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- PDB-4p59: HER3 extracellular domain in complex with Fab fragment of MOR09825 -

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Basic information

Entry
Database: PDB / ID: 4p59
TitleHER3 extracellular domain in complex with Fab fragment of MOR09825
Components
  • (MOR09825 Fab fragment ...) x 2
  • Receptor tyrosine-protein kinase erbB-3
KeywordsSignaling protein / immune system / Her3 receptor / therapeutic antibody / Fab fragment / anti-Her3
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 / ERBB2 Regulates Cell Motility / growth factor binding / PI3K events in ERBB2 signaling / lateral plasma membrane / Schwann cell development / negative regulation of signal transduction / Signaling by ERBB2 / extrinsic apoptotic signaling pathway in absence of ligand / myelination / Downregulation of ERBB2:ERBB3 signaling / neurogenesis / SHC1 events in ERBB2 signaling / basal plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signaling by ERBB2 TMD/JMD mutants / wound healing / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / regulation of cell population proliferation / heart development / 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
24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Receptor L-domain / Furin-like cysteine-rich domain ...24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / 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 / Ribbon / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSprague, E.R.
CitationJournal: Cancer Res. / Year: 2013
Title: An antibody that locks HER3 in the inactive conformation inhibits tumor growth driven by HER2 or neuregulin.
Authors: Garner, A.P. / Bialucha, C.U. / Sprague, E.R. / Garrett, J.T. / Sheng, Q. / Li, S. / Sineshchekova, O. / Saxena, P. / Sutton, C.R. / Chen, D. / Chen, Y. / Wang, H. / Liang, J. / Das, R. / ...Authors: Garner, A.P. / Bialucha, C.U. / Sprague, E.R. / Garrett, J.T. / Sheng, Q. / Li, S. / Sineshchekova, O. / Saxena, P. / Sutton, C.R. / Chen, D. / Chen, Y. / Wang, H. / Liang, J. / Das, R. / Mosher, R. / Gu, J. / Huang, A. / Haubst, N. / Zehetmeier, C. / Haberl, M. / Elis, W. / Kunz, C. / Heidt, A.B. / Herlihy, K. / Murtie, J. / Schuller, A. / Arteaga, C.L. / Sellers, W.R. / Ettenberg, S.A.
History
DepositionMar 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Feb 25, 2015Group: Derived calculations
Revision 1.4Mar 18, 2015Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
H: MOR09825 Fab fragment heavy chain
L: MOR09825 Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4208
Polymers117,9073
Non-polymers1,5125
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-12 kcal/mol
Surface area48220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.226, 140.939, 180.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody MOR09825 Fab fragment heavy chain


Mass: 25480.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody MOR09825 Fab fragment light chain


Mass: 23262.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein / Non-polymers , 2 types, 4 molecules A

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


Mass: 69164.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB3, HER3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: P21860, receptor protein-tyrosine kinase
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 5 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 3 / 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

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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: 3.5 Å3/Da / Density % sol: 64.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM bis-tris pH 6.5, 16% (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→111.03 Å / Num. all: 22112 / Num. obs: 22112 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 74.13 Å2 / Rpim(I) all: 0.053 / Rrim(I) all: 0.139 / Rsym value: 0.118 / Net I/av σ(I): 6.714 / Net I/σ(I): 14.6 / Num. measured all: 148197
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.4-3.586.80.4611.72158831670.2080.4613.899.9
3.58-3.87.10.3192.52139830340.140.3195.6100
3.8-4.066.90.2173.61966128370.0960.2177.9100
4.06-4.396.70.1515.21785326530.0680.15111.3100
4.39-4.816.30.1057.41544924380.050.10515.3100
4.81-5.386.50.0948.31457222310.0430.09417.2100
5.38-6.216.90.0918.61366119750.040.09117.9100
6.21-7.66.60.06911.31116016820.0320.06922.3100
7.6-10.756.10.03222.4804813240.0160.03238.8100
10.75-111.0276.20.02426.548077710.0110.02454.198.9

