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- PDB-8s1m: Crystal structure of human GABARAP fused to EGFR (1076-1099) -

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Basic information

Entry
Database: PDB / ID: 8s1m
TitleCrystal structure of human GABARAP fused to EGFR (1076-1099)
ComponentsEpidermal growth factor receptor,Gamma-aminobutyric acid receptor-associated protein
KeywordsPROTEIN BINDING / Atg8 / Receptor-trafficking
Function / homology
Function and homology information


positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of protein kinase C activity / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation ...positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of protein kinase C activity / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / diterpenoid metabolic process / Shc-EGFR complex / cellular response to nitrogen starvation / ovulation cycle / tongue development / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / microtubule associated complex / positive regulation of mucus secretion / epidermal growth factor binding / response to UV-A / PLCG1 events in ERBB2 signaling / midgut development / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / hydrogen peroxide metabolic process / ERBB2-EGFR signaling pathway / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Macroautophagy / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / response to cobalamin / Signaling by ERBB4 / eyelid development in camera-type eye / beta-tubulin binding / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / axoneme / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / autophagosome membrane / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / autophagosome maturation / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / smooth endoplasmic reticulum / positive regulation of bone resorption / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / protein targeting / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / positive regulation of phosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / sperm midpiece / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / cellular response to epidermal growth factor stimulus / EGFR Transactivation by Gastrin / transmembrane receptor protein tyrosine kinase activity / cellular response to cadmium ion / GRB2 events in ERBB2 signaling / autophagosome / positive regulation of DNA repair / neurogenesis / SHC1 events in ERBB2 signaling / regulation of ERK1 and ERK2 cascade / cellular response to dexamethasone stimulus / ossification / positive regulation of synaptic transmission, glutamatergic / positive regulation of epithelial cell proliferation / neuron projection morphogenesis / epithelial cell proliferation / basal plasma membrane / positive regulation of superoxide anion generation / positive regulation of DNA replication / Signal transduction by L1 / cellular response to estradiol stimulus / liver regeneration / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / positive regulation of protein localization to plasma membrane / cellular response to amino acid stimulus
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / : / 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 ...Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / : / 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 / Ubiquitin-like domain superfamily / 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
Gamma-aminobutyric acid receptor-associated protein / Epidermal growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsUeffing, A. / Willbold, D. / Weiergraeber, O.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)267205415 Germany
CitationJournal: To Be Published
Title: Crystal structure of human GABARAP fused to EGFR (1076-1099)
Authors: Ueffing, A. / Willbold, D. / Weiergraeber, O.H.
History
DepositionFeb 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epidermal growth factor receptor,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0333
Polymers16,9051
Non-polymers1282
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-9 kcal/mol
Surface area8320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.280, 101.280, 101.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Epidermal growth factor receptor,Gamma-aminobutyric acid receptor-associated protein / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1 / GABA(A) receptor-associated protein / MM46


Mass: 16905.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: EGFR(1052-1075) fused to N-terminus of GABARAP,EGFR(1052-1075) fused to N-terminus of GABARAP,EGFR(1052-1075) fused to N-terminus of GABARAP,EGFR(1052-1075) fused to N-terminus of GABARAP
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1, GABARAP, FLC3B, HT004 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T1
References: UniProt: P00533, UniProt: O95166, receptor protein-tyrosine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 M ammonium acetate 0.085 M sodium citrate 25.5% PEG 4000 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.05→41.35 Å / Num. obs: 11007 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 57.43 Å2 / CC1/2: 1 / Net I/σ(I): 21.91
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 20.1 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 798 / CC1/2: 0.365 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→41.35 Å / SU ML: 0.3497 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.7698
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2298 881 8 %
Rwork0.2033 10126 -
obs0.2055 11007 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.05 Å2
Refinement stepCycle: LAST / Resolution: 2.05→41.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 7 26 1134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041138
X-RAY DIFFRACTIONf_angle_d0.59481544
X-RAY DIFFRACTIONf_chiral_restr0.0468162
X-RAY DIFFRACTIONf_plane_restr0.0055204
X-RAY DIFFRACTIONf_dihedral_angle_d11.5576418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.180.40871460.35181673X-RAY DIFFRACTION100
2.18-2.350.30271430.25791645X-RAY DIFFRACTION100
2.35-2.580.34411470.26681699X-RAY DIFFRACTION100
2.58-2.960.30591450.23731664X-RAY DIFFRACTION100
2.96-3.720.22781470.20771694X-RAY DIFFRACTION100
3.73-41.350.18931530.17511751X-RAY DIFFRACTION99.84
Refinement TLS params.Method: refined / Origin x: 24.4256493167 Å / Origin y: 31.1975939398 Å / Origin z: 2.16098169233 Å
111213212223313233
T0.386848936778 Å20.0550449820105 Å2-0.0353183916793 Å2-0.451103376113 Å20.0578505207026 Å2--0.42219720681 Å2
L1.65674720866 °2-0.0183746016812 °21.08267444432 °2-2.57421731231 °2-2.26322604844 °2--10.8447455466 °2
S0.0286636801497 Å °-0.180672592778 Å °-0.0669441849072 Å °-0.151410705142 Å °0.0153015575625 Å °0.10811406743 Å °0.0495992078987 Å °-0.267105557002 Å °-0.0362477197034 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 1 through 117 )

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