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- PDB-8vdd: Crystal structure of Proinsulin C-peptide bound to HLA-DQ8 -

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Basic information

Entry
Database: PDB / ID: 8vdd
TitleCrystal structure of Proinsulin C-peptide bound to HLA-DQ8
Components
  • (MHC class II HLA-DQ- ...) x 2
  • Proinsulin C-peptide (InsC8-22)
KeywordsIMMUNE SYSTEM / pMHC II complex
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / 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 fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion ...antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / 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 fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / positive regulation of D-glucose import / Regulation of insulin secretion / negative regulation of proteolysis / positive regulation of protein secretion / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / negative regulation of protein catabolic process / regulation of synaptic plasticity / hormone activity / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen / MHC class II protein complex / vasodilation / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / adaptive immune response / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome membrane / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / negative regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding
Similarity search - Function
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-like ...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-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class II HLA-DQ-beta-1 / Insulin / MHC class II HLA-DQ-alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTran, T.M. / Lim, J.J. / Loh, T.Y. / Mannering, I.S. / Rossjohn, J. / Reid, H.H.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1123586 Australia
CitationJournal: J.Biol.Chem. / Year: 2024
Title: A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8.
Authors: Tran, M.T. / Lim, J.J. / Loh, T.J. / Mannering, S.I. / Rossjohn, J. / Reid, H.H.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 4, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class II HLA-DQ-alpha chain
B: MHC class II HLA-DQ-beta-1
C: Proinsulin C-peptide (InsC8-22)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4325
Polymers45,1183
Non-polymers3132
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-30 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.833, 40.698, 92.604
Angle α, β, γ (deg.)90.000, 109.518, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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MHC class II HLA-DQ- ... , 2 types, 2 molecules AB

#1: Protein MHC class II HLA-DQ-alpha chain / DQA1*03:01 (DQ8-alpha chain)


Mass: 21124.516 Da / Num. of mol.: 1 / Mutation: I75C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Cell line (production host): High Five (BTI-Tn-5B1-4) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B / References: UniProt: Q30069
#2: Protein MHC class II HLA-DQ-beta-1 / DQB1*03:02 (DQ8-beta chain)


Mass: 22605.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Plasmid: pZip3 / Cell line (production host): High Five (BTI-Tn-5B1-4) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B / References: UniProt: O19707

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Protein/peptide / Sugars , 2 types, 2 molecules C

#3: Protein/peptide Proinsulin C-peptide (InsC8-22)


Mass: 1388.461 Da / Num. of mol.: 1 / Mutation: G9E, L11C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Plasmid: pZip3 / Cell line (production host): High Five (BTI-Tn-5B1-4) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B / References: UniProt: P01308
#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.: 1 / 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

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Non-polymers , 2 types, 53 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M K Na tartrate, 14% w/v PEG 20,000 with seeding and additive C8 silver bullet

