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- PDB-4z78: Weak TCR binding to an unstable insulin epitope drives type 1 diabetes -

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Basic information

Entry
Database: PDB / ID: 4z78
TitleWeak TCR binding to an unstable insulin epitope drives type 1 diabetes
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-D alpha chain
  • Insulin
KeywordsIMMUNE SYSTEM / Immunoglobulin / H-2Kd / Type 1 Diabetes
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / antigen processing and presentation of exogenous peptide antigen via MHC class I / MHC class I protein binding / positive regulation of protein autophosphorylation / inner ear development / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / regulation of transmembrane transporter activity / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / activation of protein kinase B activity / positive regulation of insulin receptor signaling pathway / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / transport vesicle / nitric oxide-cGMP-mediated signaling / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / : / : / negative regulation of receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / positive regulation of glycolytic process / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / endosome lumen / cellular response to iron ion / acute-phase response / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of cell differentiation / Regulation of insulin secretion / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / wound healing / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / negative regulation of protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / hormone activity / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / regulation of synaptic plasticity / positive regulation of neuron projection development / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / Golgi lumen
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Insulin / H-2 class I histocompatibility antigen, K-D alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.304 Å
Model detailsG9GF in H-2Kd, Orthorhombic form
AuthorsRizkallah, P.J. / Cole, D.K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Distortion of the Major Histocompatibility Complex Class I Binding Groove to Accommodate an Insulin-derived 10-Mer Peptide.
Authors: Motozono, C. / Pearson, J.A. / De Leenheer, E. / Rizkallah, P.J. / Beck, K. / Trimby, A. / Sewell, A.K. / Wong, F.S. / Cole, D.K.
History
DepositionApr 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-D alpha chain
B: Beta-2-microglobulin
C: Insulin
D: H-2 class I histocompatibility antigen, K-D alpha chain
E: Beta-2-microglobulin
F: Insulin
G: H-2 class I histocompatibility antigen, K-D alpha chain
H: Beta-2-microglobulin
I: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,89729
Polymers136,1699
Non-polymers1,72720
Water6,557364
1
A: H-2 class I histocompatibility antigen, K-D alpha chain
B: Beta-2-microglobulin
C: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,14412
Polymers45,3903
Non-polymers7559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-86 kcal/mol
Surface area19180 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-D alpha chain
E: Beta-2-microglobulin
F: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,02010
Polymers45,3903
Non-polymers6317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-84 kcal/mol
Surface area19010 Å2
MethodPISA
3
G: H-2 class I histocompatibility antigen, K-D alpha chain
H: Beta-2-microglobulin
I: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7327
Polymers45,3903
Non-polymers3424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-27 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.170, 151.570, 182.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22G
13B
23E
14B
24H
15D
25G
16E
26H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA0 - 2761 - 277
21PROPRODD0 - 2761 - 277
12PROPROAA0 - 2761 - 277
22PROPROGG0 - 2761 - 277
13METMETBB0 - 991 - 100
23METMETEE0 - 991 - 100
14METMETBB0 - 991 - 100
24METMETHH0 - 991 - 100
15PROPRODD0 - 2761 - 277
25PROPROGG0 - 2761 - 277
16METMETEE0 - 991 - 100
26METMETHH0 - 991 - 100

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 2 types, 6 molecules ADGBEH

#1: Protein H-2 class I histocompatibility antigen, K-D alpha chain / Leukocyte antigen heavy chain / H-2K(D)


Mass: 32353.016 Da / Num. of mol.: 3 / Fragment: UNP residues 22-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P01902
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 3 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P61769

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Protein/peptide , 1 types, 3 molecules CFI

#3: Protein/peptide Insulin


Mass: 1157.363 Da / Num. of mol.: 3 / Fragment: UNP residues 39-48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: synthetic construct (others) / References: UniProt: P01308

