrosine kinase
#2: Antibody Anti-ErbB3 Fab heavy chain


Mass: 24252.021 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)
#3: Antibody Anti-ErbB3 Fab light chain


Mass: 22663.936 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)
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium acetate, 20%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→46.63 Å / Num. obs: 42145 / % possible obs: 99.2 % / Redundancy: 2 % / Biso Wilson estimate: 36.1 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.09686 / Net I/σ(I): 6.56
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5366 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 4195 / CC1/2: 0.647 / CC star: 0.886 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→46.63 Å / SU ML: 0.365 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.8568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 1247 2.96 %
Rwork0.2026 40878 -
obs0.2043 42125 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.33 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9402 0 98 39 9539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00979728
X-RAY DIFFRACTIONf_angle_d1.177913236
X-RAY DIFFRACTIONf_chiral_restr0.06681496
X-RAY DIFFRACTIONf_plane_restr0.00911698
X-RAY DIFFRACTIONf_dihedral_angle_d20.21323499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.33511370.27854528X-RAY DIFFRACTION99.76
2.6-2.720.31251340.27114516X-RAY DIFFRACTION99.32
2.72-2.860.34931360.2664520X-RAY DIFFRACTION99.19
2.86-3.040.37751400.25284542X-RAY DIFFRACTION99.77
3.04-3.280.30011440.23984544X-RAY DIFFRACTION99.66
3.28-3.610.26851360.21164502X-RAY DIFFRACTION98.68
3.61-4.130.24541380.17784580X-RAY DIFFRACTION99.68
4.13-5.20.1921410.14764541X-RAY DIFFRACTION98.76
5.2-46.630.19061410.17124605X-RAY DIFFRACTION98.18

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