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.4refinement
PDB_EXTRACT3.14data extraction
BUSTER2.11.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M6B

1m6b


Resolution: 3.4→111.03 Å / Cor.coef. Fo:Fc: 0.8891 / Cor.coef. Fo:Fc free: 0.8422 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.494
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1132 5.12 %RANDOM
Rwork0.1842 ---
obs0.1874 22111 99.79 %-
Displacement parametersBiso max: 246.71 Å2 / Biso mean: 97.29 Å2 / Biso min: 32.14 Å2
Baniso -1Baniso -2Baniso -3
1-3.8681 Å20 Å20 Å2
2--25.5365 Å20 Å2
3----29.4046 Å2
Refinement stepCycle: final / Resolution: 3.4→111.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7733 0 98 3 7834
Biso mean--130.68 46.64 -
Num. residues----1013
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2724SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes187HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1181HARMONIC5
X-RAY DIFFRACTIONt_it8050HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1055SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8811SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8050HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg10961HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion25.59
LS refinement shellResolution: 3.4→3.57 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2498 156 5.42 %
Rwork0.1923 2720 -
all0.1955 2876 -
obs--99.79 %
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)
11.9062-1.4869-0.80846.44470.52292.594-0.1135-0.578-0.5890.80580.03991.08850.3578-0.31740.0736-0.354-0.0910.2367-0.21160.05640.4219-49.5842-84.9384-31.9008
22.1944-0.65310.78437.90830.93470.04090.0162-0.3473-0.43290.58650.0371-0.24070.0764-0.3081-0.0532-0.14470.0140.0159-0.30240.0937-0.0005-39.9567-56.1696-34.6455
34.51780.56240.61012.95140.29744.2372-0.2024-0.2153-0.0418-0.24710.25290.4097-0.5079-1.0885-0.0505-0.04260.298-0.17730.32090.0044-0.4508-26.5765-33.718910.8075
41.51230.11110.63083.0236-0.08155.0016-0.1725-0.1714-0.05440.5121-0.1149-0.8701-0.5780.25890.2874-0.22610.0943-0.209-0.30830.05810.2444-24.1172-27.2704-33
54.4482-2.0929-0.32393.06591.09882.478-0.1566-0.11420.15740.64470.0237-0.13710.28180.2250.1329-0.04630.028-0.0605-0.14430.0070.0399-50.2437-23.3191-34.5204
64.69922.75091.72733.22541.16380.64180.0074-0.06560.2182-0.17060.01280.4849-0.1181-0.3372-0.0202-0.1568-0.0166-0.1007-0.20430.08960.3709-77.0941-14.1345-46.1947
74.9862-1.73860.91753.2333-0.28550.64330.08140.7665-0.0008-0.8017-0.2331-0.42940.10080.21470.1516-0.06190.08870.014-0.0142-0.0097-0.0692-47.1279-27.5556-56.4203
84.076-3.3108-0.37296.71553.25225.68550.03910.6490.725-0.6974-0.18220.6099-0.5084-0.11460.1431-0.26710.015-0.1943-0.2220.2040.3758-75.9494-5.0488-59.8187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|26 - A|207 }A26 - 207
2X-RAY DIFFRACTION2{ A|208 - A|328 }A208 - 328
3X-RAY DIFFRACTION3{ A|329 - A|518 }A329 - 518
4X-RAY DIFFRACTION4{ A|519 - A|631 }A519 - 631
5X-RAY DIFFRACTION5{ H|2 - H|117 }H2 - 117
6X-RAY DIFFRACTION6{ H|118 - H|217 }H118 - 217
7X-RAY DIFFRACTION7{ L|1 - L|106 }L1 - 106
8X-RAY DIFFRACTION8{ L|107 - L|211 }L107 - 211

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