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- PDB-7mxh: CD1c with antigen analogue 3 -

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Basic information

Entry
Database: PDB / ID: 7mxh
TitleCD1c with antigen analogue 3
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein
KeywordsLIPID BINDING PROTEIN / IMMUNE SYSTEM / lipid / CD1c / antigen-presenting / tuberculosis
Function / homology
Function and homology information


glycolipid binding / T cell activation involved in immune response / 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 ...glycolipid binding / T cell activation involved in immune response / 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 / lysosome / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / 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
DODECANE / MALONIC ACID / (2S)-2,3-dihydroxypropyl hexadecanoate / Chem-ZQ7 / T-cell surface glycoprotein CD1b / T-cell surface glycoprotein CD1c / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsCao, T.P. / Shahine, A. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Rational design of a hydrolysis-resistant mycobacterial phosphoglycolipid antigen presented by CD1c to T cells.
Authors: Reijneveld, J.F. / Marino, L. / Cao, T.P. / Cheng, T.Y. / Dam, D. / Shahine, A. / Witte, M.D. / Filippov, D.V. / Suliman, S. / van der Marel, G.A. / Moody, D.B. / Minnaard, A.J. / Rossjohn, ...Authors: Reijneveld, J.F. / Marino, L. / Cao, T.P. / Cheng, T.Y. / Dam, D. / Shahine, A. / Witte, M.D. / Filippov, D.V. / Suliman, S. / van der Marel, G.A. / Moody, D.B. / Minnaard, A.J. / Rossjohn, J. / Codee, J.D.C. / Van Rhijn, I.
History
DepositionMay 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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 CD1c/T-cell surface glycoprotein CD1b chimeric protein
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2478
Polymers44,5742
Non-polymers1,6736
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-14 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.569, 72.734, 98.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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 CD1c/T-cell surface glycoprotein CD1b chimeric protein


Mass: 31957.742 Da / Num. of mol.: 1 / Mutation: N52Q, N57Q, K108G, N128Q, Y242G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1C, CD1B / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P29017, UniProt: P29016
#2: Protein Beta-2-microglobulin


Mass: 12616.132 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Cell line (production host): HEK293S / 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, 126 molecules

#4: Chemical ChemComp-ZQ7 / 2,6-anhydro-1-deoxy-1,1-difluoro-1-[(R)-hydroxy{[(4S,8S,12S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-D-glycero-D-galacto-heptitol


Mass: 742.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H77F2O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#6: Chemical ChemComp-ZP7 / (2S)-2,3-dihydroxypropyl hexadecanoate


Mass: 330.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H38O4
#7: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 100 mM CHES, 1.05 M sodium citrate, 25 mM triglycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.11→44.16 Å / Num. obs: 23737 / % possible obs: 99.94 % / Redundancy: 2 % / Biso Wilson estimate: 33.55 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.04496 / Rpim(I) all: 0.04496 / Rrim(I) all: 0.06358 / Net I/σ(I): 8.29
Reflection shellResolution: 2.11→2.185 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4378 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 2342 / CC1/2: 0.639 / CC star: 0.883 / Rpim(I) all: 0.4378 / Rrim(I) all: 0.6192 / % possible all: 99.91

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874-000refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7MX4

7mx4


Resolution: 2.11→44.16 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1187 5 %
Rwork0.2076 --
obs0.21 23732 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→44.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 99 121 3318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093283
X-RAY DIFFRACTIONf_angle_d1.1684441
X-RAY DIFFRACTIONf_dihedral_angle_d20.956472
X-RAY DIFFRACTIONf_chiral_restr0.06461
X-RAY DIFFRACTIONf_plane_restr0.007565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.210.34541390.27642791X-RAY DIFFRACTION100
2.21-2.320.3021480.25172754X-RAY DIFFRACTION100
2.32-2.470.28131540.24182768X-RAY DIFFRACTION100
2.47-2.660.33151550.24712774X-RAY DIFFRACTION100
2.66-2.930.30881460.2352810X-RAY DIFFRACTION100
2.93-3.350.23551480.20432803X-RAY DIFFRACTION100
3.35-4.220.20961320.1792874X-RAY DIFFRACTION100
4.22-44.160.23011650.18542971X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.6716 Å / Origin y: -18.1859 Å / Origin z: 16.0199 Å
111213212223313233
T0.1664 Å2-0.0206 Å20.0118 Å2-0.2033 Å2-0.0162 Å2--0.1958 Å2
L0.6231 °2-0.3689 °20.2237 °2-0.9227 °2-0.5783 °2--0.8517 °2
S-0.0211 Å °0.0035 Å °-0.0025 Å °0.0106 Å °-0.0316 Å °-0.0194 Å °0.051 Å °-0.0103 Å °0.0604 Å °
Refinement TLS groupSelection details: all

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