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- PDB-5kwg: Crystal structure of extracellular domain of HER2 in complex with... -

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Basic information

Entry
Database: PDB / ID: 5kwg
TitleCrystal structure of extracellular domain of HER2 in complex with Fcab H10-03-6
Components
  • Ig gamma-1 chain C region
  • Receptor tyrosine-protein kinase erbB-2
KeywordsIMMUNE SYSTEM / antibody engineering / immunoglobulin G1 / Fc fragment / glycosylations / CH3 domain / Fcab / human epidermal growth factor receptor 2 / HER2/neu / erbB-2 / cell surface receptor
Function / homology
Function and homology information


negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / Fc-gamma receptor I complex binding / regulation of microtubule-based process / ErbB-3 class receptor binding / complement-dependent cytotoxicity ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / Fc-gamma receptor I complex binding / regulation of microtubule-based process / ErbB-3 class receptor binding / complement-dependent cytotoxicity / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse / IgG immunoglobulin complex / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / antibody-dependent cellular cytotoxicity / PLCG1 events in ERBB2 signaling / Classical antibody-mediated complement activation / neuromuscular junction development / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / positive regulation of Rho protein signal transduction / Initial triggering of complement / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / enzyme-linked receptor protein signaling pathway / positive regulation of transcription by RNA polymerase I / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of cell adhesion / FCGR activation / positive regulation of protein targeting to membrane / Role of phospholipids in phagocytosis / regulation of angiogenesis / coreceptor activity / Schwann cell development / Signaling by ERBB2 / immunoglobulin complex, circulating / cellular response to epidermal growth factor stimulus / immunoglobulin receptor binding / cell surface receptor protein tyrosine kinase signaling pathway / GRB2 events in ERBB2 signaling / myelination / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / Downregulation of ERBB2:ERBB3 signaling / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / FCGR3A-mediated IL10 synthesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neurogenesis / regulation of ERK1 and ERK2 cascade / basal plasma membrane / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of epithelial cell proliferation / positive regulation of translation / FCGR3A-mediated phagocytosis / antigen binding / Signaling by ERBB2 TMD/JMD mutants / B cell receptor signaling pathway / positive regulation of MAP kinase activity / wound healing / Signaling by ERBB2 ECD mutants / neuromuscular junction / neuron differentiation / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / Regulation of actin dynamics for phagocytic cup formation / cellular response to growth factor stimulus / Downregulation of ERBB2 signaling / ruffle membrane / peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / myelin sheath / presynaptic membrane / heart development / antibacterial humoral response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / positive regulation of MAPK cascade
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. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Tyrosine-protein kinase, active site / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsHumm, A. / Lobner, E. / Goritzer, K. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K.
Funding support Austria, 2items
OrganizationGrant numberCountry
Christian Doppler Research AssociationChristian Doppler Laboratory for Antibody Engineering Austria
Austrian Science FundFWF W1224 (Doctoral Program on Biomolecular Technology of Proteins , BioToP) Austria
CitationJournal: Structure / Year: 2017
Title: Fcab-HER2 Interaction: a Menage a Trois. Lessons from X-Ray and Solution Studies.
Authors: Lobner, E. / Humm, A.S. / Goritzer, K. / Mlynek, G. / Puchinger, M.G. / Hasenhindl, C. / Ruker, F. / Traxlmayr, M.W. / Djinovic-Carugo, K. / Obinger, C.
History
DepositionJul 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
C: Receptor tyrosine-protein kinase erbB-2
A: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)95,2782
Polymers95,2782
Non-polymers00
Water00
1
C: Receptor tyrosine-protein kinase erbB-2
A: Ig gamma-1 chain C region

C: Receptor tyrosine-protein kinase erbB-2
A: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)190,5564
Polymers190,5564
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
MethodPISA
Unit cell
Length a, b, c (Å)109.770, 109.770, 176.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Receptor tyrosine-protein kinase erbB-2 / Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / ...Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / Tyrosine kinase-type cell surface receptor HER2 / p185erbB2


