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- PDB-5my6: Crystal structure of a HER2-Nb complex -

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Basic information

Entry
Database: PDB / ID: 5my6
TitleCrystal structure of a HER2-Nb complex
Components
  • Nanobody 2Rs15d
  • Receptor tyrosine-protein kinase erbB-2
KeywordsTRANSFERASE / Nanobody / Her2 / EGFR family / radio-labeling
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 / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse ...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 / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / neuromuscular junction development / positive regulation of Rho protein signal transduction / ERBB2 Activates PTK6 Signaling / 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 / positive regulation of protein targeting to membrane / regulation of angiogenesis / coreceptor activity / Schwann cell development / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / myelination / Downregulation of ERBB2:ERBB3 signaling / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / neurogenesis / basal plasma membrane / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of translation / positive regulation of epithelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / neuromuscular junction / Signaling by ERBB2 ECD mutants / neuron differentiation / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / cellular response to growth factor stimulus / Downregulation of ERBB2 signaling / ruffle membrane / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / presynaptic membrane / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / positive regulation of MAPK cascade / early endosome / cell surface receptor signaling pathway / receptor complex / endosome membrane / intracellular signal transduction / apical plasma membrane / positive regulation of protein phosphorylation / protein heterodimerization activity / protein phosphorylation / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane
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. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.246 Å
AuthorsSterckx, Y.G.-J. / D'Huyvetter, M. / Devoogdt, N.
Funding support Belgium, 5items
OrganizationGrant numberCountry
FWO-Vlaanderen Belgium
Innoviris.Brussels Belgium
Stichting Tegen Kanker Belgium
BAEF Belgium
Germaine Eisendrath-Dubois Foundation Belgium
CitationJournal: Clin. Cancer Res. / Year: 2017
Title: (131)I-labeled Anti-HER2 Camelid sdAb as a Theranostic Tool in Cancer Treatment.
Authors: D'Huyvetter, M. / De Vos, J. / Xavier, C. / Pruszynski, M. / Sterckx, Y.G.J. / Massa, S. / Raes, G. / Caveliers, V. / Zalutsky, M.R. / Lahoutte, T. / Devoogdt, N.
History
DepositionJan 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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 2.1Jan 17, 2024Group: 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-2
B: Nanobody 2Rs15d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0376
Polymers81,2072
Non-polymers8304
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint2 kcal/mol
Surface area30720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.520, 113.520, 137.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#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: 68564.859 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): HEK293F / Production host: Homo sapiens (human)
References: UniProt: P04626, receptor protein-tyrosine kinase
#2: Antibody Nanobody 2Rs15d


Mass: 12642.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6

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Sugars , 2 types, 2 molecules

#3: 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.: 1 / Source method: isolated from a natural source
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
#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.: 1 / Source method: isolated from a natural source / 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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Non-polymers , 2 types, 372 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.25 / Details: 100 mM HEPES pH 7.25, 10% 2-propanol, 22% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.246→47.794 Å / Num. all: 162919 / Num. obs: 49524 / % possible obs: 98.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 39.5 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.1031 / Net I/σ(I): 9.65
Reflection shellResolution: 2.246→2.326 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 4790 / Num. unique obs: 4790 / CC1/2: 0.664 / Rrim(I) all: 0.7091 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S78

