[English] 日本語
Yorodumi
- PDB-4xst: Structure of the endoglycosidase-H treated L1-CR domains of the h... -

+
Open data


ID or keywords:

Loading...

-
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 / IRS activation / yolk / : / Insulin receptor recycling / embryonic liver development / 3-phosphoinositide-dependent protein kinase binding / Signal attenuation ...response to vanadate(3-) / Insulin receptor signalling cascade / Signaling by Insulin receptor / IRS activation / yolk / : / Insulin receptor recycling / embryonic liver development / 3-phosphoinositide-dependent protein kinase binding / Signal attenuation / positive regulation of glycoprotein biosynthetic process / lipoic acid binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / response to resveratrol / regulation of hydrogen peroxide metabolic process / alternative mRNA splicing, via spliceosome / negative regulation of glycogen biosynthetic process / regulation of female gonad development / positive regulation of meiotic cell cycle / cellular response to zinc ion starvation / positive regulation of developmental growth / insulin-like growth factor II binding / male sex determination / exocrine pancreas development / response to vitamin D / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / negative regulation of transporter activity / positive regulation of kinase activity / positive regulation of protein-containing complex disassembly / cargo receptor activity / response to manganese ion / response to food / dendritic spine maintenance / insulin binding / PTB domain binding / regulation of gluconeogenesis / adrenal gland development / neuronal cell body membrane / Signaling by Insulin receptor / response to testosterone / IRS activation / protein tyrosine kinase activator activity / response to starvation / fat cell differentiation / negative regulation of feeding behavior / amyloid-beta clearance / activation of protein kinase activity / positive regulation of respiratory burst / regulation of embryonic development / positive regulation of receptor internalization / transport across blood-brain barrier / insulin receptor substrate binding / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / response to tumor necrosis factor / response to glucose / phosphatidylinositol 3-kinase binding / heart morphogenesis / peptidyl-tyrosine autophosphorylation / positive regulation of phosphorylation / response to glucocorticoid / dendrite membrane / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / activation of protein kinase B activity / cerebellum development / positive regulation of glycolytic process / response to hormone / response to nutrient levels / Insulin receptor signalling cascade / receptor-mediated endocytosis / positive regulation of mitotic nuclear division / liver development / negative regulation of protein phosphorylation / response to activity / response to organic substance / learning / molecular function activator activity / caveola / liver regeneration / hippocampus development / positive regulation of glucose import / animal organ morphogenesis / response to insulin / positive regulation of MAP kinase activity / receptor internalization / receptor protein-tyrosine kinase / memory / cellular response to growth factor stimulus / peptidyl-tyrosine phosphorylation / cellular response to insulin stimulus / male gonad development / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of nitric oxide biosynthetic process / late endosome / glucose homeostasis
Similarity search - Function
24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 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 ...24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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 / N-Acetylglucosamine


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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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: 0

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

-
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|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more