Mass: 69507.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB2, HER2, MLN19, NEU, NGL / Cell line (production host): CHO Lec1 / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P04626, receptor protein-tyrosine kinase
#2: Protein Ig gamma-1 chain C region


Mass: 25770.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Plasmid: Plasmid / Cell line (production host): HEK 293-6E / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P01857

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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: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 50 mM Citric acid, 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 5, 2015 / Details: CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 4.3→47.532 Å / Num. all: 55512 / Num. obs: 8755 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 174.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1898 / Net I/σ(I): 6.48
Reflection shellResolution: 4.3→4.454 Å / Redundancy: 6 % / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 0.99 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2247: ???)refinement
EDNAdata collection
XDSv.Oct-2015data reduction
XDSv.Oct-2015data scaling
PHENIX1.10-2247phasing
XDSv.Oct-2015data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K33

5k33


Resolution: 4.3→47.532 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 41.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3686 1606 9.97 %
Rwork0.3237 --
obs0.3283 8754 99.86 %
all-16114 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.3→47.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6025 0 0 0 6025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026191
X-RAY DIFFRACTIONf_angle_d0.5958437
X-RAY DIFFRACTIONf_dihedral_angle_d8.4583755
X-RAY DIFFRACTIONf_chiral_restr0.043928
X-RAY DIFFRACTIONf_plane_restr0.0041105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3004-4.43910.36581520.39981300X-RAY DIFFRACTION100
4.4391-4.59760.38011470.38381344X-RAY DIFFRACTION100
4.5976-4.78160.39811420.38851353X-RAY DIFFRACTION100
4.7816-4.9990.37011500.37321289X-RAY DIFFRACTION100
4.999-5.26220.40321530.38831291X-RAY DIFFRACTION100
5.2622-5.59140.40061440.3711321X-RAY DIFFRACTION100
5.5914-6.02230.38231380.37981332X-RAY DIFFRACTION100
6.0223-6.6270.43871370.35591321X-RAY DIFFRACTION100
6.627-7.58250.35761480.31171323X-RAY DIFFRACTION100
7.5825-9.54050.36331430.32371315X-RAY DIFFRACTION100
9.5405-47.53470.33741520.24791319X-RAY DIFFRACTION100
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)
17.1196-3.6312-0.39736.04773.0571.9273-0.5614-0.3228-0.03510.75890.3911-1.04120.7263-0.06250.00012.02990.00120.11382.1659-0.14531.893955.59812.872-4.5736
21.6341-1.44720.70835.1544-2.52111.1892-0.41220.4997-1.3225-0.66860.1748-0.36580.6561-0.522501.80870.0383-0.03271.9913-0.14992.417949.1028.113-34.0927
30.80081.38051.81974.92052.23434.7181-0.94270.08130.1631.6293-0.3841.31510.19490.4945-0.91070.99570.4459-0.02492.8202-0.47071.918226.324521.8094-45.9081
41.8583-0.8748-2.24940.6570.95332.7242-1.4850.089-0.14551.07481.74310.4087-1.66410.9454-0.00112.8479-0.13060.11274.0218-0.60183.0939-31.27718.0373-42.8983
52.2005-4.88320.39292.0011-0.26325.1080.3010.1919-0.6339-2.5214-2.1043-1.4654-1.1603-0.0601-0.83511.9031-0.2515-0.63333.0847-0.25972.89423.77686.1212-61.562
65.37330.69274.38210.1060.52673.56780.4543-0.3188-0.54590.5668-1.82370.1535-0.60350.0382-0.00062.16980.333-0.11252.9564-0.56422.2004-3.45936.2524-50.1383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 224 )
2X-RAY DIFFRACTION2chain 'C' and (resid 225 through 429 )
3X-RAY DIFFRACTION3chain 'C' and (resid 430 through 575 )
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 346 )
5X-RAY DIFFRACTION5chain 'A' and (resid 347 through 364 )
6X-RAY DIFFRACTION6chain 'A' and (resid 365 through 443 )

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