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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 / homologyProtein kinases ATP-binding region signature. / Receptor L-domain / Tyrosine-protein kinase, insulin-like receptor / Signal attenuation / IRS activation / Insulin-like / Immunoglobulin-like fold / Protein kinase-like domain superfamily / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / COPI-mediated anterograde transport ...Protein kinases ATP-binding region signature. / Receptor L-domain / Tyrosine-protein kinase, insulin-like receptor / Signal attenuation / IRS activation / Insulin-like / Immunoglobulin-like fold / Protein kinase-like domain superfamily / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / COPI-mediated anterograde transport / Insulin processing / Growth factor receptor cysteine-rich domain superfamily / Signaling by Insulin receptor / Tyrosine-protein kinase, active site / Furin-like repeat / Regulation of insulin secretion / Protein kinase domain / Furin-like cysteine-rich domain / Basic-leucine zipper domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Insulin / Fibronectin type III / Insulin receptor signalling cascade / Protein kinase, ATP binding site / Synthesis, secretion, and deacylation of Ghrelin / Receptor L-domain superfamily / Basic-leucine zipper (bZIP) domain signature. / Basic region leucine zipper / Protein tyrosine kinase / Receptor L domain / Furin-like cysteine rich region / Insulin family signature. / Protein kinase domain profile. / Receptor tyrosine kinase class II signature. / Insulin/IGF/Relaxin family / Insulin-like superfamily / Insulin receptor recycling / Basic-leucine zipper (bZIP) domain profile. / Fibronectin type-III domain profile. / Amyloid fiber formation / Fibronectin type III superfamily / Insulin, conserved site / Insulin family / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, catalytic domain / Regulation of gene expression in beta cells / Tyrosine-protein kinase, receptor class II, conserved site / regulation of female gonad development / positive regulation of meiotic cell cycle / exocrine pancreas development / positive regulation of developmental growth / anatomical structure development / male sex determination / insulin-like growth factor II binding / insulin receptor complex / insulin-like growth factor I binding / insulin-activated receptor activity / positive regulation of protein complex disassembly / cargo receptor activity / 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 / regulation of embryonic development / adrenal gland development / RNA polymerase II transcription regulator recruiting activity / dendritic spine maintenance / PTB domain binding / nitrogen catabolite activation of transcription from RNA polymerase II promoter / dendrite membrane / insulin binding / positive regulation of transcription initiation from RNA polymerase II promoter / amyloid-beta clearance / epidermis development / negative regulation of glycogen catabolic process / alpha-beta T cell activation / negative regulation of fatty acid metabolic process / negative regulation of NAD(P)H oxidase activity / negative regulation of feeding behavior / cellular amino acid biosynthetic process / regulation of cellular amino acid metabolic process / positive regulation of respiratory burst / regulation of protein secretion / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein oligomerization / positive regulation of peptide hormone secretion / insulin receptor substrate binding / positive regulation of autophagy / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of blood vessel diameter / heart morphogenesis / regulation of transmembrane transporter activity / positive regulation of lipid biosynthetic process / positive regulation of dendritic spine maintenance / negative regulation of protein secretion / negative regulation of gluconeogenesis / negative regulation of reactive oxygen species biosynthetic process / negative regulation of lipid catabolic process / transformation of host cell by virus / positive regulation of cellular protein metabolic process
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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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-0247
  • Imaged by UCSF Chimera
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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 / 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

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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 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 / Nominal defocus max: 2500 / Nominal defocus min: 1000 / Cs: 2.7 / C2 aperture diameter: 50 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 16 / Electron dose: 1.85 / 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
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 / 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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