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- PDB-2xpg: Crystal structure of a MHC class I-peptide complex -

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Basic information

Entry
Database: PDB / ID: 2xpg
TitleCrystal structure of a MHC class I-peptide complex
Components
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-3 ALPHA CHAIN
  • MYELIN PROTEOLIPID PROTEIN
KeywordsIMMUNE SYSTEM / AUTOIMMUNITY / MULTIPLE SCLEROSIS
Function / homology
Function and homology information


positive regulation of calcium ion transmembrane transport / structural constituent of myelin sheath / axon ensheathment / central nervous system myelination / astrocyte development / integrin alphav-beta3 complex / AMPA selective glutamate receptor signaling pathway / long-chain fatty acid biosynthetic process / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target ...positive regulation of calcium ion transmembrane transport / structural constituent of myelin sheath / axon ensheathment / central nervous system myelination / astrocyte development / integrin alphav-beta3 complex / AMPA selective glutamate receptor signaling pathway / long-chain fatty acid biosynthetic process / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / axon development / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / substantia nigra development / : / : / 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 / lumenal side of endoplasmic reticulum membrane / 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 / positive regulation of type II interferon production / 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 / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / myelin sheath / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / chemical synaptic transmission / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / positive regulation of cell migration / inflammatory response / Amyloid fiber formation
Similarity search - Function
Myelin proteolipid protein PLP / Myelin proteolipid protein PLP, conserved site / Myelin proteolipid protein (PLP or lipophilin) / Myelin proteolipid protein signature 1. / Myelin proteolipid protein signature 2. / Myelin proteolipid protein (PLP or lipophilin) / 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 ...Myelin proteolipid protein PLP / Myelin proteolipid protein PLP, conserved site / Myelin proteolipid protein (PLP or lipophilin) / Myelin proteolipid protein signature 1. / Myelin proteolipid protein signature 2. / Myelin proteolipid protein (PLP or lipophilin) / 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
HLA class I histocompatibility antigen, A alpha chain / Myelin proteolipid protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMcMahon, R.M. / Friis, L. / Siebold, C. / Friese, M.A. / Fugger, L. / Jones, E.Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of Hla-A0301 in Complex with a Peptide of Proteolipid Protein: Insights Into the Role of Hla-A Alleles in Susceptibility to Multiple Sclerosis
Authors: Mcmahon, R.M. / Friis, L. / Siebold, C. / Friese, M.A. / Fugger, L. / Jones, E.Y.
History
DepositionAug 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references / 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 1.3Oct 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: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-3 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: MYELIN PROTEOLIPID PROTEIN


Theoretical massNumber of molelcules
Total (without water)44,3343
Polymers44,3343
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-16.6 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.140, 65.550, 107.210
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 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-3 ALPHA CHAIN / HLA-A3 / MHC CLASS I ANTIGEN A*3


Mass: 31628.838 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: P04439
#2: Protein BETA-2-MICROGLOBULIN / HLA-A3


Mass: 11574.885 Da / Num. of mol.: 1 / Fragment: BETA2-MICROGLOBULIN FORM PI 5.3, RESIDUES 22-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: P61769
#3: Protein/peptide MYELIN PROTEOLIPID PROTEIN / PLP PEPTIDE / PLP / LIPOPHILIN


Mass: 1130.333 Da / Num. of mol.: 1 / Fragment: RESIDUES 45-53 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P60201
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M BIS-TRIS-PROPANE, PH 8.0, 0.2 M NA/K PHOSPHATE, 20% (V/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9699 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 14030 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 34.93 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.1
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DUZ

1duz


Resolution: 2.6→19.75 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 694 5 %
Rwork0.19 --
obs0.193 13957 99.8 %
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.3 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.8684 Å20 Å20 Å2
2--8.9522 Å20 Å2
3----2.0838 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 0 16 3124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033195
X-RAY DIFFRACTIONf_angle_d0.7184330
X-RAY DIFFRACTIONf_dihedral_angle_d14.0521170
X-RAY DIFFRACTIONf_chiral_restr0.053443
X-RAY DIFFRACTIONf_plane_restr0.003569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80020.36771170.27282622X-RAY DIFFRACTION100
2.8002-3.08110.31011460.23422586X-RAY DIFFRACTION100
3.0811-3.52470.27491570.19342614X-RAY DIFFRACTION100
3.5247-4.43250.21091500.16382645X-RAY DIFFRACTION100
4.4325-19.75130.19871240.16892796X-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)
10.40830.12170.21251.0286-0.17270.1774-0.0221-0.0337-0.07550.09030.0391-0.0051-0.0663-0.138-0.00840.03790.0248-0.00090.05520.0002-0.005911.2798-4.566-11.3491
20.3374-0.1351-0.00550.0962-0.11020.39040.0151-0.04620.18960.0107-0.0617-0.0916-0.030.02140.04090.0788-0.01020.0150.091-0.00420.172743.5927-10.9477-23.5697
30.4121-0.33980.18330.4754-0.12960.28620.13440.0235-0.0203-0.1264-0.07760.0342-0.0564-0.0327-0.02930.07040.0417-0.00580.04670.00330.015823.6352-10.1987-34.8551
40.2195-0.330.16730.5578-0.3030.1712-0.1554-0.20340.01410.14840.1651-0.0266-0.0838-0.0871-0.00830.23560.0926-0.08450.23330.00440.17975.0371-3.0578-6.7923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:181)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 182:274)
3X-RAY DIFFRACTION3CHAIN B AND (RESID 2:98)
4X-RAY DIFFRACTION4CHAIN C AND (RESID 1:9)

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