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- PDB-7qvk: NM-02 in complex with HER2-ECD -

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Basic information

Entry
Database: PDB / ID: 7qvk
TitleNM-02 in complex with HER2-ECD
Components
  • NM-02
  • Receptor tyrosine-protein kinase erbB-2
KeywordsONCOPROTEIN / receptor tyrosine protein kinase
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 / RNA polymerase I core binding / immature T cell proliferation in thymus / semaphorin receptor complex / regulation of microtubule-based process / ErbB-3 class receptor binding / motor neuron axon guidance ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / RNA polymerase I core binding / immature T cell proliferation in thymus / semaphorin receptor complex / regulation of microtubule-based process / ErbB-3 class receptor binding / motor neuron axon guidance / Sema4D induced cell migration and growth-cone collapse / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / neurotransmitter receptor localization to postsynaptic specialization membrane / enzyme-linked receptor protein signaling pathway / neuromuscular junction development / positive regulation of Rho protein signal transduction / ERBB2-ERBB3 signaling pathway / 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 / positive regulation of MAP kinase activity / positive regulation of transcription by RNA polymerase I / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / oligodendrocyte differentiation / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / Schwann cell development / coreceptor activity / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / myelination / transmembrane receptor protein tyrosine kinase activity / GRB2 events in ERBB2 signaling / positive regulation of cell adhesion / SHC1 events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / cell surface receptor protein tyrosine kinase signaling pathway / basal plasma membrane / Constitutive Signaling by Overexpressed ERBB2 / cellular response to epidermal growth factor stimulus / peptidyl-tyrosine phosphorylation / positive regulation of translation / positive regulation of epithelial cell proliferation / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / Signaling by ERBB2 TMD/JMD mutants / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / receptor tyrosine kinase binding / Signaling by ERBB2 KD Mutants / cellular response to growth factor stimulus / ruffle membrane / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / heart development / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / protein tyrosine kinase activity / basolateral plasma membrane / early endosome / cell surface receptor signaling pathway / cell population proliferation / protein phosphorylation / receptor complex / endosome membrane / positive regulation of MAPK cascade / intracellular signal transduction / apical plasma membrane / protein heterodimerization activity / signaling receptor binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol
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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Camelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCowan, R. / Hall, G. / Carr, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Plos One / Year: 2023
Title: Co-crystallisation and humanisation of an anti-HER2 single-domain antibody as a theranostic tool.
Authors: Sawmynaden, K. / Wong, N. / Davies, S. / Cowan, R. / Brown, R. / Tang, D. / Henry, M. / Tickle, D. / Matthews, D. / Carr, M. / Bakrania, P. / Hoi Ting, H. / Hall, G.
History
DepositionJan 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Derived calculations / Category: citation / citation_author / pdbx_struct_assembly
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_assembly.details
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Receptor tyrosine-protein kinase erbB-2
BBB: NM-02
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7654
Polymers83,9572
Non-polymers8082
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint1 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.767, 105.767, 185.882
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 69622.977 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 NM-02


Mass: 14334.452 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster)
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / 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
Has ligand of interestN
Has protein modificationY

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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: 3.578768 Å3/Da / Density % sol: 65.65199 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 13% PEG6000 (w/v), 0.1 M MES pH 6.5, 7% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96872 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96872 Å / Relative weight: 1
ReflectionResolution: 3.1→65.324 Å / Num. obs: 22490 / % possible obs: 100 % / Redundancy: 19.2 % / Biso Wilson estimate: 101.26 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.1
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 19.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4001 / CC1/2: 0.34 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MY6

5my6


Resolution: 3.1→65.324 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.777 / Cross valid method: FREE R-VALUE / ESU R: 1.38 / ESU R Free: 0.497
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.3299 1186 5.284 %Random selection
Rwork0.2751 21261 --
all0.278 ---
obs0.2747 22447 99.858 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 105.683 Å2
Baniso -1Baniso -2Baniso -3
1--3.441 Å2-1.721 Å20 Å2
2---3.441 Å2-0 Å2
3---11.163 Å2
Refinement stepCycle: LAST / Resolution: 3.1→65.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4783 0 53 0 4836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134963
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174457
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.6586767
X-RAY DIFFRACTIONr_angle_other_deg2.5861.58610284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73522.627255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89115764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7871530
X-RAY DIFFRACTIONr_chiral_restr0.050.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025706
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021139
X-RAY DIFFRACTIONr_nbd_refined0.2230.21145
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2510.24754
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22367
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22326
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2125
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0820.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1070.29
X-RAY DIFFRACTIONr_nbd_other0.1920.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5860.21
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1420.21
X-RAY DIFFRACTIONr_mcbond_it5.05211.3372504
X-RAY DIFFRACTIONr_mcbond_other5.05311.3352503
X-RAY DIFFRACTIONr_mcangle_it8.35816.9833123
X-RAY DIFFRACTIONr_mcangle_other8.35716.9853124
X-RAY DIFFRACTIONr_scbond_it4.34511.632459
X-RAY DIFFRACTIONr_scbond_other4.34511.632459
X-RAY DIFFRACTIONr_scangle_it7.34617.3553644
X-RAY DIFFRACTIONr_scangle_other7.34517.3563645
X-RAY DIFFRACTIONr_lrange_it11.966134.5545371
X-RAY DIFFRACTIONr_lrange_other11.966134.5725372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.399570.4471538X-RAY DIFFRACTION99.563
3.18-3.2670.456950.4171511X-RAY DIFFRACTION99.9378
3.267-3.3620.418800.3941447X-RAY DIFFRACTION100
3.362-3.4660.361030.3651423X-RAY DIFFRACTION100
3.466-3.5790.415750.3561380X-RAY DIFFRACTION100
3.579-3.7050.366530.3021362X-RAY DIFFRACTION100
3.705-3.8450.281860.2731287X-RAY DIFFRACTION100
3.845-4.0010.279700.2581248X-RAY DIFFRACTION100
4.001-4.1790.283780.2531195X-RAY DIFFRACTION99.9215
4.179-4.3830.25570.2231156X-RAY DIFFRACTION100
4.383-4.620.275690.2021099X-RAY DIFFRACTION100
4.62-4.90.203570.1961026X-RAY DIFFRACTION100
4.9-5.2380.307570.2181003X-RAY DIFFRACTION99.9057
5.238-5.6580.274400.226916X-RAY DIFFRACTION100
5.658-6.1970.338420.234863X-RAY DIFFRACTION100
6.197-6.9280.277460.234774X-RAY DIFFRACTION100
6.928-7.9970.389510.243680X-RAY DIFFRACTION100
7.997-9.790.281320.251593X-RAY DIFFRACTION100
9.79-13.8260.373200.258481X-RAY DIFFRACTION100
13.826-65.3240.534180.458279X-RAY DIFFRACTION97.3771

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