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- PDB-2xfx: cattle MHC class I N01301 presenting an 11mer from Theileria parva -

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Basic information

Entry
Database: PDB / ID: 2xfx
Titlecattle MHC class I N01301 presenting an 11mer from Theileria parva
Components
  • BETA-2-MICROGLOBULIN
  • MHC CLASS 1
  • UNCHARACTERIZED PROTEIN
KeywordsIMMUNE SYSTEM / MAJOR HISTOCOMPATIBILITY / EAST COAST FEVER / THEILERIOSIS
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / immune response / lysosomal membrane / extracellular region / membrane
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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
Beta-2-microglobulin / MHC class 1 / Uncharacterized protein
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
THEILERIA PARVA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMacdonald, I.K. / Harkiolaki, M. / Hunt, L. / Morrison, W.I. / Connelley, T. / Graham, S.P. / Jones, E.Y. / Flower, D.R. / Ellis, S.A.
CitationJournal: Plos Pathog. / Year: 2010
Title: Mhc Class I Bound to an Immunodominant Theileria Parva Epitope Demonstrates Unconventional Presentation to T Cell Receptors.
Authors: Macdonald, I.K. / Harkiolaki, M. / Hunt, L. / Connelley, T. / Carroll, A.V. / Machugh, N.D. / Graham, S.P. / Jones, E.Y. / Morrison, W.I. / Flower, D.R. / Ellis, S.A.
History
DepositionMay 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 6, 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: MHC CLASS 1
B: BETA-2-MICROGLOBULIN
C: UNCHARACTERIZED PROTEIN


Theoretical massNumber of molelcules
Total (without water)45,2703
Polymers45,2703
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-17 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.611, 97.888, 123.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC CLASS 1 / N01301


Mass: 32251.480 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-297
Source method: isolated from a genetically manipulated source
Details: MHC CLASS I ALPHA CHAIN / Source: (gene. exp.) BOS TAURUS (domestic cattle) / Strain: BRITISH FRIESIAN CATTLE / Plasmid: POPIN-I / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTABLUE (DE3) / References: UniProt: Q30291
#2: Protein BETA-2-MICROGLOBULIN / LACTOLLIN


Mass: 11724.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Strain: BRITISH FRIESIAN CATTLE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTABLUE (DE3) / References: UniProt: P01888
#3: Protein/peptide UNCHARACTERIZED PROTEIN


Mass: 1294.558 Da / Num. of mol.: 1 / Fragment: 214-224 / Source method: isolated from a natural source / Source: (natural) THEILERIA PARVA (eukaryote) / References: UniProt: Q4MYJ2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.99 Å3/Da / Density % sol: 58.9 % / Description: NONE
Crystal growpH: 7 / Details: 20% PEG 8000, 50MM POTASSIUM PHOSPHATE, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 44056 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0070refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AGF

1agf


Resolution: 1.9→45.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.667 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 2207 5.1 %RANDOM
Rwork0.1978 ---
obs0.1998 41373 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.304 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 0 149 3341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0213282
X-RAY DIFFRACTIONr_bond_other_d0.0010.022320
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9474450
X-RAY DIFFRACTIONr_angle_other_deg1.033.0025568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12323.352182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12715546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.581533
X-RAY DIFFRACTIONr_chiral_restr0.1260.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02712
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 159 -
Rwork0.311 3042 -
obs--99.72 %
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)
10.49820.1841-0.58050.88540.1322.35970.05130.010.03590.2245-0.03790.00610.08920.0034-0.01340.14240.0059-0.00910.0135-0.01960.057877.021439.038430.1836
20.55610.14070.74990.58231.22073.1165-0.0031-0.0666-0.0723-0.1886-0.00870.045-0.36430.05740.01180.1339-0.01290.01370.1103-0.00250.049978.584361.25432.9747
30.714-0.15360.28360.21460.2881.0068-0.03970.0499-0.037-0.022-0.0215-0.0027-0.1256-0.11370.06120.05780.0243-0.00510.0701-0.01860.106672.719740.81493.7307
42.8356-0.9062-1.67611.26510.95051.1702-0.1725-0.1393-0.0724-0.00930.1360.00890.06510.10720.03640.0780.01950.00660.0970.00450.082473.40436.0306-4.7008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 99
2X-RAY DIFFRACTION2A181 - 277
3X-RAY DIFFRACTION3A1 - 180
4X-RAY DIFFRACTION4C8 - 18

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