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- EMDB-21418: Leg region of the closed conformation of the human type 1 insulin... -

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Basic information

Entry
Database: EMDB / ID: EMD-21418
TitleLeg region of the closed conformation of the human type 1 insulin-like growth factor receptor ectodomain in complex with human insulin-like growth factor II
Map dataleg part of the close conformation
Sample
  • Complex: Leg region of the open-leg conformation of the human type 1 insulin-like growth factor receptor ectodomain in complex with human insulin-like growth factor II
    • Protein or peptide: Leucine-zippered human type 1 insulin-like growth factor receptor ectodomain
KeywordsType 1 insulin-like growth factor receptor / Insulin-like growth factor II / ectodomain receptor / tyrosine kinase / SIGNALING PROTEIN
Function / homology
Function and homology information


cardiac atrium development / negative regulation of cholangiocyte apoptotic process / protein kinase complex / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / insulin-like growth factor binding / protein transporter activity / IRS-related events triggered by IGF1R / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / protein kinase complex / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / insulin-like growth factor binding / protein transporter activity / IRS-related events triggered by IGF1R / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / nitrogen catabolite activation of transcription from RNA polymerase II promoter / FCERI mediated MAPK activation / protein localization to nuclear periphery / cellular response to aldosterone / Activation of the AP-1 family of transcription factors / cellular response to zinc ion starvation / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / insulin receptor complex / cellular response to testosterone stimulus / insulin-like growth factor I binding / transcytosis / insulin receptor activity / negative regulation of hepatocyte apoptotic process / alphav-beta3 integrin-IGF-1-IGF1R complex / Oxidative Stress Induced Senescence / response to alkaloid / cellular response to angiotensin / positive regulation of protein-containing complex disassembly / dendritic spine maintenance / insulin binding / response to L-glutamate / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / positive regulation of axon regeneration / positive regulation of cytokinesis / positive regulation of osteoblast proliferation / TFIID-class transcription factor complex binding / amyloid-beta clearance / regulation of JNK cascade / Respiratory syncytial virus (RSV) attachment and entry / amino acid biosynthetic process / insulin receptor substrate binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / G-protein alpha-subunit binding / response to vitamin E / estrous cycle / positive regulation of transcription initiation by RNA polymerase II / negative regulation of MAPK cascade / SHC-related events triggered by IGF1R / cellular response to nutrient levels / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / cellular response to transforming growth factor beta stimulus / T-tubule / cellular response to amino acid starvation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to dexamethasone stimulus / cerebellum development / insulin-like growth factor receptor signaling pathway / axonogenesis / cellular response to estradiol stimulus / hippocampus development / cellular response to glucose stimulus / response to nicotine / positive regulation of smooth muscle cell proliferation / insulin receptor binding / receptor protein-tyrosine kinase / caveola / cellular response to mechanical stimulus / RNA polymerase II transcription regulator complex / cellular response to amyloid-beta / cellular senescence / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / protein tyrosine kinase activity / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / protein autophosphorylation / positive regulation of MAPK cascade / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / positive regulation of cell migration / immune response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / intracellular membrane-bounded organelle / neuronal cell body / chromatin binding
Similarity search - Function
: / Tyrosine-protein kinase, insulin-like receptor / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. ...: / Tyrosine-protein kinase, insulin-like receptor / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / 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 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
General control transcription factor GCN4 / Insulin-like growth factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.21 Å
AuthorsXu Y / Kirk NS
Funding support Australia, United Kingdom, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1128553 Australia
Wellcome Trust209407/Z/17/ United Kingdom
CitationJournal: Structure / Year: 2020
Title: How IGF-II Binds to the Human Type 1 Insulin-like Growth Factor Receptor.
Authors: Yibin Xu / Nicholas S Kirk / Hariprasad Venugopal / Mai B Margetts / Tristan I Croll / Jarrod J Sandow / Andrew I Webb / Carlie A Delaine / Briony E Forbes / Michael C Lawrence /
Abstract: Human type 1 insulin-like growth factor receptor (IGF-1R) signals chiefly in response to the binding of insulin-like growth factor I. Relatively little is known about the role of insulin-like growth ...Human type 1 insulin-like growth factor receptor (IGF-1R) signals chiefly in response to the binding of insulin-like growth factor I. Relatively little is known about the role of insulin-like growth factor II signaling via IGF-1R, despite the affinity of insulin-like growth factor II for IGF-1R being within an order of magnitude of that of insulin-like growth factor I. Here, we describe the cryoelectron microscopy structure of insulin-like growth factor II bound to a leucine-zipper-stabilized IGF-1R ectodomain, determined in two conformations to a maximum average resolution of 3.2 Å. The two conformations differ in the relative separation of their respective points of membrane entry, and comparison with the structure of insulin-like growth factor I bound to IGF-1R reveals long-suspected differences in the way in which the critical C domain of the respective growth factors interact with IGF-1R.
History
DepositionFeb 19, 2020-
Header (metadata) releaseMay 13, 2020-
Map releaseMay 13, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vwj
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vwj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21418.png

Downloads & links

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Map

FileDownload / File: emd_21418.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationleg part of the close conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.33727473 - 1.6974219
Average (Standard dev.)0.0008719653 (±0.02055146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z424.000424.000424.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.3371.6970.001

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Supplemental data

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Sample components

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Entire : Leg region of the open-leg conformation of the human type 1 insul...

