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- PDB-1jk8: Crystal structure of a human insulin peptide-HLA-DQ8 complex -

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Basic information

Entry
Database: PDB / ID: 1jk8
TitleCrystal structure of a human insulin peptide-HLA-DQ8 complex
Components
  • (MHC class II HLA-DQ8) x 2
  • insulin B peptide
KeywordsIMMUNE SYSTEM / HLA-DQ8 / insulin B peptide / type 1 diabetes / autoimmunity
Function / homology
Function and homology information


: / MHC class II receptor activity / transport vesicle membrane / negative regulation of NAD(P)H oxidase activity / 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 ...: / MHC class II receptor activity / transport vesicle membrane / negative regulation of NAD(P)H oxidase activity / 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 / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of peptide hormone secretion / plasma membrane => GO:0005886 / Regulation of gene expression in beta cells / positive regulation of respiratory burst / humoral immune response / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / Generation of second messenger molecules / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / PD-1 signaling / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / 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 / negative regulation of lipid catabolic process / type II interferon-mediated signaling pathway / 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 / Insulin receptor recycling / insulin-like growth factor receptor binding / MHC class II antigen presentation / 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 / trans-Golgi network membrane / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / lumenal side of endoplasmic reticulum membrane / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / clathrin-coated endocytic vesicle membrane / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / ER to Golgi transport vesicle membrane / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / peptide antigen assembly with MHC class II protein complex / Golgi lumen / vasodilation / MHC class II protein complex / positive regulation of protein localization to nucleus / peptide antigen binding / endocytic vesicle membrane / glucose metabolic process / regulation of protein localization / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / glucose homeostasis / Downstream TCR signaling / cell-cell signaling / insulin receptor signaling pathway / MHC class II protein complex binding / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Insulin ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Insulin / HLA class II histocompatibility antigen, DQ alpha 1 chain / HLA class II histocompatibility antigen, DQ beta 1 chain / HLA class II histocompatibility antigen, DQ alpha 1 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLee, K.H. / Wucherpfennig, K.W. / Wiley, D.C.
CitationJournal: Nat.Immunol. / Year: 2001
Title: Structure of a human insulin peptide-HLA-DQ8 complex and susceptibility to type 1 diabetes.
Authors: Lee, K.H. / Wucherpfennig, K.W. / Wiley, D.C.
History
DepositionJul 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.temp
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class II HLA-DQ8
B: MHC class II HLA-DQ8
C: insulin B peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7684
Polymers44,5473
Non-polymers2211
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-34 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.034, 42.862, 87.467
Angle α, β, γ (deg.)90.00, 102.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MHC class II HLA-DQ8


Mass: 20734.102 Da / Num. of mol.: 1 / Fragment: alpha chain (DQA1*0301)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04225, UniProt: P01909*PLUS
#2: Protein MHC class II HLA-DQ8


Mass: 22333.100 Da / Num. of mol.: 1 / Fragment: beta chain (DQB1*0302)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01920
#3: Protein/peptide insulin B peptide


Mass: 1479.721 Da / Num. of mol.: 1 / Fragment: peptide (9-SHLVEALYLVCGERG-23) / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS).
References: GenBank: 3776078, UniProt: P01308*PLUS
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: PEG 8000, magnesium acetate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-5 mg/mlprotein1drop
218-25 %PEG80001reservoir
3100 mMglycine1reservoir
4100 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 18183 / % possible obs: 95 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.103
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 95 %
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / Rmerge(I) obs: 0.362

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.16 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1016975.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1765 9.9 %RANDOM
Rwork0.224 ---
obs0.224 17854 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.6514 Å2 / ksol: 0.335285 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å24.06 Å2
2--4.63 Å20 Å2
3----5.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 14 70 3201
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it2.371.5
X-RAY DIFFRACTIONc_mcangle_it3.842
X-RAY DIFFRACTIONc_scbond_it3.322
X-RAY DIFFRACTIONc_scangle_it4.532.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 257 9.7 %
Rwork0.3 2396 -
obs--83.7 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.65
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Lowest resolution: 2.42 Å / Rfactor Rfree: 0.311 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.315

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