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- EMDB-30227: The conformation C4 for the ectodomain of the full-length human i... -

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Basic information

Entry
Database: EMDB / ID: EMD-30227
TitleThe conformation C4 for the ectodomain of the full-length human insulin receptor in apo.
Map data
Sample
  • Complex: Human Insulin Receptor
    • Protein or peptide: Human Insulin Receptor
Function / homology
Function and homology information


regulation of female gonad development / positive regulation of meiotic cell cycle / positive regulation of developmental growth / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly ...regulation of female gonad development / positive regulation of meiotic cell cycle / positive regulation of developmental growth / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly / cargo receptor activity / dendritic spine maintenance / insulin binding / PTB domain binding / adrenal gland development / neuronal cell body membrane / Signaling by Insulin receptor / IRS activation / activation of protein kinase activity / amyloid-beta clearance / positive regulation of respiratory burst / positive regulation of receptor internalization / regulation of embryonic development / transport across blood-brain barrier / insulin receptor substrate binding / positive regulation of glycogen biosynthetic process / epidermis development / Signal attenuation / phosphatidylinositol 3-kinase binding / heart morphogenesis / dendrite membrane / Insulin receptor recycling / neuron projection maintenance / positive regulation of glycolytic process / activation of protein kinase B activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / learning / caveola / positive regulation of glucose import / insulin-like growth factor receptor binding / positive regulation of MAP kinase activity / receptor internalization / receptor protein-tyrosine kinase / memory / cellular response to growth factor stimulus / peptidyl-tyrosine phosphorylation / cellular response to insulin stimulus / male gonad development / positive regulation of nitric oxide biosynthetic process / late endosome / insulin receptor signaling pathway / glucose homeostasis / amyloid-beta binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / receptor complex / endosome membrane / positive regulation of cell migration / symbiont entry into host cell / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / protein domain specific binding / external side of plasma membrane / axon / protein phosphorylation / positive regulation of cell population proliferation / protein-containing complex binding / regulation of DNA-templated transcription / GTP binding / positive regulation of DNA-templated transcription / extracellular exosome / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / 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 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.4 Å
AuthorsYu D / Zhang X / Sun J / Li X / Wu Z / Han X / Fan C / Ma Y / Ouyang Q / Wang T
CitationJournal: To Be Published
Title: Insulin Binding Induced the Ectodomain Conformational Dynamics in the Full-length Human Insulin Receptor
Authors: Yu D / Zhang X / Sun J / Li X / Wu Z / Han X / Fan C / Ma Y / Ouyang Q / Wang T
History
DepositionApr 13, 2020-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30227.png

Downloads & links

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Map

FileDownload / File: emd_30227.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.37 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.009826387 - 0.042384468
Average (Standard dev.)0.0007176414 (±0.0029201333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 219.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z219.200219.200219.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0100.0420.001

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Supplemental data

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Half map: #1

Fileemd_30227_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30227_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Insulin Receptor

EntireName: Human Insulin Receptor
Components
  • Complex: Human Insulin Receptor
    • Protein or peptide: Human Insulin Receptor

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Supramolecule #1: Human Insulin Receptor

SupramoleculeName: Human Insulin Receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Human Insulin Receptor

