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- PDB-7pl4: Structure of Insulin receptor-related receptor's transmembrane domain -

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Basic information

Entry
Database: PDB / ID: 7pl4
TitleStructure of Insulin receptor-related receptor's transmembrane domain
ComponentsInsulin receptor-related protein beta chain
KeywordsTRANSFERASE / PROTEIN / TRANSMEMBRANE DOMAIN / Insulin receptor-related receptor / RECEPTOR / IRR
Function / homology
Function and homology information


cellular response to alkaline pH / male sex determination / insulin receptor complex / insulin receptor activity / insulin receptor substrate binding / phosphatidylinositol 3-kinase binding / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / actin cytoskeleton organization ...cellular response to alkaline pH / male sex determination / insulin receptor complex / insulin receptor activity / insulin receptor substrate binding / phosphatidylinositol 3-kinase binding / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / actin cytoskeleton organization / protein autophosphorylation / receptor complex / axon / ATP 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 / 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 receptor-related protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBershatsky, Y.V. / Nadezhdin, K.D. / Bocharova, O.V. / Bocharov, E.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation18-14-00375 Russian Federation
CitationJournal: To Be Published
Title: Structure of Insulin-like growth factor 1 receptor's transmembrane domain
Authors: Bershatsky, Y.V. / Nadezhdin, K.D. / Bocharova, O.V. / Bocharov, E.V.
History
DepositionAug 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin receptor-related protein beta chain


Theoretical massNumber of molelcules
Total (without water)3,2441
Polymers3,2441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3240 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Insulin receptor-related protein beta chain


Mass: 3243.968 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSRR, IRR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14616

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-15N TROSY
131isotropic12D 1H-13C CT HSQC
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-13C HSQC aromatic
161isotropic13D HNCO
171isotropic13D HNCA
181isotropic13D HN(CO)CA
191isotropic13D CBCA(CO)NH
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: micelle
Contents: 0.5 mM [U-100% 13C; U-100% 15N] IRRtm, 100 mM [U-99% 2H] DPC, 0.3 mM Sodium azide, 30 mM KH2PO4, 20 mM K2HPO4, 95% H2O/5% D2O
Label: 13C 15N / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMIRRtm[U-100% 13C; U-100% 15N]1
100 mMDPC[U-99% 2H]1
0.3 mMSodium azidenatural abundance1
30 mMKH2PO4natural abundance1
20 mMK2HPO4natural abundance1
Sample conditionsIonic strength: 0.1 M / Label: conditions / pH: 6.7 / Pressure: AMBIENT Pa / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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