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- PDB-7om4: Nanobody EgB4 bound to the full extracellular EGFR-EGF complex -

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Basic information

Entry
Database: PDB / ID: 7om4
TitleNanobody EgB4 bound to the full extracellular EGFR-EGF complex
Components
  • Epidermal growth factor
  • Epidermal growth factor receptor
  • Nanobody EgB4
KeywordsIMMUNE SYSTEM / EGFR / nanobody / cancer / signaling
Function / homology
Function and homology information


negative regulation of secretion / positive regulation of hyaluronan biosynthetic process / negative regulation of cholesterol efflux / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / positive regulation of epithelial tube formation / Wnt receptor activity / regulation of calcium ion import / positive regulation of protein localization to early endosome / regulation of protein localization to cell surface ...negative regulation of secretion / positive regulation of hyaluronan biosynthetic process / negative regulation of cholesterol efflux / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / positive regulation of epithelial tube formation / Wnt receptor activity / regulation of calcium ion import / positive regulation of protein localization to early endosome / regulation of protein localization to cell surface / Wnt-protein binding / positive regulation of ubiquitin-dependent protein catabolic process / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / regulation of receptor signaling pathway via JAK-STAT / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / NFE2L2 regulating tumorigenic genes / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / epidermal growth factor receptor binding / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / branching morphogenesis of an epithelial tube / intracellular vesicle / Signaling by EGFR / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / eyelid development in camera-type eye / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / positive regulation of receptor internalization / regulation of JNK cascade / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / mammary gland alveolus development / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / canonical Wnt signaling pathway / positive regulation of DNA binding / GAB1 signalosome / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / positive regulation of endothelial cell proliferation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / cellular response to cadmium ion / positive regulation of DNA repair / ERK1 and ERK2 cascade / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of endothelial cell migration / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / positive regulation of mitotic nuclear division / positive regulation of synaptic transmission, glutamatergic / cellular response to dexamethasone stimulus / ossification / neurogenesis / regulation of ERK1 and ERK2 cascade / guanyl-nucleotide exchange factor activity / basal plasma membrane / neuron projection morphogenesis / positive regulation of superoxide anion generation / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation
Similarity search - Function
Pro-epidermal growth factor / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / : / Calcium-binding EGF domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor ...Pro-epidermal growth factor / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / : / Calcium-binding EGF 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 / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Furin-like repeat / Furin-like repeats / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / 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 / 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
Epidermal growth factor receptor / Pro-epidermal growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.05 Å
AuthorsZeronian, M.R. / Janssen, B.J.C.
CitationJournal: Bmc Mol Cell Biol / Year: 2022
Title: Structural insights into the non-inhibitory mechanism of the anti-EGFR EgB4 nanobody.
Authors: Zeronian, M.R. / Doulkeridou, S. / van Bergen En Henegouwen, P.M.P. / Janssen, B.J.C.
History
DepositionMay 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Refinement description
Category: citation / citation_author / pdbx_refine_tls_group
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 / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epidermal growth factor receptor
C: Epidermal growth factor
B: Nanobody EgB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,68210
Polymers90,1343
Non-polymers1,5487
Water00
1
A: Epidermal growth factor receptor
C: Epidermal growth factor
B: Nanobody EgB4
hetero molecules

A: Epidermal growth factor receptor
C: Epidermal growth factor
B: Nanobody EgB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,36420
Polymers180,2686
Non-polymers3,09714
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Unit cell
Length a, b, c (Å)307.610, 307.610, 135.138
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


Mass: 69709.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1 / Production host: Homo sapiens (human)
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Protein Epidermal growth factor / Urogastrone


Mass: 6229.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGF / Production host: Escherichia coli (E. coli) / References: UniProt: P01133
#3: Antibody Nanobody EgB4


Mass: 14195.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#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.: 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
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: 10.27 Å3/Da / Density % sol: 88.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M LiSO4, 0.1 M glycine pH 10.5, 1.1 M sodium dihydrogen phosphate and 0.72 M dipotassium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 6.05→153.81 Å / Num. obs: 6321 / % possible obs: 91.8 % / Redundancy: 9.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.065 / Rrim(I) all: 0.199 / Net I/σ(I): 7.8
Reflection shellResolution: 6.05→7.15 Å / Rmerge(I) obs: 1.995 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 632 / CC1/2: 0.548 / Rpim(I) all: 0.642 / Rrim(I) all: 2.099

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
REFMACrefinement
PHASERphasing
STARANISOdata scaling
XDSdata reduction
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NJP

3njp


Resolution: 6.05→153.81 Å / SU ML: 0.97 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3268 289 4.58 %
Rwork0.2959 6023 -
obs0.2968 6312 65.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 853.59 Å2 / Biso mean: 534.9126 Å2 / Biso min: 329.55 Å2
Refinement stepCycle: final / Resolution: 6.05→153.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 98 0 6206
Biso mean--590.86 --
Num. residues----791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
6.05-7.620.3872590.34741344140330
7.62-153.810.32222300.29174679490999
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)
18.5214-1.77262.43069.3187-2.54262.79081.9523.7151-2.5254-4.6518-2.603-0.63651.90542.1426-0.58711.15982.0389-0.85633.81070.00833.761-0.8129-139.79928.9155
24.65385.3482-0.26298.4444-1.20440.28460.32630.52573.4759-0.1731.40324.99271.31643.28370.42144.59560.1711.83556.3750.31734.155626.5878-155.9186.5412
32.4524-3.2501-2.80842.27925.64845.12270.87194.9432-0.4979-7.6097-2.03360.364-1.97660.6929-3.78362.2134-1.89550.03091.85720.79326.179632.3034-120.63543.8855
43.9991.8014.98410.59271.96076.161.01424.4911-3.7477-2.4360.6982-6.97271.00873.74084.90666.013-0.56811.77443.69310.69966.972173.2898-121.4915-6.0565
53.8046-2.4861-3.78291.59621.82485.08932.59611.82851.3974-1.12061.4087-2.2924-5.0255-0.036714.5801-1.34433.43481.68932.23780.4834.8811-13.5327-165.694429.8871
60.99863.6252.82221.992.0178.3461-2.976-3.24662.45816.213-2.89832.8309-0.6836-0.9447-46.68446.04731.6807-3.81644.3425-1.48488.27619.7614-118.378612.0874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 1:189)A1 - 189
2X-RAY DIFFRACTION1chain A and (resid 701:703)A701 - 703
3X-RAY DIFFRACTION2chain A and resid 190:309A190 - 309
4X-RAY DIFFRACTION3chain A and (resid 310:480)A310 - 480
5X-RAY DIFFRACTION3chain A and (resid 704:706)A704 - 706
6X-RAY DIFFRACTION4chain A and (resid 481:614)A481 - 614
7X-RAY DIFFRACTION4chain A and (resid 707)A707
8X-RAY DIFFRACTION5chain BB1 - 130
9X-RAY DIFFRACTION6chain CC5 - 51

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