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.6→43.64 Å / Num. obs: 17563 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 35.35 Å2 / CC1/2: 0.951 / Rpim(I) all: 0.141 / Rrim(I) all: 0.346 / Net I/σ(I): 3.6
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2117 / CC1/2: 0.758 / Rpim(I) all: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
autoXDSdata reduction
Coot0.9.8.92model building
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→43.64 Å / SU ML: 0.4023 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2798 859 4.89 %
Rwork0.221 16703 -
obs0.2238 17562 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 20 52 3040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293077
X-RAY DIFFRACTIONf_angle_d0.56524200
X-RAY DIFFRACTIONf_chiral_restr0.0446465
X-RAY DIFFRACTIONf_plane_restr0.0055545
X-RAY DIFFRACTIONf_dihedral_angle_d12.92841094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.760.36321670.26332692X-RAY DIFFRACTION99.48
2.76-2.980.28931300.25792773X-RAY DIFFRACTION99.55
2.98-3.280.3141380.23572754X-RAY DIFFRACTION99.62
3.28-3.750.26661320.21222798X-RAY DIFFRACTION99.86
3.75-4.720.23871490.1942778X-RAY DIFFRACTION100
4.72-43.640.27811430.21942908X-RAY DIFFRACTION99.77
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)
13.858939070641.18851218231-1.050721481970.6151055607280.01188238124851.310447625640.0434334785777-0.008602761310840.677021049539-0.380716595358-0.01722148303310.250945844358-0.491781661810.107726830733-0.276188958210.634531573148-0.03947325261750.06361896103520.033737687764-0.09563326686550.34128790652424.9283561542-13.076646001625.0120480832
22.90655539167-1.28537076533-1.318685126420.96146245622-0.5594142472963.89395158682-0.06484168056920.177790637349-0.279368331957-0.210007434547-0.01980087878320.2611399188140.0925136201943-0.6566668755440.3097483636030.3623602082830.01888196203080.01209330133520.12920708712-0.08012750512590.27210159901118.0221082488-22.675230589125.130911623
33.26191798301-0.901978058041-0.8083774540664.84336221609-0.2946585437054.7690646365-0.0902768718370.132407312835-0.349550847056-0.215957860965-0.205401279847-0.2993515129240.517712863118-0.0832994768850.3390512062580.4101393939680.01126719248580.1025992661870.139989226925-0.002039163576310.33192256197928.5461689156-27.695441127919.5025616219
44.48178020432-1.19544161294-0.388375867974.26505409561.235844769695.2455714473-0.0923914608936-0.445160936634-0.08561599512680.3677352154310.2677168659190.04386849896990.479475448023-0.651329367614-0.06061656398280.427448888367-0.05009340701530.07026382043490.2694094101720.02017877308750.16958685246116.688523901-23.345750752937.184793685
51.992850044270.304048178279-1.626749020131.693310953-0.4598646463892.984335125880.006883079861960.2074569772760.3023552878520.08325958739810.3382440192930.219834269429-0.295060081809-1.40686533675-0.2491673972130.3052445748990.1061941504470.08164411073331.07523724520.1231108270380.3794674717663.66910533139-12.360599644428.8444314437
62.639993425791.056949706190.3559915634781.96891123782-2.101964916823.304301425090.1438766682320.1270829461110.132049473939-0.3149866879120.32459771216-0.106273875019-0.085200962792-0.0987606966344-0.5130976535830.427889345907-0.110325936084-0.02622352978481.40807266249-0.07429545159240.40649625372816.8350762579-16.2604873073-1.79810556422
70.177368708342-0.221900704306-0.7238594284150.5240791013260.3528035486424.09780114976-0.03032040444990.260637214587-0.117077486866-0.04659817829610.1581207039060.09660006691580.133190983392-0.361016430835-0.1555030125360.3147428270250.0459886322117-0.07040432348371.177158626260.006276145078670.30942760687211.3910953399-19.108520111710.5683244879
89.605171761342.65251917195.098075732399.083321582974.682699559183.99037995070.3002305564270.9839433297180.166131226682-0.00459269172143-0.7194448243170.7551403234081.06607726803-0.8977073279490.5119058544990.446798282535-0.06174512388580.07992618987020.9164900704820.0237136902340.37984280044110.0316700967-28.39420751213.50480304727
93.26121097327-1.28419052643-0.01821271420038.084799213954.239926442432.36559646427-0.1328264864110.6159024580840.4885217364450.777218421031-0.335383793192-0.070821445010.414277548658-0.2106828455390.3788315678580.415904985159-0.05871184039350.003042949340820.3628996977650.1226503092040.34961283286316.5020416899-14.352378928420.3306542596
100.120078698274-0.03723390799390.06935141134942.13407985411-0.1608057795010.0486336363940.1888216200840.162974213965-0.0307461396384-0.685939402152-0.3393814479610.4547610405870.0833882668309-1.19436845767-0.07402417422650.610255740428-0.097088526749-0.1195259959911.51017971566-0.04622098902630.36023101136111.0590679345-22.46071804240.945305830379
110.1189940192810.0310047578720.08962805381130.7716074008670.8959938733093.4936049760.2358103684170.3089021935460.333860590626-0.117815755794-0.2426513787960.185462873724-0.324664753342-0.458812684566-0.08544472168630.4847276438180.04559637124890.04692153745931.997351608710.03715133875510.5931900913.81334574752-15.94556732977.12809763676
120.951021929412-0.384211546982-0.7712725698030.6526770425710.8492332508483.5151191104-0.0584156167747-0.06593740853820.2050393120510.09366493002590.0885205762121-0.0601533296378-0.1765999978010.18981544838-0.04050643237880.3796742661640.02779021220140.02565742835030.03170981248440.0001224729935690.25323659240227.276073549-12.732183306232.1959508867
133.162704257510.562725488593-1.060754625246.064843458-2.518906609277.23411271312-0.01470295182440.5158959621740.386257446516-0.3334870249620.1130429145490.494724530889-0.318274775639-0.520383880714-0.1037946193430.3304506163310.007712017291120.003346991610250.3452277534810.03151369204140.25854155373728.6018846953-4.03460607582-4.79641944027
149.61626108169-0.697174030096-6.112427360935.555008703440.5977822182868.03374920159-0.4497348615770.439625545095-0.3699141733450.4598354016540.101881857422-0.1171027484770.47594173968-0.2501366175310.4405891888080.5312751113420.02653499118490.01768199494550.1379579569160.02762638147480.21285181029126.7824555392-22.077788427535.9740295157
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 15 )AA0 - 151 - 16
22chain 'A' and (resid 16 through 27 )AA16 - 2717 - 28
33chain 'A' and (resid 28 through 56 )AA28 - 5629 - 57
44chain 'A' and (resid 57 through 77 )AA57 - 7758 - 78
55chain 'A' and (resid 78 through 88 )AA78 - 8879 - 89
66chain 'A' and (resid 89 through 102 )AA89 - 10290 - 103
77chain 'A' and (resid 103 through 123 )AA103 - 123104 - 124
88chain 'A' and (resid 124 through 135 )AA124 - 135125 - 136
99chain 'A' and (resid 136 through 147 )AA136 - 147137 - 148
1010chain 'A' and (resid 148 through 167 )AA148 - 167149 - 168
1111chain 'A' and (resid 168 through 182 )AA168 - 182169 - 183
1212chain 'B' and (resid 4 through 97 )BC4 - 971 - 94
1313chain 'B' and (resid 98 through 190 )BC98 - 19095 - 177
1414chain 'C' and (resid -2 through 12 )CE-2 - 121 - 15

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