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- PDB-1k3a: Structure of the Insulin-like Growth Factor 1 Receptor Kinase -

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Basic information

Entry
Database: PDB / ID: 1k3a
TitleStructure of the Insulin-like Growth Factor 1 Receptor Kinase
Components
  • insulin receptor substrate 1
  • insulin-like growth factor 1 receptor
KeywordsTRANSFERASE / protein kinase / tyrosine kinase / tyrosine phosphorylation / protein-substrate complex
Function / homology
Function and homology information


protein kinase complex / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / protein transporter activity / IRS-related events triggered by IGF1R / positive regulation of glucose metabolic process / positive regulation of fatty acid beta-oxidation / transcytosis / IRS-mediated signalling / insulin receptor complex ...protein kinase complex / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / protein transporter activity / IRS-related events triggered by IGF1R / positive regulation of glucose metabolic process / positive regulation of fatty acid beta-oxidation / transcytosis / IRS-mediated signalling / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly / Activated NTRK3 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / alphav-beta3 integrin-IGF-1-IGF1R complex / Signaling by Leptin / cellular response to fatty acid / regulation of JNK cascade / Signaling by LTK / dendritic spine maintenance / PI3K/AKT activation / insulin binding / Signaling by ALK / IRS activation / amyloid-beta clearance / Respiratory syncytial virus (RSV) attachment and entry / insulin receptor substrate binding / insulin-like growth factor receptor activity / PI3K Cascade / SOS-mediated signalling / peptidyl-tyrosine autophosphorylation / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / Signal attenuation / SHC-related events triggered by IGF1R / insulin receptor activity / Growth hormone receptor signaling / phosphatidylinositol 3-kinase binding / negative regulation of MAPK cascade / insulin-like growth factor receptor binding / signaling adaptor activity / phosphotyrosine residue binding / Interleukin-7 signaling / SH2 domain binding / negative regulation of insulin receptor signaling pathway / insulin-like growth factor receptor signaling pathway / protein kinase C binding / positive regulation of D-glucose import / insulin receptor binding / cellular response to glucose stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of insulin secretion / receptor protein-tyrosine kinase / response to insulin / caveola / cellular response to insulin stimulus / Signaling by ALK fusions and activated point mutants / cytokine-mediated signaling pathway / cellular response to amyloid-beta / Constitutive Signaling by Aberrant PI3K in Cancer / insulin receptor signaling pathway / glucose homeostasis / PIP3 activates AKT signaling / signaling receptor complex adaptor activity / positive regulation of cold-induced thermogenesis / protein autophosphorylation / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / Extra-nuclear estrogen signaling / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / immune response / cilium / positive regulation of cell migration / axon / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / negative regulation of apoptotic process / nucleolus / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
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) / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain ...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) / 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. / Pleckstrin homology domain / 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. / PH-like domain superfamily / Tyrosine-protein kinase, active site / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Insulin-like growth factor 1 receptor / Insulin receptor substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFavelyukis, S. / Till, J.H. / Hubbard, S.R. / Miller, W.T.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure and autoregulation of the insulin-like growth factor 1 receptor kinase.
Authors: Favelyukis, S. / Till, J.H. / Hubbard, S.R. / Miller, W.T.
History
DepositionOct 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE RESIDUE CORRESPONDS TO RESIDUE FROM A SYNTHETIC PEPTIDE. IT WAS ADDED TO MODIFY THE ...SEQUENCE THE RESIDUE CORRESPONDS TO RESIDUE FROM A SYNTHETIC PEPTIDE. IT WAS ADDED TO MODIFY THE SEQUENCE TO BE SUITABLE FOR ACTIVITY ASSAYS

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: insulin-like growth factor 1 receptor
B: insulin receptor substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5143
Polymers36,0092
Non-polymers5051
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-5 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.624, 111.018, 93.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailstetramer of 2 alpha and 2 beta chains linked by disulfide bonds.

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Components

#1: Protein insulin-like growth factor 1 receptor


Mass: 34410.199 Da / Num. of mol.: 1 / Fragment: beta chain, kinase domain (residues 988-1286)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFast-Bac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P08069, EC: 2.7.1.112
#2: Protein/peptide insulin receptor substrate 1 / IRS-1


Mass: 1598.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: P35568
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, sodium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
21 mMMg AMP-PCP1drop
31 mMpeptide1drop
416 %(w/v)PEG80001reservoir
5100 mMHEPES1reservoirpH7.5
60.15 M1reservoirNaCl
72 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9725 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2001
RadiationMonochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 2.1→28.07 Å / Num. all: 24941 / Num. obs: 24941 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.048
Reflection shellResolution: 2.1→2.18 Å / Rsym value: 0.254 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 279673 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.254

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ir3

1ir3


Resolution: 2.1→28.07 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 387254.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2381 9.8 %RANDOM
Rwork0.212 ---
all0.212 24265 --
obs0.212 24265 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.8196 Å2 / ksol: 0.357892 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2--3.88 Å20 Å2
3----5.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 31 158 2548
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it0.991.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it5.112
X-RAY DIFFRACTIONc_scangle_it6.692.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 390 9.9 %
Rwork0.231 3533 -
obs-3533 96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2DNA-RNA.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3WATER_REP.PARAM&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4ION.PARAM&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5PARAMCSDX.MISC&_1_TOPOLOGY_INFILE_5
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor Rfree: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
X-RAY DIFFRACTIONc_mcbond_it0.991.5
X-RAY DIFFRACTIONc_scbond_it5.112
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scangle_it6.692.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.275 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.231

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