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- PDB-3w12: Insulin receptor ectodomain construct comprising domains L1-CR in... -

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Basic information

Entry
Database: PDB / ID: 3w12
TitleInsulin receptor ectodomain construct comprising domains L1-CR in complex with high-affinity insulin analogue [D-PRO-B26]-DTI-NH2, alpha-CT peptide(704-719) and FAB 83-7
Components
  • (Insulin receptor ...) x 2
  • (monoclonal antibody fab 83-7 fragment - ...) x 2
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE RECEPTOR/HORMONE/IMMUNE SYSTEM / CELL SURFACE RECEPTOR/IMMUNE SYSTEM / INSULIN RECEPTOR / IR ECTODOMAIN / CT PEPTIDE / INSULIN / HORMONE RECEPTOR-HORMONE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of female gonad development / positive regulation of meiotic cell cycle / positive regulation of developmental growth / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly ...regulation of female gonad development / positive regulation of meiotic cell cycle / positive regulation of developmental growth / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly / cargo receptor activity / dendritic spine maintenance / insulin binding / PTB domain binding / negative regulation of NAD(P)H oxidase activity / neuronal cell body membrane / adrenal gland development / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / amyloid-beta clearance / positive regulation of peptide hormone secretion / activation of protein kinase activity / Regulation of gene expression in beta cells / positive regulation of respiratory burst / regulation of embryonic development / positive regulation of receptor internalization / transport across blood-brain barrier / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / insulin receptor substrate binding / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / epidermis development / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / phosphatidylinositol 3-kinase binding / negative regulation of lipid catabolic process / heart morphogenesis / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / dendrite membrane / Insulin receptor recycling / insulin-like growth factor receptor binding / receptor-mediated endocytosis / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / learning / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / caveola / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / positive regulation of MAP kinase activity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / receptor internalization / receptor protein-tyrosine kinase / memory / cellular response to growth factor stimulus / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus
Similarity search - Function
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. / Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. ...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. / Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily / 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 / 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 / Insulin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.301 Å
AuthorsLawrence, M.C. / Smith, B.J. / Brzozowsk, A.M.
CitationJournal: Nature / Year: 2013
Title: How insulin engages its primary binding site on the insulin receptor
Authors: Menting, J.G. / Whittaker, J. / Margetts, M.B. / Whittaker, L.J. / Kong, G.K.-W. / Smith, B.J. / Watson, C.J. / Zakova, L. / Kletvikova, E. / Jiracek, J. / Chan, S.J. / Steiner, D.F. / ...Authors: Menting, J.G. / Whittaker, J. / Margetts, M.B. / Whittaker, L.J. / Kong, G.K.-W. / Smith, B.J. / Watson, C.J. / Zakova, L. / Kletvikova, E. / Jiracek, J. / Chan, S.J. / Steiner, D.F. / Dodson, G.G. / Brzozowski, A.M. / Weiss, M.A. / Ward, C.W. / Lawrence, M.C.
History
DepositionNov 6, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Sep 4, 2013Group: Database references
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.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Insulin receptor domains L1-CR
C: monoclonal antibody fab 83-7 fragment - heavy chain
D: monoclonal antibody fab 83-7 fragment - light chain
A: Insulin A chain
B: Insulin B chain
F: Insulin receptor alpha-CT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,92210
Polymers68,1456
Non-polymers1,7784
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-18 kcal/mol
Surface area27370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.488, 169.488, 169.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23

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Components

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Insulin receptor ... , 2 types, 2 molecules EF

#1: Protein Insulin receptor domains L1-CR / insulin receptor L1-CR (IR310.T) / Insulin receptor subunit alpha


Mass: 35503.934 Da / Num. of mol.: 1 / Fragment: UNP residues 28-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Cell (production host): CHO CELL / Cell line (production host): LEC8 MUTANT / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P06213, receptor protein-tyrosine kinase
#6: Protein/peptide Insulin receptor alpha-CT peptide / Insulin receptor subunit alpha


Mass: 1922.143 Da / Num. of mol.: 1 / Fragment: UNP residues 731-746 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: P06213, receptor protein-tyrosine kinase

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Protein/peptide , 2 types, 2 molecules AB

