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- PDB-3bu5: Crystal structure of the insulin receptor kinase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3bu5
TitleCrystal structure of the insulin receptor kinase in complex with IRS2 KRLB peptide and ATP
Components
  • Insulin receptor substrate 2
  • insulin receptor subunit beta
KeywordsTRANSFERASE / IRK / KRLB / IRS2 / ATP / 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 / positive regulation of type B pancreatic cell proliferation / SOS-mediated signalling / PI3K/AKT activation / Erythropoietin activates RAS / PI3K Cascade / IRS activation / Interleukin-7 signaling ...IRS-mediated signalling / IRS-related events triggered by IGF1R / Signaling by Erythropoietin / positive regulation of type B pancreatic cell proliferation / SOS-mediated signalling / PI3K/AKT activation / Erythropoietin activates RAS / PI3K Cascade / IRS activation / Interleukin-7 signaling / Signal attenuation / 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 / regulation of female gonad development / positive regulation of meiotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of developmental growth / positive regulation of fatty acid beta-oxidation / insulin-like growth factor II binding / phosphatidylinositol 3-kinase activator activity / RET signaling / type B pancreatic cell proliferation / male sex determination / exocrine pancreas development / mammary gland development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / transmembrane receptor protein tyrosine kinase adaptor activity / negative regulation of B cell apoptotic process / positive regulation of protein-containing complex disassembly / cargo receptor activity / dendritic spine maintenance / positive regulation of mesenchymal cell proliferation / insulin binding / PTB domain binding / negative regulation of kinase activity / adrenal gland development / neuronal cell body membrane / Signaling by Insulin receptor / IRS activation / activation of protein kinase activity / positive regulation of epithelial cell migration / 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 / response to glucose / heart morphogenesis / positive regulation of B cell proliferation / dendrite membrane / 14-3-3 protein binding / 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 / cellular response to glucose stimulus / insulin-like growth factor receptor binding / positive regulation of MAP kinase activity / insulin receptor binding / positive regulation of insulin secretion / brain development / 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 / cell migration / late endosome / insulin receptor signaling pathway / glucose homeostasis / protein-macromolecule adaptor activity / amyloid-beta binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein phosphatase binding / protein tyrosine kinase activity / cell population proliferation / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / receptor complex
Similarity search - Function
Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Phosphotyrosine-binding 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 ...Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Phosphotyrosine-binding 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 / PH domain / Growth factor receptor cysteine-rich domain superfamily / PH domain profile. / Fibronectin type III domain / Pleckstrin homology domain. / Pleckstrin homology 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. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
ADENOSINE-5'-TRIPHOSPHATE / Insulin receptor / Insulin receptor substrate 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,2814
Polymers36,7492
Non-polymers5312
Water3,873215
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.750, 84.428, 50.601
Angle α, β, γ (deg.)90.00, 112.88, 90.00
Int Tables number4
Space group name H-MP1211

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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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.87 %
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

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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: 2.1→50 Å / Num. all: 21034 / Num. obs: 19937 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.7 / Num. unique all: 21034 / Rsym value: 0.325 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.63 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.904 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.222 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23927 1078 5.1 %RANDOM
Rwork0.19391 ---
obs0.19625 19937 99.24 %-
all-21034 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.301 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å2-0.03 Å2
2--0.04 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 32 215 2658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222498
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9853396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10223.947114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30615410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0591517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021887
X-RAY DIFFRACTIONr_nbd_refined0.1890.21230
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21690
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2209
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.216
X-RAY DIFFRACTIONr_mcbond_it0.6941.51576
X-RAY DIFFRACTIONr_mcangle_it1.11122447
X-RAY DIFFRACTIONr_scbond_it1.67331072
X-RAY DIFFRACTIONr_scangle_it2.5064.5949
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 83 -
Rwork0.239 1453 -
obs--98.97 %

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