[English] 日本語
Yorodumi
- PDB-3bu3: Crystal structure of the insulin receptor kinase in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bu3
TitleCrystal structure of the insulin receptor kinase in complex with IRS2 KRLB peptide
Components
  • Insulin receptor substrate 2
  • insulin receptor subunit beta
KeywordsTRANSFERASE / IRK / KRLB / IRS2 / insulin receptor / substrate / Alternative splicing / ATP-binding / Carbohydrate metabolism / Cleavage on pair of basic residues / Diabetes mellitus / Disease mutation / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / Transmembrane / Tyrosine-protein kinase / Transducer
Function / homology
Function and homology information


IRS-mediated signalling / IRS-related events triggered by IGF1R / Signaling by Erythropoietin / SOS-mediated signalling / PI3K/AKT activation / positive regulation of type B pancreatic cell proliferation / Erythropoietin activates RAS / PI3K Cascade / Interleukin-7 signaling / IRS activation ...IRS-mediated signalling / IRS-related events triggered by IGF1R / Signaling by Erythropoietin / SOS-mediated signalling / PI3K/AKT activation / positive regulation of type B pancreatic cell proliferation / Erythropoietin activates RAS / PI3K Cascade / Interleukin-7 signaling / IRS activation / Signal attenuation / negative regulation of kinase activity / epithelial cell migration / negative regulation of long-chain fatty acid import across plasma membrane / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / RAF/MAP kinase cascade / PIP3 activates AKT signaling / cellular response to peptide / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of female gonad development / positive regulation of meiotic cell cycle / RET signaling / phosphatidylinositol 3-kinase activator activity / positive regulation of fatty acid beta-oxidation / insulin-like growth factor II binding / positive regulation of developmental growth / type B pancreatic cell proliferation / male sex determination / insulin receptor complex / insulin-like growth factor I binding / mammary gland development / transmembrane receptor protein tyrosine kinase adaptor activity / exocrine pancreas development / positive regulation of protein-containing complex disassembly / dendritic spine maintenance / cargo receptor activity / positive regulation of mesenchymal cell proliferation / insulin binding / negative regulation of B cell apoptotic process / neuronal cell body membrane / adrenal gland development / PTB domain binding / Signaling by Insulin receptor / IRS activation / positive regulation of respiratory burst / amyloid-beta clearance / regulation of embryonic development / positive regulation of receptor internalization / protein kinase activator activity / insulin receptor substrate binding / positive regulation of epithelial cell migration / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / phosphatidylinositol 3-kinase binding / transport across blood-brain barrier / response to glucose / heart morphogenesis / activation of protein kinase B activity / Insulin receptor recycling / insulin-like growth factor receptor binding / 14-3-3 protein binding / positive regulation of B cell proliferation / dendrite membrane / neuron projection maintenance / positive regulation of MAP kinase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / insulin-like growth factor receptor signaling pathway / positive regulation of glycolytic process / learning / positive regulation of D-glucose import / insulin receptor binding / placental growth factor receptor activity / cellular response to glucose stimulus / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / brain development / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of insulin secretion / caveola / receptor internalization / memory / cellular response to insulin stimulus / male gonad development
Similarity search - Function
Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site ...Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / 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 / PH domain / PH domain profile. / Pleckstrin homology domain. / Growth factor receptor cysteine-rich domain superfamily / Pleckstrin homology domain / 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 / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Insulin receptor / Insulin receptor substrate 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWu, J. / Hubbard, S.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural and biochemical characterization of the KRLB region in insulin receptor substrate-2.
Authors: Wu, J. / Tseng, Y.D. / Xu, C.F. / Neubert, T.A. / White, M.F. / Hubbard, S.R.
History
DepositionDec 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: insulin receptor subunit beta
B: Insulin receptor substrate 2


Theoretical massNumber of molelcules
Total (without water)36,7492
Polymers36,7492
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.759, 84.932, 50.708
Angle α, β, γ (deg.)90.00, 113.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein insulin receptor subunit beta / IR / CD220 antigen


Mass: 35033.660 Da / Num. of mol.: 1 / Fragment: protein kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P06213, receptor protein-tyrosine kinase
#2: Protein/peptide Insulin receptor substrate 2 / IRS-2 / 4PS


Mass: 1715.769 Da / Num. of mol.: 1 / Fragment: UNP residues 620-634 / Source method: obtained synthetically
Details: The sequence of this peptide natually exists in Mus Musculus.
References: UniProt: P81122
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG8000 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorDetector: CCD / Date: Apr 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 43554 / Num. obs: 41344 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 22.9
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.8 / Num. unique all: 43554 / Rsym value: 0.347 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→46.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.98 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.101 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 2186 5 %RANDOM
Rwork0.20193 ---
obs0.20281 41344 99.44 %-
all-43554 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20.09 Å2
2---0.35 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 0 267 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222509
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9683406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4325309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71423.932117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49215414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6031517
X-RAY DIFFRACTIONr_chiral_restr0.0860.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021923
X-RAY DIFFRACTIONr_nbd_refined0.1950.21229
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21748
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.212
X-RAY DIFFRACTIONr_mcbond_it0.7911.51588
X-RAY DIFFRACTIONr_mcangle_it1.23722488
X-RAY DIFFRACTIONr_scbond_it2.05131047
X-RAY DIFFRACTIONr_scangle_it3.1334.5918
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 157 -
Rwork0.262 2986 -
obs--96.71 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more