#4: Protein/peptide Insulin A chain


Mass: 2383.698 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: semi-synthetic modification of porcine insulin derived from porcine pancreas
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#5: Protein/peptide Insulin B chain


Mass: 2938.408 Da / Num. of mol.: 1 / Fragment: UNP residues 25-50 / Source method: obtained synthetically
Details: semi-synthetic modification of porcine insulin derived from porcine pancreas
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308

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Antibody , 2 types, 2 molecules CD

#2: Antibody monoclonal antibody fab 83-7 fragment - heavy chain


Mass: 12712.239 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA CELL / Production host: Mus musculus (house mouse)
#3: Antibody monoclonal antibody fab 83-7 fragment - light chain


Mass: 12684.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA CELL / Production host: Mus musculus (house mouse)

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Sugars , 3 types, 4 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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

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Details

Sequence detailsHIS E 144 IS NATURAL VARIANT RS1051692. THE SEQUENCE OF CHIAN F IS ISOFORM SHORT OF INSULIN ...HIS E 144 IS NATURAL VARIANT RS1051692. THE SEQUENCE OF CHIAN F IS ISOFORM SHORT OF INSULIN RECEPTOR, P06213-2. B26 TYR MUTATED TO D-PRO; B27-B30 ARE DELETED; B26 C-TERMINUS IS FINISHED WITH CONH2 (CARBOXYAMIDE) NOT A COOH GROUP.

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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: 6.074 Å3/Da / Density % sol: 79.749 % / Mosaicity: 0.13 °
Crystal growpH: 8
Details: 0.9-1.1M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE-HCL, 0.02% SODIUM AZIDE, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 4.301→169.488 Å / Num. all: 11280 / Num. obs: 11280 / % possible obs: 99.7 % / Redundancy: 8.8 % / Rsym value: 0.188 / Net I/σ(I): 7.8
Reflection shellResolution: 4.3→4.53 Å / Redundancy: 8.8 % / Rmerge(I) obs: 2.697 / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LOH, 2WRW

3loh
PDB Unreleased entry

2wrw


Resolution: 4.301→29.08 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.831 / Occupancy max: 1 / Occupancy min: 0.7 / SU B: 157.305 / SU ML: 0.857 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.998 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3492 538 4.8 %RANDOM
Rwork0.2887 ---
obs0.2913 11259 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 443.43 Å2 / Biso mean: 238.7561 Å2 / Biso min: 127.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 4.301→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4454 0 117 0 4571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194698
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9856387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9955557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6724.3207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.27415768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5211523
X-RAY DIFFRACTIONr_chiral_restr0.1040.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213497
LS refinement shellResolution: 4.301→4.412 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 46 -
Rwork0.332 763 -
all-809 -
obs--100 %
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)
11.9974-0.52711.01864.0538-1.55773.52530.02-0.02330.2538-0.0851-0.1329-0.33280.1390.36460.11290.95190.04050.17350.610.08830.563129.01120.671169.9892
22.8479-0.44920.412711.09060.76789.7993-0.4002-1.22980.83191.24230.6601-0.9499-1.8834-0.2182-0.25981.41860.5296-0.17091.3372-0.40410.562823.721624.9254110.2745
36.43463.1292-0.34887.18172.39491.6695-0.0542-0.56030.35590.86830.24570.36080.3066-0.6527-0.19151.09140.2528-0.06411.8360.46020.17499.5939.7163103.8221
436.160310.589812.760521.9651-19.055632.04450.05210.11263.06630.07960.742.42760.006-0.8875-0.79210.95120.36820.62850.70760.02621.078422.198736.554942.7027
514.8872-6.54296.51443.051-2.73853.04291.7281.66280.3947-1.2128-1.5249-0.25270.5470.1764-0.20312.31771.63140.43053.43970.31130.86131.725532.246343.2281
612.58395.982-11.33837.00833.017227.21691.2487-0.0612-0.8971-0.0382-0.0288-1.379-2.28470.0373-1.21991.63230.13130.09730.92970.25640.86422.701927.500151.7357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E5 - 310
2X-RAY DIFFRACTION1E401 - 409
3X-RAY DIFFRACTION2C1 - 116
4X-RAY DIFFRACTION3D1 - 114
5X-RAY DIFFRACTION4A1 - 21
6X-RAY DIFFRACTION5B7 - 21
7X-RAY DIFFRACTION6F705 - 715

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