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- PDB-8ukv: Crystal structure of nanobody/VHH domain of 34E5 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8ukv
TitleCrystal structure of nanobody/VHH domain of 34E5 in complex with the extracellular region of the epidermal growth factor variant III (EGFRvIII)
Components
  • Epidermal growth factor receptor
  • Nanobody/VHH domain 34E5
KeywordsTRANSFERASE/IMMUNE SYSTEM / cell surface receptor / glycoprotein / extracellular / glioblastoma / oncogenic variant / nanobody / VHH domain / Camelid VH domain / antibody / antigen / antibody complex / transferase-immune system complex / TRANSFERASE
Function / homology
Function and homology information


multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A ...multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / Signaling by EGFR / intracellular vesicle / negative regulation of epidermal growth factor receptor signaling pathway / eyelid development in camera-type eye / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / protein tyrosine kinase activator activity / Respiratory syncytial virus (RSV) attachment and entry / Signaling by ERBB4 / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hair follicle development / MAP kinase kinase kinase activity / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / salivary gland morphogenesis / Signaling by ERBB2 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / EGFR Transactivation by Gastrin / transmembrane receptor protein tyrosine kinase activity / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / ossification / NOTCH3 Activation and Transmission of Signal to the Nucleus / positive regulation of DNA repair / basal plasma membrane / cellular response to epidermal growth factor stimulus / EGFR downregulation / positive regulation of DNA replication / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Signal transduction by L1 / positive regulation of protein localization to plasma membrane / cellular response to amino acid stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Downregulation of ERBB2 signaling / cell-cell adhesion / Signaling by ERBB2 ECD mutants / receptor protein-tyrosine kinase / Signaling by ERBB2 KD Mutants / negative regulation of protein catabolic process / positive regulation of miRNA transcription / kinase binding / ruffle membrane / epidermal growth factor receptor signaling pathway / positive regulation of protein phosphorylation / cell morphogenesis / neuron differentiation / positive regulation of fibroblast proliferation / HCMV Early Events / Constitutive Signaling by Aberrant PI3K in Cancer / actin filament binding / Cargo recognition for clathrin-mediated endocytosis / cell junction / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / Clathrin-mediated endocytosis / PIP3 activates AKT signaling / ATPase binding / virus receptor activity / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / double-stranded DNA binding / protein tyrosine kinase activity / early endosome membrane / protein phosphatase binding / nuclear membrane / basolateral plasma membrane / learning or memory / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / endosome 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 / 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
Epidermal growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsStayrook, S.E. / Ferguson, K.M. / Bagchi, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA198164 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA112552 United States
CitationJournal: Structure / Year: 2024
Title: Structural insights into the role and targeting of EGFRvIII.
Authors: Bagchi, A. / Stayrook, S.E. / Xenaki, K.T. / Starbird, C.A. / Doulkeridou, S. / El Khoulati, R. / Roovers, R.C. / Schmitz, K.R. / van Bergen En Henegouwen, P.M.P. / Ferguson, K.M.
History
DepositionOct 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 18, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 25, 2024Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.4Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Epidermal growth factor receptor
B: Epidermal growth factor receptor
C: Nanobody/VHH domain 34E5
D: Nanobody/VHH domain 34E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4368
Polymers109,9424
Non-polymers1,4944
Water00
1
A: Epidermal growth factor receptor
C: Nanobody/VHH domain 34E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6174
Polymers54,9712
Non-polymers6462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint4 kcal/mol
Surface area23330 Å2
MethodPISA
2
B: Epidermal growth factor receptor
D: Nanobody/VHH domain 34E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8204
Polymers54,9712
Non-polymers8492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint7 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.291, 80.361, 91.841
Angle α, β, γ (deg.)106.92, 103.50, 104.56
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 39226.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1 / Variant: VAR_066493 / Plasmid: PFASTBAC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Antibody Nanobody/VHH domain 34E5


Mass: 15744.366 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-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


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: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 70-90 micromolar protein, 15-20% PEG 3350, 100 mM ammonium phosphate, pH 7.4, +20% PEG400 for cryo

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.755→47.31 Å / Num. obs: 40641 / % possible obs: 94.3 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.058 / Rrim(I) all: 0.114 / Χ2: 0.97 / Net I/σ(I): 9
Reflection shellResolution: 2.76→2.87 Å / % possible obs: 70 % / Redundancy: 3.9 % / Rmerge(I) obs: 1.954 / Num. measured all: 13150 / Num. unique obs: 3379 / CC1/2: 0.333 / Rpim(I) all: 1.143 / Rrim(I) all: 2.266 / Χ2: 0.94 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.94→46.55 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 33.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 1681 4.86 %
Rwork0.2149 --
obs0.2168 34614 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.94→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6641 0 98 0 6739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056873
X-RAY DIFFRACTIONf_angle_d0.8699307
X-RAY DIFFRACTIONf_dihedral_angle_d6.812971
X-RAY DIFFRACTIONf_chiral_restr0.0551041
X-RAY DIFFRACTIONf_plane_restr0.0071216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.030.49551140.39692773X-RAY DIFFRACTION98
3.03-3.120.43321260.37782761X-RAY DIFFRACTION98
3.12-3.240.35841540.33232708X-RAY DIFFRACTION98
3.24-3.370.33961160.28932769X-RAY DIFFRACTION99
3.37-3.520.33291590.26092746X-RAY DIFFRACTION99
3.52-3.70.2691360.23022773X-RAY DIFFRACTION99
3.7-3.940.26411620.20832725X-RAY DIFFRACTION99
3.94-4.240.23041530.17552743X-RAY DIFFRACTION99
4.24-4.670.16961390.14842763X-RAY DIFFRACTION99
4.67-5.340.16621530.15242734X-RAY DIFFRACTION98
5.34-6.720.25351450.20592748X-RAY DIFFRACTION99
6.72-46.550.231240.20012690X-RAY DIFFRACTION96

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