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- PDB-3to4: Structure of mouse Valpha14Vbeta2-mouseCD1d-alpha-Galactosylceramide -

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Basic information

Entry
Database: PDB / ID: 3to4
TitleStructure of mouse Valpha14Vbeta2-mouseCD1d-alpha-Galactosylceramide
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2 microglobulin
  • NKT Valpha14 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
  • NKT Vbeta2 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
KeywordsIMMUNE SYSTEM / mouse CD1d / mouse NKT
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / positive regulation of NK T cell activation / NK T cell differentiation / 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 ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / positive regulation of NK T cell activation / NK T cell differentiation / 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 thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / antigen processing and presentation / positive regulation of interleukin-4 production / regulation of immune response / cellular defense response / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / Neutrophil degranulation / cell adhesion molecule binding / T cell receptor binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / late endosome / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / histone binding / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / lysosome / learning or memory / early endosome / endosome membrane / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol / cytoplasm
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 / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-AGH / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPatel, O. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Vbeta2 natural killer T cell antigen receptor-mediated recognition of CD1d-glycolipid antigen.
Authors: Patel, O. / Pellicci, D.G. / Uldrich, A.P. / Sullivan, L.C. / Bhati, M. / McKnight, M. / Richardson, S.K. / Howell, A.R. / Mallevaey, T. / Zhang, J. / Bedel, R. / Besra, G.S. / Brooks, A.G. ...Authors: Patel, O. / Pellicci, D.G. / Uldrich, A.P. / Sullivan, L.C. / Bhati, M. / McKnight, M. / Richardson, S.K. / Howell, A.R. / Mallevaey, T. / Zhang, J. / Bedel, R. / Besra, G.S. / Brooks, A.G. / Kjer-Nielsen, L. / McCluskey, J. / Porcelli, S.A. / Gapin, L. / Rossjohn, J. / Godfrey, D.I.
History
DepositionSep 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2 microglobulin
C: NKT Valpha14 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
D: NKT Vbeta2 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1788
Polymers98,4534
Non-polymers1,7254
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12320 Å2
ΔGint-54 kcal/mol
Surface area38190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.211, 82.594, 238.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 34662.012 Da / Num. of mol.: 1 / Fragment: UNP residues 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBacp10pH / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P11609
#2: Protein Beta-2 microglobulin /


Mass: 11660.350 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m, RP23-34E24.5-001, mCG_11606 / Plasmid: pBacp10pH / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91XJ8, UniProt: P01887*PLUS

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Antibody , 2 types, 2 molecules CD

#3: Antibody NKT Valpha14 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)


Mass: 23235.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FOR CHAIN C, RESIDUES 1 TO 116 IS MOUSE VARIABLE DOMAIN AND 117-207 IS HUMAN CONSTANT DOMAIN
Source: (gene. exp.) HOMO SAPIENS, Mus musculus / Plasmid: pET30b / Production host: Escherichia coli (E. coli)
#4: Antibody NKT Vbeta2 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)


Mass: 28895.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FOR CHAIN D, RESIDUES 1 TO 117 IS MOUSE VARIABLE DOMAIN AND 118-247 IS HUMAN CONSTANT DOMAIN.
Source: (gene. exp.) HOMO SAPIENS, Mus musculus / Plasmid: pET30b / Production host: Escherichia coli (E. coli)

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Sugars , 3 types, 4 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-AGH / N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE / Alpha-Galactosylceramide


Type: D-saccharide / Mass: 858.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C50H99NO9
#7: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 , 1 types, 5 molecules

#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SWISS-PROT ENTRY P11609 CONFLICTS WITH BRADBURY ET AL., 1988 WHICH SUGGESTS A HISTIDINE IN ...THE SWISS-PROT ENTRY P11609 CONFLICTS WITH BRADBURY ET AL., 1988 WHICH SUGGESTS A HISTIDINE IN PLACE OF ASPARTATE. SEQUENCE IN THIS PDB AGREES WITH THE CITATION. RESIDUES AT THE END OF CHAIN C 'ENDGGGCK' ARE TAG REGION AND NOT PART OF THE ORIGINAL PROTEIN. RESIDUES AT THE END OF CHAIN D 'QDRGGGCD' ARE TAG REGION AND NOT PART OF THE ORIGINAL PROTEIN

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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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG 10K, 0.1M ammonium acetate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95453 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95453 Å / Relative weight: 1
ReflectionResolution: 3.1→82.64 Å / Num. obs: 22054 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 64.6 Å2 / Rmerge(I) obs: 0.241 / Net I/σ(I): 10.3
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.243 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3160 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HE7

3he7


Resolution: 3.1→78.05 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.875 / SU B: 47.693 / SU ML: 0.379 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26753 1131 5.1 %RANDOM
Rwork0.21708 ---
all0.21965 20978 --
obs0.21965 20916 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.466 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å2-0 Å2-0 Å2
2--1.36 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 3.1→78.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6375 0 116 5 6496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216680
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.949119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3345813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99523.919296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.43615974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3221533
X-RAY DIFFRACTIONr_chiral_restr0.0630.21011
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215105
X-RAY DIFFRACTIONr_mcbond_it0.2031.54094
X-RAY DIFFRACTIONr_mcangle_it0.40426581
X-RAY DIFFRACTIONr_scbond_it0.57332586
X-RAY DIFFRACTIONr_scangle_it1.0084.52538
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 87 -
Rwork0.288 1442 -
obs-1529 96.35 %
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)
12.3159-0.89850.80454.766-0.12424.3740.0259-0.24940.0856-0.0427-0.21390.2182-0.2043-0.30760.18790.1188-0.0809-0.00720.232-0.14570.1501-14.2613-4.0794-74.4457
25.1436-0.5559-0.30875.40053.72626.401-0.29260.25210.5277-0.52020.1456-0.0027-0.29070.21870.1470.1913-0.0565-0.09450.13420.0980.1177-21.7313-6.4906-113.3597
33.86750.2050.0562.7807-1.884311.2092-0.26160.21440.5667-0.29490.0456-0.3164-0.24631.24170.2160.1419-0.1179-0.01810.235-0.01650.1976-5.4335-1.8496-101.4778
44.46841.31042.56684.01875.024310.05370.0034-0.36490.28320.3009-0.42240.38410.0949-0.90910.4190.103-0.10850.05880.2844-0.11260.1415-4.90025.2134-41.699
511.3081-4.8302-1.88429.49991.798713.39620.02080.7412-0.1806-0.6805-0.1933-0.1503-0.1804-0.14150.17250.3257-0.0166-0.04170.1634-0.0710.054617.263314.2038-14.7517
610.7810.81114.31834.65853.01547.87250.59490.2648-0.87160.08780.0917-0.47770.99080.543-0.68660.39880.0162-0.0290.1653-0.09250.20549.9515-9.9422-49.7294
75.5773-2.6878-5.07065.71665.838613.5628-0.33640.5525-1.26920.1446-0.50630.43350.88670.05670.84280.19250.1076-0.01920.2343-0.21650.5321.7475-2.1158-19.9619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 186
2X-RAY DIFFRACTION1A1
3X-RAY DIFFRACTION1A301
4X-RAY DIFFRACTION1A302
5X-RAY DIFFRACTION1A303 - 304
6X-RAY DIFFRACTION2A187 - 299
7X-RAY DIFFRACTION3B2 - 99
8X-RAY DIFFRACTION4C1 - 113
9X-RAY DIFFRACTION5C114 - 207
10X-RAY DIFFRACTION6D3 - 116
11X-RAY DIFFRACTION7D117 - 247

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