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Basic information

Entry
Database: PDB / ID: 8fhl
TitleStructure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial
KeywordsIMMUNE SYSTEM / MHC / neoepitope / Mouse / Pdpr
Function / homology
Function and homology information


pyruvate dehydrogenase (lipoamide) phosphatase complex / Regulation of pyruvate dehydrogenase (PDH) complex / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response ...pyruvate dehydrogenase (lipoamide) phosphatase complex / Regulation of pyruvate dehydrogenase (PDH) complex / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / mitochondrial matrix / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / plasma membrane / cytosol / cytoplasm
Similarity search - Function
FAD dependent oxidoreductase, central domain / FAD dependent oxidoreductase central domain / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / GCVT N-terminal domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / FAD dependent oxidoreductase ...FAD dependent oxidoreductase, central domain / FAD dependent oxidoreductase central domain / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / GCVT N-terminal domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / FAD dependent oxidoreductase / FAD dependent oxidoreductase / Rhodanese-like domain / 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 / : / FAD/NAD(P)-binding domain superfamily / 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 / H-2 class I histocompatibility antigen, D-D alpha chain / Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å
AuthorsCustodio, J.M.F. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118166 United States
CitationJournal: To Be Published
Title: Structure of Pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd
Authors: Custodio, J.M.F. / Baker, B.M.
History
DepositionDec 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
C: Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9034
Polymers44,8803
Non-polymers231
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-32 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.091, 86.359, 211.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein H-2 class I histocompatibility antigen, D-D alpha chain / H-2D(D)


Mass: 32265.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01900
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial / PDPr


Mass: 954.145 Da / Num. of mol.: 1 / Fragment: neoepitope (UNP residues 627-635) / Mutation: V632L / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8NCN5
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium isothiocyanate, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→41.343 Å / Num. obs: 29908 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.055 / Rrim(I) all: 0.195 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2215 / CC1/2: 0.367

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8D5F

8d5f


Resolution: 2.194→41.343 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 14.236 / SU ML: 0.167 / Cross valid method: FREE R-VALUE / ESU R: 0.252 / ESU R Free: 0.203 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2479 1110 4.941 %
Rwork0.2096 21353 -
all0.212 --
obs-22463 99.113 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 50.643 Å2
Baniso -1Baniso -2Baniso -3
1--2.124 Å2-0 Å2-0 Å2
2--5.423 Å20 Å2
3----3.299 Å2
Refinement stepCycle: LAST / Resolution: 2.194→41.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 1 42 2865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0112899
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.6673937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.319530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88610429
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.43510144
X-RAY DIFFRACTIONr_chiral_restr0.0860.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022223
X-RAY DIFFRACTIONr_nbd_refined0.220.21155
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21913
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2910.2111
X-RAY DIFFRACTIONr_metal_ion_refined0.0610.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.27
X-RAY DIFFRACTIONr_mcbond_it3.5824.0141401
X-RAY DIFFRACTIONr_mcangle_it5.0087.1671732
X-RAY DIFFRACTIONr_scbond_it5.184.381498
X-RAY DIFFRACTIONr_scangle_it7.4087.82205
X-RAY DIFFRACTIONr_lrange_it10.45148.76711492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.194-2.250.321940.2711423X-RAY DIFFRACTION90.784
2.25-2.3120.32870.2411501X-RAY DIFFRACTION100
2.312-2.3790.227840.2251473X-RAY DIFFRACTION100
2.379-2.4520.259610.2221458X-RAY DIFFRACTION99.9342
2.452-2.5320.252740.2261379X-RAY DIFFRACTION99.8625
2.532-2.620.278760.2271369X-RAY DIFFRACTION100
2.62-2.7190.242650.2151321X-RAY DIFFRACTION100
2.719-2.8290.275640.2161233X-RAY DIFFRACTION100
2.829-2.9540.278600.2311248X-RAY DIFFRACTION99.8473
2.954-3.0980.283400.2281152X-RAY DIFFRACTION97.8654
3.098-3.2640.269530.2061096X-RAY DIFFRACTION99.913
3.264-3.4610.273640.2051051X-RAY DIFFRACTION100
3.461-3.6980.231340.193997X-RAY DIFFRACTION99.9031
3.698-3.9920.233570.18935X-RAY DIFFRACTION100
3.992-4.3690.194540.173853X-RAY DIFFRACTION100
4.369-4.8780.193350.173792X-RAY DIFFRACTION99.6385
4.878-5.6190.293310.187690X-RAY DIFFRACTION99.8615
5.619-6.850.254360.254597X-RAY DIFFRACTION99.061
6.85-9.5580.191250.191485X-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)
10.2049-0.1740.45350.5047-0.26481.69340.0064-0.03870.0219-0.1241-0.0476-0.04690.09750.0060.04130.07930.01880.02240.0703-0.00620.037-10.1694-15.080627.7244
21.0851-0.55731.80411.5415-1.65945.74220.0353-0.2021-0.01290.10370.0690.1198-0.4982-0.3896-0.10430.11480.00560.01410.041-0.00020.0105-16.94950.444319.1034
33.23650.3071-0.95592.4162-1.03690.66650.0468-0.18430.13450.2517-0.0385-0.0662-0.06860.0569-0.00820.2329-0.01920.01040.14540.020.1774-6.4295-16.444546.7186
Refinement TLS groupSelection: ALL

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