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- EMDB-30230: Cryo-EM Structure for the Insulin Binding Region in the Ectodomai... -

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Basic information

Entry
Database: EMDB / ID: EMD-30230
TitleCryo-EM Structure for the Insulin Binding Region in the Ectodomain of the Full-length Human Insulin Receptor in Complex with 1 Insulin
Map data
Sample
  • Complex: Human Insulin Receptor Complexed with 1 Insulin
    • Complex: Insulin receptor
      • Protein or peptide: Insulin receptor
    • Complex: Insulin
      • Protein or peptide: Insulin fusion
KeywordsHuman Insulin Receptor / Full-length / Ectodomain / Insulin / Conformation. / SIGNALING PROTEIN
Function / homology
Function and homology information


cellular response to oxygen-containing compound / regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity ...cellular response to oxygen-containing compound / regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / 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 / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / PTB domain binding / adrenal gland development / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / activation of protein kinase activity / Signaling by Insulin receptor / IRS activation / Insulin processing / neuronal cell body membrane / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / amyloid-beta clearance / positive regulation of receptor internalization / regulation of amino acid metabolic process / regulation of embryonic development / negative regulation of respiratory burst involved in inflammatory response / insulin receptor substrate binding / positive regulation of dendritic spine maintenance / transport across blood-brain barrier / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / epidermis development / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / phosphatidylinositol 3-kinase binding / positive regulation of lipid biosynthetic process / heart morphogenesis / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / dendrite membrane / neuron projection maintenance / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / positive regulation of nitric-oxide synthase activity / learning / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / positive regulation of D-glucose import / Regulation of insulin secretion / negative regulation of proteolysis / positive regulation of protein secretion / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / positive regulation of MAP kinase activity / wound healing / negative regulation of protein catabolic process / regulation of synaptic plasticity / receptor protein-tyrosine kinase / hormone activity / caveola / receptor internalization / cellular response to growth factor stimulus / memory / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen
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. / Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. ...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. / Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Insulin / Insulin / Insulin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 14, 2020-
Header (metadata) releaseApr 14, 2021-
Map releaseApr 14, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bw8
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bw8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30230.png

Downloads & links

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Map

FileDownload / File: emd_30230.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 160 pix.
= 219.2 Å		1.37 Å/pix.
x 160 pix.
= 219.2 Å		1.37 Å/pix.
x 160 pix.
= 219.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.034 / Movie #1: 0.034
Minimum - Maximum-0.10747145 - 0.3242215
Average (Standard dev.)0.00035316858 (±0.0043336763)
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/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1070.3240.000

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Supplemental data

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Mask #1

Fileemd_30230_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30230_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_30230_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Human Insulin Receptor Complexed with 1 Insulin

EntireName: Human Insulin Receptor Complexed with 1 Insulin
Components
  • Complex: Human Insulin Receptor Complexed with 1 Insulin
    • Complex: Insulin receptor
      • Protein or peptide: Insulin receptor
    • Complex: Insulin
      • Protein or peptide: Insulin fusion

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Supramolecule #1: Human Insulin Receptor Complexed with 1 Insulin

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

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Supramolecule #2: Insulin receptor

SupramoleculeName: Insulin receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Insulin

SupramoleculeName: Insulin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: Insulin receptor

