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- PDB-3jvg: Crystal Structure of chicken CD1-1 -

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Basic information

Entry
Database: PDB / ID: 3jvg
TitleCrystal Structure of chicken CD1-1
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1A1 antigen
KeywordsIMMUNE SYSTEM / cd1 / T-Cell / lipid / antigen / Transmembrane / Disulfide bond / Immune response / Immunoglobulin domain / MHC I / Polymorphism / Secreted
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Neutrophil degranulation / cellular response to iron ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Neutrophil degranulation / cellular response to iron ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular region / 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 / 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
Unknown ligand / T-cell surface glycoprotein CD1A1 antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDvir, H. / Wang, J. / Zajonc, D.M.
CitationJournal: J.Immunol. / Year: 2010
Title: Structural basis for lipid-antigen recognition in avian immunity.
Authors: Dvir, H. / Wang, J. / Ly, N. / Dascher, C.C. / Zajonc, D.M.
History
DepositionSep 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: T-cell surface glycoprotein CD1A1 antigen
B: T-cell surface glycoprotein CD1A1 antigen
C: Beta-2-microglobulin
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,68716
Polymers85,2894
Non-polymers1,39812
Water5,909328
1
A: T-cell surface glycoprotein CD1A1 antigen
C: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3438
Polymers42,6442
Non-polymers6996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-18 kcal/mol
Surface area18110 Å2
MethodPISA
2
B: T-cell surface glycoprotein CD1A1 antigen
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3438
Polymers42,6442
Non-polymers6996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-18 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.839, 112.124, 201.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
/ NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein T-cell surface glycoprotein CD1A1 antigen


Mass: 31581.990 Da / Num. of mol.: 2 / Fragment: ecto domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CD1A1, chicken cd1.1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf-9 / References: UniProt: A5HUM9
#2: Protein Beta-2-microglobulin


Mass: 11062.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B2M, beta-2-microglobulin / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF-9 / References: UniProt: P21611

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Sugars , 1 types, 6 molecules

#5: 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.: 6
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 , 3 types, 334 molecules

#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20% PEG 4000, 0.2 M NH4F, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→43.1 Å / Num. all: 48254 / Num. obs: 47868 / Observed criterion σ(F): 3.5 / Redundancy: 7.1 % / Rsym value: 0.07

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3dbx

3dbx


Resolution: 2.2→43.06 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.191 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25203 2420 5.1 %RANDOM
Rwork0.21573 ---
obs0.21762 45372 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.779 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---0.17 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5738 0 208 328 6274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226093
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.9798246
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71923.488258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99515945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6631535
X-RAY DIFFRACTIONr_chiral_restr0.140.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214521
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8321.53630
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64525880
X-RAY DIFFRACTIONr_scbond_it2.7432463
X-RAY DIFFRACTIONr_scangle_it4.3814.52365
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1056medium positional0.140.5
22C392medium positional0.050.5
11A1019loose positional0.265
22C383loose positional0.25
11B1056medium thermal0.432
22D392medium thermal0.432
11B1019loose thermal0.7910
22D383loose thermal0.6710
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 165 -
Rwork0.237 3207 -
obs--95.77 %
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)
12.1825-1.27550.0471.29220.3382.0708-0.03470.21030.06020.0946-0.0004-0.0143-0.0421-0.08080.0350.1784-0.0207-0.02220.34240.01260.0168-0.93656.696-2.155
21.40610.2573-1.57142.6606-2.40425.1783-0.0287-0.1208-0.10750.3613-0.06810.08870.04210.02080.09670.3517-0.0218-0.00030.251-0.01260.07429.6336.31426.725
33.72450.832-2.00421.62060.2292.8006-0.03140.1251-0.1081-0.11090.0173-0.06890.1057-0.04820.01410.18790.0168-0.01650.2448-0.00290.0309-4.93654.63144.24
44.0679-0.79111.86011.7595-0.07092.6563-0.0755-0.17910.07840.06080.0303-0.0598-0.127-0.05560.04520.2083-0.01470.02030.2429-0.00790.028915.22957.43520.716
52.06341.0931-0.12241.24720.2281.851-0.0081-0.2387-0.0426-0.0856-0.01490.00770.0154-0.04140.02310.16980.01490.02280.33420.0220.0188-21.22255.18867.575
61.4136-0.6471.75773.8004-1.85133.65770.04310.10590.0329-0.7073-0.13740.0419-0.0620.08410.09430.4320.0431-0.00340.2526-0.02990.0397-10.56575.72838.641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B6 - 179
2X-RAY DIFFRACTION1B1
3X-RAY DIFFRACTION1B283
4X-RAY DIFFRACTION1B284
5X-RAY DIFFRACTION1B285
6X-RAY DIFFRACTION1B286
7X-RAY DIFFRACTION1D99
8X-RAY DIFFRACTION2B180 - 277
9X-RAY DIFFRACTION3C1 - 98
10X-RAY DIFFRACTION4D1 - 98
11X-RAY DIFFRACTION5A6 - 179
12X-RAY DIFFRACTION5A1
13X-RAY DIFFRACTION5A283
14X-RAY DIFFRACTION5A284
15X-RAY DIFFRACTION5A285
16X-RAY DIFFRACTION5A286
17X-RAY DIFFRACTION5A287
18X-RAY DIFFRACTION6A180 - 277

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