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- PDB-4xst: Structure of the endoglycosidase-H treated L1-CR domains of the h... -

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Basic information

Entry
Database: PDB / ID: 4xst
TitleStructure of the endoglycosidase-H treated L1-CR domains of the human insulin receptor in complex with residues 697-719 of the human insulin receptor (A-isoform)
Components(Insulin receptor) x 2
KeywordsHormone/Hormone receptor / Insulin receptor / Insulin micro-receptor / Hormone-Hormone receptor complex
Function / homology
Function and homology information


response to vanadate(3-) / Insulin receptor signalling cascade / Signaling by Insulin receptor / yolk / IRS activation / 3-phosphoinositide-dependent protein kinase binding / positive regulation of glycoprotein biosynthetic process / Insulin receptor recycling / embryonic liver development / lipoic acid binding ...response to vanadate(3-) / Insulin receptor signalling cascade / Signaling by Insulin receptor / yolk / IRS activation / 3-phosphoinositide-dependent protein kinase binding / positive regulation of glycoprotein biosynthetic process / Insulin receptor recycling / embryonic liver development / lipoic acid binding / Signal attenuation / response to resveratrol / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of hydrogen peroxide metabolic process / negative regulation of glycogen biosynthetic process / regulation of female gonad development / positive regulation of meiotic cell cycle / cellular response to zinc ion starvation / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / insulin receptor complex / insulin-like growth factor I binding / response to vitamin D / exocrine pancreas development / positive regulation of protein-containing complex disassembly / nuclear lumen / response to manganese ion / dendritic spine maintenance / cargo receptor activity / response to food / insulin binding / neuronal cell body membrane / regulation of gluconeogenesis / adrenal gland development / PTB domain binding / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / response to starvation / fat cell differentiation / response to testosterone / 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 / response to tumor necrosis factor / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / phosphatidylinositol 3-kinase binding / transport across blood-brain barrier / positive regulation of phosphorylation / response to glucose / heart morphogenesis / response to glucocorticoid / activation of protein kinase B activity / Insulin receptor recycling / response to hormone / insulin-like growth factor receptor binding / dendrite membrane / neuron projection maintenance / positive regulation of MAP kinase activity / positive regulation of mitotic nuclear division / cerebellum development / Insulin receptor signalling cascade / receptor-mediated endocytosis / liver development / hippocampus development / positive regulation of glycolytic process / liver regeneration / learning / animal organ morphogenesis / response to activity / positive regulation of D-glucose import / response to insulin / response to nutrient levels / placental growth factor receptor activity / 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 / receptor protein-tyrosine kinase / cellular response to growth factor stimulus / peptidyl-tyrosine phosphorylation / caveola / receptor internalization
Similarity search - Function
Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-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. / Alpha-Beta Horseshoe ...Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-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. / Alpha-Beta Horseshoe / 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 / Ribbon / 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Insulin receptor / Insulin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMenting, J.G. / Lawrence, C.F. / Kong, G.K.-W. / Lawrence, M.C.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1005896 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1058233 Australia
CitationJournal: Structure / Year: 2015
Title: Structural Congruency of Ligand Binding to the Insulin and Insulin/Type 1 Insulin-like Growth Factor Hybrid Receptors.
Authors: Menting, J.G. / Lawrence, C.F. / Kong, G.K. / Margetts, M.B. / Ward, C.W. / Lawrence, M.C.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Insulin receptor
F: Insulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2478
Polymers39,0242
Non-polymers1,2236
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-8 kcal/mol
Surface area15830 Å2
MethodPISA
2
E: Insulin receptor
F: Insulin receptor
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)241,48248
Polymers234,14312
Non-polymers7,33936
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area31460 Å2
ΔGint-206 kcal/mol
Surface area80780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.718, 158.718, 85.912
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Insulin receptor / IR


Mass: 36231.762 Da / Num. of mol.: 1 / Fragment: L1-CR, UNP residues 28-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Cell line (production host): LEC 8 MUTANT CHO CELL / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P06213, receptor protein-tyrosine kinase
#2: Protein/peptide Insulin receptor / IR


Mass: 2792.128 Da / Num. of mol.: 1 / Fragment: Alpha-CT peptide, UNP residues 697-719 / Source method: obtained synthetically / Details: Chemical synthesis / Source: (synth.) Rattus norvegicus (Norway rat)
References: UniProt: P15127, receptor protein-tyrosine kinase
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
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: 4 Å3/Da / Density % sol: 69.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.45 M (NH4)2SO4 + 10 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2013
RadiationMonochromator: Double crystal monochromator (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→79.36 Å / Num. obs: 13240 / % possible obs: 99.9 % / Redundancy: 21.2 % / Biso Wilson estimate: 104.21 Å2 / Rmerge(I) obs: 0.5 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3-3.121.20.2650.8930.625370119811989.14100
3.1-3.20.4710.63710.8823521107110716.512100
3.2-3.30.6440.47321.23206299369364.836100
3.3-40.9320.17243.3392458429242831.76399.8
4-60.9920.37211.0984046395939590.381100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Cootmodel building
PHASERphasing
XSCALEdata scaling
XDSdata reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HR7

2hr7


Resolution: 3→79.36 Å / Cor.coef. Fo:Fc: 0.9262 / Cor.coef. Fo:Fc free: 0.8882 / SU R Cruickshank DPI: 0.571 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.606 / SU Rfree Blow DPI: 0.341 / SU Rfree Cruickshank DPI: 0.34
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 650 4.91 %RANDOM
Rwork0.2169 ---
obs0.2191 13240 99.88 %-
Displacement parametersBiso mean: 113.7 Å2
Baniso -1Baniso -2Baniso -3
1-8.4842 Å20 Å20 Å2
2--8.4842 Å20 Å2
3----16.9684 Å2
Refine analyzeLuzzati coordinate error obs: 0.626 Å
Refinement stepCycle: LAST / Resolution: 3→79.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 76 0 2507
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012581HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.243515HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d896SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes368HARMONIC5
X-RAY DIFFRACTIONt_it2581HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.57
X-RAY DIFFRACTIONt_other_torsion16.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion345SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2795SEMIHARMONIC4
LS refinement shellResolution: 3→3.24 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2724 131 4.93 %
Rwork0.2514 2526 -
all0.2524 2657 -
obs--99.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.195-0.9413-0.09673.1180.15281.6217-0.0871-0.2062-0.06280.3845-0.20080.08130.0428-0.33740.2879-0.3842-0.04180.2262-0.3198-0.21040.350751.677839.3999-4.2425
21.401-3.30566.96527.2478-4.12521.78140.06680.4880.1682-0.3179-0.23310.3209-0.1048-0.50660.1663-0.37780.14390.0649-0.1322-0.43690.463631.778546.0375-13.6857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ E|* }
2X-RAY DIFFRACTION2{ F|* }

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