1s78


Resolution: 2.246→47.794 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 2476 5 %RANDOM
Rwork0.1848 47045 --
obs0.1866 49521 98.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.42 Å2 / Biso mean: 49.2832 Å2 / Biso min: 18.87 Å2
Refinement stepCycle: final / Resolution: 2.246→47.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5109 0 54 370 5533
Biso mean--81.35 48.02 -
Num. residues----671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065352
X-RAY DIFFRACTIONf_angle_d0.8737298
X-RAY DIFFRACTIONf_chiral_restr0.065810
X-RAY DIFFRACTIONf_plane_restr0.005957
X-RAY DIFFRACTIONf_dihedral_angle_d13.3823242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2456-2.28880.29411300.2672466259693
2.2888-2.33550.28741350.25162572270799
2.3355-2.38630.31191360.24542572270898
2.3863-2.44180.2851380.243626252763100
2.4418-2.50290.28381380.233326202758100
2.5029-2.57060.26861380.221926252763100
2.5706-2.64620.25881380.21122615275399
2.6462-2.73160.27311370.20342605274299
2.7316-2.82920.23691380.20782618275699
2.8292-2.94250.24961350.20282566270197
2.9425-3.07640.22221380.18232638277699
3.0764-3.23850.27811390.18732630276999
3.2385-3.44140.21081370.17482606274398
3.4414-3.7070.2091390.17272641278099
3.707-4.07990.20521360.1542582271897
4.0799-4.66980.14821390.14252647278698
4.6698-5.88180.21581410.16082663280497
5.8818-47.80470.18161440.20262754289896
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)
11.88780.50920.5192.07960.47431.48850.01150.1962-0.1989-0.12370.018-0.15210.08090.225-0.02570.21790.0460.01290.27110.00760.214323.4189-31.2554-24.5569
20.204-0.35850.38142.0885-0.0651.4245-0.05550.22290.0664-0.2617-0.05770.2868-0.02980.11430.09530.365-0.0074-0.02860.27950.05810.28379.6718-13.1916-41.0491
31.89680.06340.40451.72640.41571.96090.03510.3222-0.0399-0.3821-0.00050.20910.1062-0.2165-0.03970.3212-0.0112-0.0960.2833-0.02750.3276-10.8399-45.9289-40.1611
46.1062-0.784-3.0245.2999-1.03172.69790.2478-0.4830.4290.6021-0.2396-0.8577-0.68641.13920.12250.3191-0.1129-0.01180.5319-0.01960.300321.8809-16.27612.9409
52.35110.6745-1.26271.7311-1.1784.01950.3608-0.41120.0560.2226-0.34250.1597-0.51470.3562-0.00090.2322-0.02710.020.2875-0.00310.26212.5458-18.01961.7922
67.8066-1.5019-0.33417.4672-3.36679.313-0.2696-0.2265-0.6554-0.22690.0715-0.02481.55460.61520.20220.45380.09180.05810.38980.05120.333114.9762-29.1095-2.9746
75.0882.8757-1.74325.6963-0.67793.5838-0.08080.3202-0.1826-0.30510.00310.0636-0.012-0.50640.01460.25990.04590.03610.3480.01710.2817.4925-22.4411-9.7814
86.87654.45540.2279.82080.68333.9487-0.17190.17930.3603-0.1040.29320.1656-0.432-0.2957-0.14360.29470.04130.05590.3720.02190.33227.4122-15.9544-0.7155
92.22380.8574-1.42821.6878-1.41263.0623-0.0795-0.2318-0.24120.0187-0.1692-0.06850.13250.24490.20160.24230.01440.02450.2697-0.00710.233815.1561-23.5038-2.3771
107.3-1.9659-1.42377.7515-2.08262.01670.05480.0144-0.7537-0.2963-0.39720.05850.4160.11660.31170.34560.01-0.04460.3324-0.00960.30368.8506-31.54028.2937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 233 )A24 - 233
2X-RAY DIFFRACTION2chain 'A' and (resid 234 through 318 )A234 - 318
3X-RAY DIFFRACTION3chain 'A' and (resid 319 through 575 )A319 - 575
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 7 )B1 - 7
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 33 )B8 - 33
6X-RAY DIFFRACTION6chain 'B' and (resid 34 through 45 )B34 - 45
7X-RAY DIFFRACTION7chain 'B' and (resid 46 through 63 )B46 - 63
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 82 )B64 - 82
9X-RAY DIFFRACTION9chain 'B' and (resid 83 through 108 )B83 - 108
10X-RAY DIFFRACTION10chain 'B' and (resid 109 through 115 )B109 - 115

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