MacromoleculeName: Insulin receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 154.114516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HLYPGEVCPG MDIRNNLTRL HELENCSVIE GHLQILLMFK TRPEDFRDLS FPKLIMITDY LLLFRVYGLE SLKDLFPNLT VIRGSRLFF NYALVIFEMV HLKELGLYNL MNITRGSVRI EKNNELCYLA TIDWSRILDS VEDNYIVLNK DDNEECGDIC P GTAKGKTN ...String:
HLYPGEVCPG MDIRNNLTRL HELENCSVIE GHLQILLMFK TRPEDFRDLS FPKLIMITDY LLLFRVYGLE SLKDLFPNLT VIRGSRLFF NYALVIFEMV HLKELGLYNL MNITRGSVRI EKNNELCYLA TIDWSRILDS VEDNYIVLNK DDNEECGDIC P GTAKGKTN CPATVINGQF VERCWTHSHC QKVCPTICKS HGCTAEGLCC HSECLGNCSQ PDDPTKCVAC RNFYLDGRCV ET CPPPYYH FQDWRCVNFS FCQDLHHKCK NSRRQGCHQY VIHNNKCIPE CPSGYTMNSS NLLCTPCLGP CPKVCHLLEG EKT IDSVTS AQELRGCTVI NGSLIINIRG GNNLAAELEA NLGLIEEISG YLKIRRSYAL VSLSFFRKLR LIRGETLEIG NYSF YALDN QNLRQLWDWS KHNLTITQGK LFFHYNPKLC LSEIHKMEEV SGTKGRQERN DIALKTNGDQ ASCENELLKF SYIRT SFDK ILLRWEPYWP PDFRDLLGFM LFYKEAPYQN VTEFDGQDAC GSNSWTVVDI DPPLRSNDPK SQNHPGWLMR GLKPWT QYA IFVKTLVTFS DERRTYGAKS DIIYVQTDAT NPSVPLDPIS VSNSSSQIIL KWKPPSDPNG NITHYLVFWE RQAEDSE LF ELDYCLKGLK LPSRTWSPPF ESEDSQKHNQ SEYEDSAGEC CSCPKTDSQI LKELEESSFR KTFEDYLHNV VFVPRKTS S GTGAEDPRPS RKRRSLGDVG NVTVAVPTVA AFPNTSSTSV PTSPEEHRPF EKVVNKESLV ISGLRHFTGY RIELQACNQ DTPEERCSVA AYVSARTMPE AKADDIVGPV THEIFENNVV HLMWQEPKEP NGLIVLYEVS YRRYGDEELH LCVSRKHFAL ERGCRLRGL SPGNYSVRIR ATSLAGNGSW TEPTYFYVTD YLDVPSNIAK IIIGPLIFVF LFSVVIGSIY LFLRKRQPDG P LGPLYASS NPEYLSASDV FPCSVYVPDE WEVSREKITL LRELGQGSFG MVYEGNARDI IKGEAETRVA VKTVNESASL RE RIEFLNE ASVMKGFTCH HVVRLLGVVS KGQPTLVVME LMAHGDLKSY LRSLRPEAEN NPGRPPPTLQ EMIQMAAEIA DGM AYLNAK KFVHRDLAAR NCMVAHDFTV KIGDFGMTRD IYETDYYRKG GKGLLPVRWM APESLKDGVF TTSSDMWSFG VVLW EITSL AEQPYQGLSN EQVLKFVMDG GYLDQPDNCP ERVTDLMRMC WQFNPKMRPT FLEIVNLLKD DLHPSFPEVS FFHSE ENKA PESEELEMEF EDMENVPLDR SSHCQREEAG GRDGGSSLGF KRSYEEHIPY THMNGGKKNG RILTLPRSNP S

UniProtKB: Insulin receptor

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Macromolecule #2: Insulin fusion

MacromoleculeName: Insulin fusion / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.380529 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
FVNQHLCGSH LVEALYLVCG ERGFFYTPKT RREAEDLQGS LQPLALEGSL QKRGIVEQCC TSICSLYQLE NYCN

UniProtKB: Insulin, Insulin, Insulin

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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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
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: 5 / Number real images: 17122 / 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: 2069212
Details: Particle picking was done using EMAN2. 2D classifications were done in Relion 2.1 and good classes were selected.
Startup modelType of model: INSILICO MODEL / In silico model: Using Cryosparc
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7)
Details: Focused refinement with mask in the insulin binding region
Number images used: 439418
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: 6 / Avg.num./class: 280747 / Software - Name: RELION (ver. 3.0.7)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6pxv

chain_id: A, source_name: PDB, initial_model_type: experimental model

6pxv

chain_id: C, source_name: PDB, initial_model_type: experimental model

6pxv

chain_id: D, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 85 / Target criteria: Correlation coefficient
Output model

PDB-7bw8:
Cryo-EM Structure for the Insulin Binding Region in the Ectodomain of the Full-length Human Insulin Receptor in Complex with 1 Insulin

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