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- PDB-6hn5: Leucine-zippered human insulin receptor ectodomain with single bo... -

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Basic information

Entry
Database: PDB / ID: 6hn5
TitleLeucine-zippered human insulin receptor ectodomain with single bound insulin - "upper" membrane-distal part
Components
  • (Insulin) x 2
  • Insulin receptor,General control protein GCN4
KeywordsSIGNALING PROTEIN / insulin / insulin receptor ectodomain / signal transduction
Function / homologyTyrosine-protein kinase, receptor class II, conserved site / Tyrosine-protein kinase, insulin-like receptor / Basic region leucine zipper / Protein tyrosine kinase / Receptor L domain / Insulin/IGF/Relaxin family / Receptor L-domain superfamily / Insulin-like superfamily / Fibronectin type III superfamily / Insulin, conserved site ...Tyrosine-protein kinase, receptor class II, conserved site / Tyrosine-protein kinase, insulin-like receptor / Basic region leucine zipper / Protein tyrosine kinase / Receptor L domain / Insulin/IGF/Relaxin family / Receptor L-domain superfamily / Insulin-like superfamily / Fibronectin type III superfamily / Insulin, conserved site / Insulin family / Tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Insulin-like / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase-like domain superfamily / Growth factor receptor cysteine-rich domain superfamily / Tyrosine-protein kinase, active site / Receptor L-domain / Furin-like repeat / Protein kinase domain / Furin-like cysteine-rich domain / Basic-leucine zipper domain / Insulin / Fibronectin type III / Basic-leucine zipper (bZIP) domain signature. / Furin-like cysteine rich region / Tyrosine protein kinases specific active-site signature. / Insulin processing / Amyloid fiber formation / Insulin receptor recycling / Signaling by Insulin receptor / Insulin receptor signalling cascade / Signal attenuation / IRS activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / COPI-mediated anterograde transport / Receptor tyrosine kinase class II signature. / Regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Fibronectin type-III domain profile. / Regulation of gene expression in beta cells / Insulin family signature. / Protein kinase domain profile. / Basic-leucine zipper (bZIP) domain profile. / positive regulation of meiotic cell cycle / regulation of female gonad development / exocrine pancreas development / positive regulation of developmental growth / insulin-like growth factor II binding / insulin receptor complex / insulin-like growth factor I binding / male sex determination / insulin-activated receptor activity / positive regulation of protein complex disassembly / positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation / neuronal cell body membrane / positive regulation of cellular response to amino acid starvation / negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels / adrenal gland development / regulation of embryonic development / dendritic spine maintenance / RNA polymerase II transcription regulator recruiting activity / dendrite membrane / PTB domain binding / nitrogen catabolite activation of transcription from RNA polymerase II promoter / insulin binding / positive regulation of transcription initiation from RNA polymerase II promoter / epidermis development / amyloid-beta clearance / negative regulation of glycogen catabolic process / alpha-beta T cell activation / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / cellular amino acid biosynthetic process / negative regulation of NAD(P)H oxidase activity / regulation of cellular amino acid metabolic process / positive regulation of autophagy / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / regulation of protein secretion / insulin receptor substrate binding / negative regulation of protein oligomerization / positive regulation of peptide hormone secretion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / heart morphogenesis / negative regulation of blood vessel diameter / regulation of transmembrane transporter activity / positive regulation of lipid biosynthetic process / negative regulation of gluconeogenesis / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / negative regulation of reactive oxygen species biosynthetic process / positive regulation of cellular protein metabolic process / negative regulation of lipid catabolic process / transformation of host cell by virus / cognition / phosphatidylinositol 3-kinase binding
Function and homology information
Specimen sourceHomo sapiens (human)
Saccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsWeis, F. / Menting, J.G. / Margetts, M.B. / Chan, S.J. / Xu, Y. / Tennagels, N. / Wohlfart, P. / Langer, T. / Mueller, C.W. / Dreyer, M.K. / Lawrence, M.C.
CitationJournal: Nat Commun / Year: 2018
Title: The signalling conformation of the insulin receptor ectodomain.
Authors: Felix Weis / John G Menting / Mai B Margetts / Shu Jin Chan / Yibin Xu / Norbert Tennagels / Paulus Wohlfart / Thomas Langer / Christoph W Müller / Matthias K Dreyer / Michael C Lawrence
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 14, 2018 / Release: Nov 21, 2018

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Structure visualization

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  • EMDB-0247
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Assembly

Deposited unit
A: Insulin
B: Insulin
E: Insulin receptor,General control protein GCN4
F: Insulin receptor,General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,70715
Polyers219,2744
Non-polymers2,43311
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)9890
ΔGint (kcal/M)7
Surface area (Å2)46790
MethodPISA

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Components

#1: Protein/peptide Insulin /


Mass: 2383.698 Da / Num. of mol.: 1 / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin /


Mass: 3433.953 Da / Num. of mol.: 1 / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#3: Protein/peptide Insulin receptor,General control protein GCN4 / IR / IR / Amino acid biosynthesis regulatory protein


Mass: 106728.211 Da / Num. of mol.: 2
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: INSR, GCN4, AAS3, ARG9, YEL009C / Plasmid name: PEE14 / Strain: ATCC 204508 / S288c / Cell line (production host): Lec8 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P06213, UniProt: P03069, receptor protein-tyrosine kinase
#4: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 11 / Formula: C8H15NO6 / N-Acetylglucosamine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component

Type: COMPLEX

IDNameDetailsEntity IDParent IDSource
1Leucine zippered human insulin receptor ectodomain (IR-A isoform, "deltabeta" mutant) in complex with insulin and two Fv 83-7 modules : "upper" membrane-distal partNote: Attached to the leucine-zippered insulin receptor ectodomain are two Fv 83-7 modules. One of these is present within this map volume but it is very poorly ordered and thus left completely unmodelled. See the manuscript for further details.1,2,30MULTIPLE SOURCES
2insulin1, 21RECOMBINANT
3Leucine zippered human insulin receptor ectodomain31RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
229606Homo sapiens (human)
339606Homo sapiens (human)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
2210029Cricetulus griseus (Chinese hamster)
3332630synthetic construct (others)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
110 mMHEPES-NaOH1
20.02 %sodium azide1
SpecimenConc.: 0.094 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: PELCO easiGlow factory settings / Grid material: COPPER / Grid mesh size: 300 / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 16 sec. / Electron dose: 1.85 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2287
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20 / Used frames/image: 1-20

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Processing

SoftwareName: PHENIX / Version: 1.13-2998_1692: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimera1.11.2model fitting
8Coot0.8.7model fitting
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
20PHENIX1.13-2998-1692model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 747074
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 213867 / Algorithm: BACK PROJECTION / Number of class averages: 2 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: correlation coefficient
Atomic model buildingPDB-ID: 4ZXB

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