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- PDB-1jqh: IGF-1 receptor kinase domain -

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Basic information

Entry
Database: PDB / ID: 1jqh
TitleIGF-1 receptor kinase domain
ComponentsIGF-1 receptor kinase
KeywordsTRANSFERASE / protein kinase fold
Function / homology
Function and homology information


cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / protein transporter activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / protein transporter activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to zinc ion starvation / cellular response to aldosterone / insulin receptor complex / cellular response to testosterone stimulus / negative regulation of hepatocyte apoptotic process / insulin-like growth factor I binding / insulin receptor activity / transcytosis / response to alkaloid / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of protein-containing complex disassembly / cellular response to angiotensin / cellular response to insulin-like growth factor stimulus / response to L-glutamate / dendritic spine maintenance / insulin binding / establishment of cell polarity / negative regulation of MAPK cascade / positive regulation of axon regeneration / amyloid-beta clearance / positive regulation of cytokinesis / positive regulation of osteoblast proliferation / regulation of JNK cascade / estrous cycle / insulin receptor substrate binding / G-protein alpha-subunit binding / response to vitamin E / SHC-related events triggered by IGF1R / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / cellular response to transforming growth factor beta stimulus / T-tubule / cerebellum development / cellular response to dexamethasone stimulus / axonogenesis / insulin-like growth factor receptor signaling pathway / response to nicotine / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / caveola / cellular response to glucose stimulus / hippocampus development / positive regulation of smooth muscle cell proliferation / insulin receptor binding / receptor protein-tyrosine kinase / cellular response to mechanical stimulus / cellular response to amyloid-beta / cellular senescence / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / protein tyrosine kinase activity / response to ethanol / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / immune response / axon / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / protein-containing complex binding / negative regulation of apoptotic process / signal transduction / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
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 ...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 / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Insulin-like growth factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsPautsch, A. / Zoephel, A. / Ahorn, H. / Spevak, W. / Hauptmann, R. / Nar, H.
CitationJournal: Structure / Year: 2001
Title: Crystal structure of bisphosphorylated IGF-1 receptor kinase: insight into domain movements upon kinase activation.
Authors: Pautsch, A. / Zoephel, A. / Ahorn, H. / Spevak, W. / Hauptmann, R. / Nar, H.
History
DepositionAug 7, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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.ptnr2_symmetry / _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: IGF-1 receptor kinase
B: IGF-1 receptor kinase
C: IGF-1 receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,13810
Polymers105,3073
Non-polymers1,8317
Water4,540252
1
A: IGF-1 receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7294
Polymers35,1021
Non-polymers6273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IGF-1 receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7043
Polymers35,1021
Non-polymers6022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: IGF-1 receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7043
Polymers35,1021
Non-polymers6022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.963, 85.963, 132.204
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein IGF-1 receptor kinase


Mass: 35102.207 Da / Num. of mol.: 3 / Fragment: kinase domain / Mutation: E979G, Y980S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08069, EC: 2.7.1.112
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: magnesium chloride, Tris, ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mMAMP-PNP1drop
226-30 %PEG5000 MME1reservoir
3200 mMammonium sulfate1reservoir
4100 mMHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 27, 2000
RadiationMonochromator: Si-111 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 160185 / Num. obs: 63650 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 16.9
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6291 / Rsym value: 0.44 / % possible all: 98.7
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. measured all: 160185 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.44

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Processing

Software
NameVersionClassification
SHARPphasing
CNX2000refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→19.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2019848.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber values
Details: crystals were twinned. refinement was against twinned data with a residual that accounts for twinning.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3121 4.8 %RANDOM
Rwork0.195 ---
all-63464 --
obs-60343 99.3 %-
Displacement parametersBiso mean: 44 Å2
Baniso -1Baniso -2Baniso -3
1--5.9 Å2-0.15 Å20 Å2
2---5.9 Å20 Å2
3---11.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6931 0 109 252 7292
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it2.391.5
X-RAY DIFFRACTIONc_mcangle_it3.532
X-RAY DIFFRACTIONc_scbond_it2.392
X-RAY DIFFRACTIONc_scangle_it3.782.5
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 379 4.8 %
Rwork0.3172 9864 -
obs-7178 97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ANP_XPLO2D.PARAM
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.195 / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04
LS refinement shell
*PLUS
Rfactor Rfree: 0.311 / Rfactor Rwork: 0.3172 / Rfactor obs: 0.3172

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