MacromoleculeName: Human Insulin Receptor / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HLYPGEVCPG MDIRNNLTRL HELENCSVIE GHLQILLMFK TRPEDFRDLS FPKLIMITDY LLLFRVYGLE SLKDLFPNLT VIRGSRLFFN YALVIFEMVH LKELGLYNLM NITRGSVRIE KNNELCYLAT IDWSRILDSV EDNYIVLNKD DNEECGDICP GTAKGKTNCP ...String:
HLYPGEVCPG MDIRNNLTRL HELENCSVIE GHLQILLMFK TRPEDFRDLS FPKLIMITDY LLLFRVYGLE SLKDLFPNLT VIRGSRLFFN YALVIFEMVH LKELGLYNLM NITRGSVRIE KNNELCYLAT IDWSRILDSV EDNYIVLNKD DNEECGDICP GTAKGKTNCP ATVINGQFVE RCWTHSHCQK VCPTICKSHG CTAEGLCCHS ECLGNCSQPD DPTKCVACRN FYLDGRCVET CPPPYYHFQD WRCVNFSFCQ DLHHKCKNSR RQGCHQYVIH NNKCIPECPS GYTMNSSNLL CTPCLGPCPK VCHLLEGEKT IDSVTSAQEL RGCTVINGSL IINIRGGNNL AAELEANLGL IEEISGYLKI RRSYALVSLS FFRKLRLIRG ETLEIGNYSF YALDNQNLRQ LWDWSKHNLT ITQGKLFFHY NPKLCLSEIH KMEEVSGTKG RQERNDIALK TNGDQASCEN ELLKFSYIRT SFDKILLRWE PYWPPDFRDL LGFMLFYKEA PYQNVTEFDG QDACGSNSWT VVDIDPPLRS NDPKSQNHPG WLMRGLKPWT QYAIFVKTLV TFSDERRTYG AKSDIIYVQT DATNPSVPLD PISVSNSSSQ IILKWKPPSD PNGNITHYLV FWERQAEDSE LFELDYCLKG LKLPSRTWSP PFESEDSQKH NQSEYEDSAG ECCSCPKTDS QILKELEESS FRKTFEDYLH NVVFVPRKTS SGTGAEDPRP SRKRRSLGDV GNVTVAVPTV AAFPNTSSTS VPTSPEEHRP FEKVVNKESL VISGLRHFTG YRIELQACNQ DTPEERCSVA AYVSARTMPE AKADDIVGPV THEIFENNVV HLMWQEPKEP NGLIVLYEVS YRRYGDEELH LCVSRKHFAL ERGCRLRGLS PGNYSVRIRA TSLAGNGSWT EPTYFYVTDY LDVPSNIAKI IIGPLIFVFL FSVVIGSIYL FLRKRQPDGP LGPLYASSNP EYLSASDVFP CSVYVPDEWE VSREKITLLR ELGQGSFGMV YEGNARDIIK GEAETRVAVK TVNESASLRE RIEFLNEASV MKGFTCHHVV RLLGVVSKGQ PTLVVMELMA HGDLKSYLRS LRPEAENNPG RPPPTLQEMI QMAAEIADGM AYLNAKKFVH RDLAARNCMV AHDFTVKIGD FGMTRDIYET DYYRKGGKGL LPVRWMAPES LKDGVFTTSS DMWSFGVVLW EITSLAEQPY QGLSNEQVLK FVMDGGYLDQ PDNCPERVTD LMRMCWQFNP KMRPTFLEIV NLLKDDLHPS FPEVSFFHSE ENKAPESEEL EMEFEDMENV PLDRSSHCQR EEAGGRDGGS SLGFKRSYEE HIPYTHMNGG KKNGRILTLP RSNPS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium chloride
2.7 mMKClPotassium chloride
10.0 mMNa2HPO4Sodium phosphate dibasic
2.0 mMKH2PO4Potassium phosphate monobasic
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK III
DetailsThe sample was prepared using the gradient fixation method.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 6155 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2
Details: Images were collected in movie mode with 40 frames per 10 seconds.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.7000000000000001 µm / Calibrated magnification: 43796 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe movie stacks were motion corrected for further analysis.
Particle selectionNumber selected: 440506
Details: Particle picking was done using EMAN2. 2D classifications were done in Relion 2.1 and good classes were selected.
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: INSILICO MODEL / In silico model: Using Cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 61771
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 0.6.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Final 3D classificationNumber classes: 4 / Avg.num./class: 110126 / Software - Name: RELION (ver. 3.0.7)
FSC plot (resolution estimation)

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