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- PDB-7bw7: Cryo-EM Structure for the Ectodomain of the Full-length Human Ins... -

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Basic information

Entry
Database: PDB / ID: 7bw7
TitleCryo-EM Structure for the Ectodomain of the Full-length Human Insulin Receptor in Complex with 1 Insulin.
Components
  • Insulin fusion
  • Insulin receptor
KeywordsSIGNALING PROTEIN / Human Insulin Receptor / Full-length / Ectodomain / Apo / Conformation.
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 / dendritic spine maintenance / cargo receptor activity / insulin binding / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / PTB domain binding / positive regulation of nitric oxide mediated signal transduction / adrenal gland development / negative regulation of fatty acid metabolic process / neuronal cell body membrane / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / 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 / amyloid-beta clearance / alpha-beta T cell activation / regulation of embryonic development / positive regulation of receptor internalization / protein kinase activator activity / negative regulation of respiratory burst involved in inflammatory response / regulation of amino acid metabolic process / insulin receptor substrate binding / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / epidermis development / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / transport across blood-brain barrier / Signal attenuation / phosphatidylinositol 3-kinase binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / negative regulation of reactive oxygen species biosynthetic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / heart morphogenesis / nitric oxide-cGMP-mediated signaling / positive regulation of protein autophosphorylation / activation of protein kinase B activity / dendrite membrane / transport vesicle / Insulin receptor recycling / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / receptor-mediated endocytosis / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / learning / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / negative regulation of proteolysis / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of MAP kinase activity / positive regulation of cell differentiation / Regulation of insulin secretion / insulin receptor binding / wound healing / regulation of transmembrane transporter activity / negative regulation of protein catabolic process / receptor protein-tyrosine kinase / regulation of synaptic plasticity / caveola / hormone activity / receptor internalization / peptidyl-tyrosine phosphorylation / cellular response to growth factor stimulus / positive regulation of neuron projection development / memory / cognition / positive regulation of protein localization to nucleus
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Movie
  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-30229
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  • Superimposition on EM map
  • EMDB-30229
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Insulin receptor
C: Insulin receptor
D: Insulin fusion


Theoretical massNumber of molelcules
Total (without water)316,6103
Polymers316,6103
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5380 Å2
ΔGint-23 kcal/mol
Surface area57940 Å2

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Components

#1: Protein Insulin receptor / IR


Mass: 154114.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P06213, receptor protein-tyrosine kinase
#2: Protein Insulin fusion


Mass: 8380.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308, UniProt: A6XGL2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human Insulin Receptor Complexed with 1 InsulinCOMPLEXall0RECOMBINANT
2Insulin receptorCOMPLEX#11RECOMBINANT
3InsulinCOMPLEX#21RECOMBINANT
Molecular weightValue: 0.13 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK293T
32Saccharomyces cerevisiae (brewer's yeast)4932
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMSodium chlorideNaCl1
22.7 mMPotassium chlorideKCl1
310 mMSodium phosphate dibasicNa2HPO41
42 mMPotassium phosphate monobasicKH2PO41
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was prepared using the gradient fixation method.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 43796 X / Nominal defocus max: 2700 nm / Nominal defocus min: 700 nm / Calibrated defocus min: 700 nm / Calibrated defocus max: 2700 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording

Imaging-ID: 1 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

IDAverage exposure time (sec.)Electron dose (e/Å2)Num. of grids imagedNum. of real imagesDetails
11050517122Images were collected in movie mode with 40 frames per 10 seconds.
250
350
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.18_3845: / Classification: refinement
EM software
IDNameVersionCategoryDetailsFitting-ID
1EMAN22.21aparticle selectionPicking
2RELION2.1particle selectionFurther selection
3SerialEM3.6image acquisition
5Gctf1.06CTF correction
8UCSF Chimera1.11.2model fitting1
9Coot0.9model fitting1
11cryoSPARC0.6.5initial Euler assignment
12RELION3.0.7final Euler assignment
13RELION3.0.7classification
14RELION3.0.73D reconstruction
21PHENIX1.16model refinementReal space refinement1
29UCSF Chimera1.11.2model fitting2
30Coot0.9model fitting2
42PHENIX1.16model refinementReal space refinement2
Image processingDetails: The movie stacks were motion corrected for further analysis.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2069212
Details: Particle picking was done using EMAN2. 2D classifications were done in Relion 2.1 and good classes were selected.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1162871 / Algorithm: BACK PROJECTION / Num. of class averages: 4 / Symmetry type: POINT
Atomic model building
IDB valueProtocolSpaceTarget criteria
175FLEXIBLE FITREALCorrelation coefficient
290FLEXIBLE FITREALCorrelation coefficient
Atomic model building

Accession code: 6PXV / Initial refinement model-ID: 1 / PDB-ID: 6PXV

6pxv

/ Source name: PDB / Type: experimental model

IDPdb chain-ID 3D fitting-ID
1A1
2C1
3D1
4A2
5C2
6D2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0079032
ELECTRON MICROSCOPYf_angle_d0.99512233
ELECTRON MICROSCOPYf_dihedral_angle_d18.2221184
ELECTRON MICROSCOPYf_chiral_restr0.0581337
ELECTRON MICROSCOPYf_plane_restr0.0061568

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