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- PDB-6nux: CD1a-lipid binary complex -

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Basic information

Entry
Database: PDB / ID: 6nux
TitleCD1a-lipid binary complex
Components
  • Beta-2-microglobulin
  • CD1A protein
KeywordsIMMUNE SYSTEM / contact hypersensitivity / antigen presentation / HLA class I-like
Function / homology
Function and homology information


exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression ...exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / : / : / 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 / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / 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 / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / 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 / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 ...MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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
(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol / T-cell surface glycoprotein CD1a / Beta-2-microglobulin / CD1A protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWegrecki, M. / Le Nours, J. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Sci Immunol / Year: 2020
Title: Human T cell response to CD1a and contact dermatitis allergens in botanical extracts and commercial skin care products.
Authors: Nicolai, S. / Wegrecki, M. / Cheng, T.Y. / Bourgeois, E.A. / Cotton, R.N. / Mayfield, J.A. / Monnot, G.C. / Le Nours, J. / Van Rhijn, I. / Rossjohn, J. / Moody, D.B. / de Jong, A.
History
DepositionFeb 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD1A protein
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9336
Polymers44,5242
Non-polymers4094
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint5 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.065, 90.020, 105.262
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

#1: Protein CD1A protein


Mass: 32322.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1A / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q8N5T0, UniProt: P06126*PLUS
#2: Protein Beta-2-microglobulin


Mass: 12201.693 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
#3: Chemical ChemComp-FOF / (2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol / trans,trans-Farnesol


Mass: 222.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→45.435 Å / Num. obs: 21111 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 36.88 Å2 / Net I/σ(I): 16.7
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 27.1 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1772 / Rpim(I) all: 0.267 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J1A

5j1a


Resolution: 2.2→45.435 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 1027 4.89 %RANDOM
Rwork0.2046 ---
obs0.2068 20983 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→45.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 28 106 3132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023131
X-RAY DIFFRACTIONf_angle_d0.6014254
X-RAY DIFFRACTIONf_dihedral_angle_d12.9071805
X-RAY DIFFRACTIONf_chiral_restr0.043435
X-RAY DIFFRACTIONf_plane_restr0.004550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.3160.30521460.24862800X-RAY DIFFRACTION100
2.316-2.46110.27471490.23932785X-RAY DIFFRACTION100
2.4611-2.65110.27681500.22862803X-RAY DIFFRACTION100
2.6511-2.91790.3191530.21882801X-RAY DIFFRACTION100
2.9179-3.340.22841380.19772846X-RAY DIFFRACTION100
3.34-4.20760.20611400.18882905X-RAY DIFFRACTION100
4.2076-45.4450.2451510.19663016X-RAY DIFFRACTION100
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)
16.4088-1.3065-1.01612.6701-0.22265.57770.20940.5918-0.6595-0.1008-0.18370.050.2257-0.2721-0.12260.3765-0.02560.03570.3667-0.12490.538828.151930.745934.543
24.29650.40331.13882.80560.49493.07660.1326-0.0880.45910.09030.0307-0.0121-0.0857-0.07-0.19910.15140.00650.02980.20650.02950.31929.416562.331350.4496
33.5755-4.8877-1.2837.8834-0.11484.16290.13880.0299-0.16540.0168-0.0394-0.68570.00821.1045-0.10440.3007-0.0316-0.05180.4087-0.1020.434121.316644.21755.3215
47.16271.90220.90044.1106-3.92747.1535-0.5955-0.19790.0370.19420.63631.2919-0.0862-0.8056-0.42060.23630.0180.01750.31660.01240.5738-2.466850.69753.7677
59.7679-3.8669-1.18322.4248-1.02252.60650.16110.1846-0.0487-0.07230.01230.39140.12760.0323-0.20280.33480.0457-0.09740.216-0.05850.386211.627243.437752.4436
68.1236-1.3534-3.55733.54121.8823.5238-0.9251-0.9035-1.27980.63380.24470.2630.87280.34410.87840.50340.08340.05730.39170.15950.526513.317935.586759.6898
72.8466-0.7082-2.85212.35260.76783.3504-0.1682-0.1236-0.13020.00020.18740.22640.0699-0.1462-0.0360.3085-0.0125-0.01230.2357-0.0140.395614.509638.266949.1585
83.9564-2.8845-3.27684.24310.96387.99-0.8268-2.06880.15520.7730.67870.0463-0.2271-0.0330.08220.51570.06080.03330.5751-0.04010.42355.440143.12363.6339
90.929-0.79721.65850.6882-1.43032.9683-0.6366-1.6898-0.23780.74480.7419-0.20280.41770.84540.00160.59820.2604-0.16240.80130.060.447720.880139.928664.1109
107.0103-6.7596-6.03827.08775.97225.3046-0.0774-0.76290.7729-0.0410.4999-0.3678-0.0852-0.4402-0.60790.58820.02950.03410.7207-0.20520.73311.215156.013765.2927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 181 )
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 285 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 12 )
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 20 )
5X-RAY DIFFRACTION5chain 'B' and (resid 21 through 31 )
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 47 )
7X-RAY DIFFRACTION7chain 'B' and (resid 48 through 72 )
8X-RAY DIFFRACTION8chain 'B' and (resid 73 through 84 )
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 95 )
10X-RAY DIFFRACTION10chain 'B' and (resid 96 through 105 )

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