EntireName: Leg region of the open-leg conformation of the human type 1 insulin-like growth factor receptor ectodomain in complex with human insulin-like growth factor II
Components
  • Complex: Leg region of the open-leg conformation of the human type 1 insulin-like growth factor receptor ectodomain in complex with human insulin-like growth factor II
    • Protein or peptide: Leucine-zippered human type 1 insulin-like growth factor receptor ectodomain

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Supramolecule #1: Leg region of the open-leg conformation of the human type 1 insul...

SupramoleculeName: Leg region of the open-leg conformation of the human type 1 insulin-like growth factor receptor ectodomain in complex with human insulin-like growth factor II
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Leucine-zippered human type 1 insulin-like growth factor receptor...

MacromoleculeName: Leucine-zippered human type 1 insulin-like growth factor receptor ectodomain
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 108.937242 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLTV ITEYLLLFRV AGLESLGDLF PNLTVIRGWK LFYNYALVI FEMTNLKDIG LYNLRNITRG AIRIEKNADL CYLSTVDWSL ILDAVSNNYI VGNKPPKECG DLCPGTMEEK P MCEKTTIN ...String:
EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLTV ITEYLLLFRV AGLESLGDLF PNLTVIRGWK LFYNYALVI FEMTNLKDIG LYNLRNITRG AIRIEKNADL CYLSTVDWSL ILDAVSNNYI VGNKPPKECG DLCPGTMEEK P MCEKTTIN NEYNYRCWTT NRCQKMCPST CGKRACTENN ECCHPECLGS CSAPDNDTAC VACRHYYYAG VCVPACPPNT YR FEGWRCV DRDFCANILS AESSDSEGFV IHDGECMQEC PSGFIRNGSQ SMYCIPCEGP CPKVCEEEKK TKTIDSVTSA QML QGCTIF KGNLLINIRR GNNIASELEN FMGLIEVVTG YVKIRHSHAL VSLSFLKNLR LILGEEQLEG NYSFYVLDNQ NLQQ LWDWD HRNLTIKAGK MYFAFNPKLC VSEIYRMEEV TGTKGRQSKG DINTRNNGER ASCESDVLHF TSTTTSKNRI IITWH RYRP PDYRDLISFT VYYKEAPFKN VTEYDGQDAC GSNSWNMVDV DLPPNKDVEP GILLHGLKPW TQYAVYVKAV TLTMVE NDH IRGAKSEILY IRTNASVPSI PLDVLSASNS SSQLIVKWNP PSLPNGNLSY YIVRWQRQPQ DGYLYRHNYC SKDKIPI RK YADGTIDIEE VTENPKTEVC GGEKGPCCAC PKTEAEKQAE KEEAEYRKVF ENFLHNSIFV PRPERKRRDV MQVANTTM S SRSRNTTAAD TYNITDPEEL ETEYPFFESR VDNKERTVIS NLRPFTLYRI DIHSCNHEAE KLGCSASNFV FARTMPAEG ADDIPGPVTW EPRPENSIFL KWPEPENPNG LILMYEIKYG SQVEDQRECV SRQEYRKYGG AKLNRLNPGN YTARIQATSL SGNGSWTDP VFFYVQAKTG YENFIHRMKQ LEDKVEELLS KNYHLENEVA RLKKLVGERS SSEQKLISEE DLN

UniProtKB: Insulin-like growth factor 1 receptor, General control transcription factor GCN4

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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

Concentration0.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
24.8 mMTris-HCl
137.0 mMNaCl
2.7 mMKCl
0.02 %NaN3
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 15mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsIGFII:IGF-1R molar ratio 1.5:1

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 4585 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2057701
Startup modelType of model: OTHER
Details: Initial model was of the same ectodomain construct in complex with IGF-I (unpublished data).
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.11) / Number images used: 108899
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.11)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.11)
Final 3D classificationNumber classes: 7 / Software - Name: cryoSPARC (ver. 2.11)

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Atomic model buiding 1

Initial modelPDB ID:

5u8r


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsUCSF Chimera was used for the initial fitting and ISOLDE v 1.03b was using for flexible fitting.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6vwj:
Leg region of the closed conformation of the human type 1 insulin-like growth factor receptor ectodomain in complex with human insulin-like growth factor II

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