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- EMDB-0247: Leucine-zippered human insulin receptor ectodomain with single bo... -

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Basic information

Entry
Database: EMDB / ID: 0247
TitleLeucine-zippered human insulin receptor ectodomain with single bound insulin - "upper" membrane-distal part
Map datahuman insulin receptor ectodomain with insulin bound - "upper" membrane-distal part
SampleLeucine zippered human insulin receptor ectodomain (IR-A isoform, "deltabeta" mutant) in complex with insulin and two Fv 83-7 modules : "upper" membrane-distal part
  • insulin
  • Leucine zippered human insulin receptor ectodomain
  • (Insulin) x 2
  • Insulin receptor,General control protein GCN4
  • ligand
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
SourceHomo sapiens (human) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsWeis F / Menting JG / Margetts MB / Chan SJ / Xu Y / Tennagels N / Wohlfart P / Langer T / Mueller CW / Dreyer MK / Lawrence MC
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 ReportPDB-ID: 6hn5

SummaryFull reportAbout validation report
DateDeposition: Sep 14, 2018 / Header (metadata) release: Nov 21, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6hn5
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0247.map.gz (map file in CCP4 format, 95552 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
1.04 Å/pix.
= 299.52 Å
288 pix
1.04 Å/pix.
= 299.52 Å
288 pix
1.04 Å/pix.
= 299.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.13270356 - 0.2162133
Average (Standard dev.)0.00019532986 (0.0033116017)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin0.00.00.0
Limit287.0287.0287.0
Spacing288288288
CellA=B=C: 299.52 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z299.520299.520299.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1330.2160.000

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Supplemental data

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Sample components

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Entire Leucine zippered human insulin receptor ectodomain (IR-A isoform,...

EntireName: Leucine zippered human insulin receptor ectodomain (IR-A isoform, "deltabeta" mutant) in complex with insulin and two Fv 83-7 modules : "upper" membrane-distal part
Details: Note: 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.
Number of components: 7

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Component #1: protein, Leucine zippered human insulin receptor ectodomain (IR-A...

ProteinName: Leucine zippered human insulin receptor ectodomain (IR-A isoform, "deltabeta" mutant) in complex with insulin and two Fv 83-7 modules : "upper" membrane-distal part
Details: Note: 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.
Recombinant expression: No

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Component #2: protein, insulin

ProteinName: insulin / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

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Component #3: protein, Leucine zippered human insulin receptor ectodomain

ProteinName: Leucine zippered human insulin receptor ectodomain / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, Insulin

ProteinName: Insulin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.383698 kDa
SourceSpecies: Homo sapiens (human)

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Component #5: protein, Insulin

ProteinName: Insulin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.433953 kDa
SourceSpecies: Homo sapiens (human)

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Component #6: protein, Insulin receptor,General control protein GCN4

ProteinName: Insulin receptor,General control protein GCN4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 106.728211 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

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Component #7: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.094 mg/ml / pH: 7.5
Support filmPELCO easiGlow factory settings
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.85 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2287

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 213867
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL
Input PDB model: 4ZXB
Output model

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