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- PDB-7sh4: CD1a-phosphatidylglycerol binary structure -

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Basic information

Entry
Database: PDB / ID: 7sh4
TitleCD1a-phosphatidylglycerol binary structure
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1a
KeywordsIMMUNE SYSTEM / CD1 / antigen presentation / lipid / phospholipid
Function / homology
Function and homology information


endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression ...endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / endosome membrane / immune response / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC-I family domain / 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 ...MHC-I family domain / 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
Similarity search - Domain/homology
Chem-MW9 / DI(HYDROXYETHYL)ETHER / T-cell surface glycoprotein CD1a / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWegrecki, M. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Nat.Immunol. / Year: 2023
Title: Staphylococcal phosphatidylglycerol antigens activate human T cells via CD1a.
Authors: Monnot, G.C. / Wegrecki, M. / Cheng, T.Y. / Chen, Y.L. / Sallee, B.N. / Chakravarthy, R. / Karantza, I.M. / Tin, S.Y. / Khaleel, A.E. / Monga, I. / Uwakwe, L.N. / Tillman, A. / Cheng, B. / ...Authors: Monnot, G.C. / Wegrecki, M. / Cheng, T.Y. / Chen, Y.L. / Sallee, B.N. / Chakravarthy, R. / Karantza, I.M. / Tin, S.Y. / Khaleel, A.E. / Monga, I. / Uwakwe, L.N. / Tillman, A. / Cheng, B. / Youssef, S. / Ng, S.W. / Shahine, A. / Garcia-Vilas, J.A. / Uhlemann, A.C. / Bordone, L.A. / Han, A. / Rohde, C.H. / Ogg, G. / Moody, D.B. / Rossjohn, J. / de Jong, A.
History
DepositionOct 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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: T-cell surface glycoprotein CD1a
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5549
Polymers45,0252
Non-polymers1,5307
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.225, 89.790, 105.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein T-cell surface glycoprotein CD1a / T-cell surface antigen T6/Leu-6 / hTa1 thymocyte antigen


Mass: 32464.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1A / Production host: Homo sapiens (human) / References: UniProt: P06126
#2: Protein Beta-2-microglobulin


Mass: 12560.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Homo sapiens (human) / References: UniProt: P61769

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Sugars , 1 types, 1 molecules

#3: 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 , 5 types, 313 molecules

#4: Chemical ChemComp-MW9 / (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate / 1-stearoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol)


Mass: 777.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H81O10P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20-25% PEG 1500, 0.1M MMT pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→45.37 Å / Num. obs: 27852 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1996 / CC1/2: 0.657

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KOZ

7koz


Resolution: 2→45.37 Å / SU ML: 0.2473 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9629
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23 1079 3.88 %
Rwork0.1928 26712 -
obs0.1943 27791 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.61 Å2
Refinement stepCycle: LAST / Resolution: 2→45.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 101 307 3469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523252
X-RAY DIFFRACTIONf_angle_d0.80774398
X-RAY DIFFRACTIONf_chiral_restr0.0532449
X-RAY DIFFRACTIONf_plane_restr0.0059557
X-RAY DIFFRACTIONf_dihedral_angle_d21.49691187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.2881340.25343266X-RAY DIFFRACTION100
2.09-2.20.27961320.23143294X-RAY DIFFRACTION100
2.2-2.340.24951200.22023314X-RAY DIFFRACTION100
2.34-2.520.24171220.21693290X-RAY DIFFRACTION100
2.52-2.770.29421410.2123320X-RAY DIFFRACTION100
2.77-3.170.23851420.19423322X-RAY DIFFRACTION100
3.17-40.18571330.1723383X-RAY DIFFRACTION100
4-45.370.21611550.17173523X-RAY DIFFRACTION99.92
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)
16.25315117816-0.590861778616-0.2878747989582.37788910505-0.03591196743523.664552527610.3437002117840.626404296723-0.419022212608-0.273147628609-0.1600292865470.0577939480510.147195009595-0.0754033412437-0.146687979090.2737279011570.0126525139172-0.011116941340.241833075729-0.07336100589630.23415708637827.934819442530.721413207434.2455343284
22.53768645941-0.01297422414030.8511272855942.595666985810.3739275123482.051230112560.0085972457132-0.1049575711160.2303552360670.07339015589980.0731678349531-0.06947399392630.00292299274451-0.040170018573-0.05941590746320.1049569202260.006037453573970.01347848001260.1387011253260.01812816852210.1697116640279.6350059572362.288828654850.3816668565
38.62161225886-2.033773543660.1949013978092.46155524987-0.577269254252.63021955432-0.306614678045-0.175944999021-0.2085105717910.2260750693730.2667299570370.0536044558586-0.04692185617650.137136526301-0.03154924267010.173805053253-0.00751433728108-0.02910315152070.145940931728-0.02803989723490.1352782505311.780941394746.515151237854.6962149128
45.93377416543-0.428530315558-2.36600132231.667409163251.160649250861.37351410526-0.0894910588947-0.0460894932808-0.2416588326250.04901304886880.02442914342360.1210399812660.112506436640.003957363080350.1158683730640.2228008776520.0095694404187-0.02569776954130.1718774787550.02396542022330.1679400948713.654723067938.434838818652.7257454695
54.10990194405-3.419578695222.649007718043.49651501765-2.336984039422.47570134993-0.166210484681-1.960174830091.353102512790.3967948151690.6067883172990.56350975411-1.36797831907-1.32968198061-0.2424082832270.5031548445260.1025264365510.07953086489710.555214494205-0.06958007578280.46951659448-1.6710909199846.606586287864.7055572924
64.12468909564-2.186519830140.4283574872241.64334089448-0.1298952814190.196979715474-0.450147542725-1.89143447981-0.5118324976280.6935653382320.3058203489540.1943820740.4720052387730.409454154150.117212123250.3318949478140.109795624666-0.01175967264520.6295053094660.08933259932140.17048259747717.722347765839.552561043763.2188087358
72.22156996759-1.256880300650.5581767482630.704577763593-0.4777915132010.453745996912-0.341846146625-0.5541846255761.069613760720.8208105780591.055859959490.694150074591-1.06434294757-0.249863938226-0.2198742700910.6217045465920.1535378299440.2546657209940.488179987213-0.1182725067290.8460632239810.25476739024456.80690085765.9031016563
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 181 )AA9 - 1811 - 168
22chain 'A' and (resid 182 through 285 )AA182 - 285169 - 272
33chain 'B' and (resid 2 through 20 )BE2 - 201 - 19
44chain 'B' and (resid 21 through 72 )BE21 - 7220 - 71
55chain 'B' and (resid 73 through 78 )BE73 - 7872 - 77
66chain 'B' and (resid 79 through 95 )BE79 - 9578 - 94
77chain 'B' and (resid 96 through 107 )BE96 - 10795 - 106

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