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Non-polymers , 4 types, 384 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 4% PEG 4000, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.304→182.23 Å / Num. all: 57725 / Num. obs: 57725 / % possible obs: 100 % / Redundancy: 7.2 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.148 / Rsym value: 0.127 / Net I/av σ(I): 5.2 / Net I/σ(I): 10.4 / Num. measured all: 418482
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.367.30.9290.83023841650.3990.9293100
2.36-2.437.50.7850.93084241220.3320.7853.5100
2.43-2.57.40.69912922139400.2980.6993.9100
2.5-2.587.20.6011.22808439060.2620.6014.399.9
2.58-2.667.10.4921.42658237340.2150.4925100
2.66-2.757.40.3971.82700836550.170.3976100
2.75-2.867.10.3162.22500035380.1380.3167100
2.86-2.987.30.2552.82459733760.1090.2558.299.9
2.98-3.117.40.1913.72413032740.0820.1919.8100
3.11-3.267.30.1474.82280331160.0640.14711.4100
3.26-3.447.10.1166.12106429740.0510.11613.2100
3.44-3.647.50.097.72102528220.0380.0915.7100
3.64-3.97.10.0788.71896126800.0340.07817100
3.9-4.217.60.0689.41894525000.0280.06819.2100
4.21-4.617.40.06110.31691322970.0250.06120.9100
4.61-5.157.10.0619.71504821050.0260.06120.899.9
5.15-5.957.10.0639.71312018600.0270.06319.6100
5.95-7.297.30.0679.51166116060.0280.06719100
7.29-10.316.70.04711.8854112740.020.04721.1100
10.31-182.2360.04113.146997810.0190.04121.399.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.43 Å37.1 Å
Translation5.43 Å37.1 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.304→78.09 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2301 / WRfactor Rwork: 0.1861 / FOM work R set: 0.832 / SU B: 14.573 / SU ML: 0.174 / SU R Cruickshank DPI: 0.3705 / SU Rfree: 0.2344 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 2925 5.1 %RANDOM
Rwork0.1882 ---
obs0.1904 54718 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.6 Å2 / Biso mean: 39.766 Å2 / Biso min: 15.45 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å2-0 Å2-0 Å2
2--0.67 Å20 Å2
3---1.47 Å2
Refinement stepCycle: final / Resolution: 2.304→78.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9615 0 101 364 10080
Biso mean--65.72 37.3 -
Num. residues----1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910007
X-RAY DIFFRACTIONr_bond_other_d0.0060.029029
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.93913576
X-RAY DIFFRACTIONr_angle_other_deg1.214320733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87951156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5623.048538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.029151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.361591
X-RAY DIFFRACTIONr_chiral_restr0.1080.21377
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111304
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022531
X-RAY DIFFRACTIONr_mcbond_it1.5461.8714645
X-RAY DIFFRACTIONr_mcbond_other1.5461.8714644
X-RAY DIFFRACTIONr_mcangle_it2.542.7955794
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A158460.08
12D158460.08
21A157360.09
22G157360.09
31B58100.09
32E58100.09
41B58000.08
42H58000.08
51D156280.09
52G156280.09
61E57650.09
62H57650.09
LS refinement shellResolution: 2.304→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 222 -
Rwork0.237 3937 -
all-4159 -
obs--99.98 %
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)
12.44880.3464-0.51761.3641-0.64563.30250.0171-0.0075-0.1836-0.0609-0.0070.06660.20410.013-0.01010.0665-0.0091-0.00790.0159-0.02060.05245.726746.94958.6295
21.8416-0.33240.48356.60610.91911.8723-0.0560.11290.3443-0.11640.08430.2561-0.28470.0164-0.02830.1459-0.01390.01030.1486-0.03150.124240.140279.18125.7609
32.24710.28390.37662.56062.17635.612-0.0287-0.23850.1590.20110.0506-0.3106-0.15720.2516-0.02190.08080.0021-0.04160.071-0.05480.143157.347564.10126.2458
43.03910.7735-1.00251.2736-0.6913.28170.0011-0.159-0.31960.0151-0.00910.03780.31560.05120.00790.11240.0015-0.00470.01690.0030.085222.776621.858836.2935
51.48191.13620.43397.2192-0.41161.55080.0004-0.0850.29960.2061-0.14780.6926-0.256-0.15040.14750.19320.0031-0.01960.1962-0.0760.177416.956152.795154.9085
64.01570.1903-0.04372.6881.58815.781-0.0721-0.63650.26080.43860.0793-0.2634-0.14830.3588-0.00730.16230.0047-0.04380.1764-0.05620.143334.200937.659655.0469
73.23920.3621.54172.55570.0064.0906-0.04070.20690.1174-0.0946-0.0553-0.2472-0.22860.2370.0960.1272-0.03310.00660.03210.04570.184946.511880.050471.7466
82.16830.8421-0.68217.19870.5521.1675-0.09350.21-0.3191-0.24750.0338-0.470.21520.10850.05960.2140.02970.00910.1690.07390.212151.682346.552285.885
92.17530.19990.16732.8779-2.03534.9186-0.0172-0.1467-0.11040.21520.09030.2430.1028-0.3771-0.07310.1328-0.00890.0180.04950.02560.192434.937461.77788.1897
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D0 - 180
6X-RAY DIFFRACTION4F1 - 10
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99
9X-RAY DIFFRACTION7G0 - 180
10X-RAY DIFFRACTION7I1 - 10
11X-RAY DIFFRACTION8G181 - 276
12X-RAY DIFFRACTION9H0 - 99

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