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Basic information

Entry
Database: PDB / ID: 8fhu
TitleStructure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope 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 / positive regulation of pyruvate dehydrogenase activity / 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 ...pyruvate dehydrogenase (lipoamide) phosphatase complex / positive regulation of pyruvate dehydrogenase activity / 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 / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / protein dephosphorylation / 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 / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / 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 T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / oxidoreductase activity / learning or memory / mitochondrial matrix / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / plasma membrane / cytoplasm / cytosol
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, folate-binding domain / Aminomethyltransferase folate-binding domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / FAD dependent oxidoreductase / 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, folate-binding domain / Aminomethyltransferase folate-binding 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 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
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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 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)R35GM118166 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 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release

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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
D: H-2 class I histocompatibility antigen, D-D alpha chain
E: Beta-2-microglobulin
F: Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8998
Polymers89,8216
Non-polymers782
Water3,315184
1
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)44,9494
Polymers44,9103
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-19 kcal/mol
Surface area18960 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-D alpha chain
E: Beta-2-microglobulin
F: Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9494
Polymers44,9103
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-19 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.415, 104.564, 169.993
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111TRPTRP2 - 2742 - 274
211TRPTRP2 - 2742 - 274
322ALAALA2 - 992 - 99
422ALAALA2 - 992 - 99

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01900
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pGMT7 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01887
#3: Protein/peptide Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial / PDPr


Mass: 940.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NCN5
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 56.1 % / Description: Needle
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M Potassium thiocyanate and 20% PEG 3350

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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 EIGER 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: 1.801→50 Å / Num. obs: 81134 / % possible obs: 99 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.052 / Rrim(I) all: 0.185 / Net I/σ(I): 13.2
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 11.7 % / Num. unique obs: 3638 / CC1/2: 0.261 / % possible all: 82.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
HKL-2000data reduction
BUCCANEERmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.801→49.819 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.966 / SU ML: 0.102 / Cross valid method: FREE R-VALUE / ESU R: 0.167 / ESU R Free: 0.156 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2488 3480 5.025 %
Rwork0.2081 65774 -
all0.21 --
obs-69254 73.729 %
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: 30.284 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0 Å20 Å2
2--0.722 Å2-0 Å2
3----0.082 Å2
Refinement stepCycle: LAST / Resolution: 1.801→49.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6141 0 2 184 6327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126316
X-RAY DIFFRACTIONr_angle_refined_deg2.2371.6678577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3625742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.746561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.878101015
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.7610333
X-RAY DIFFRACTIONr_chiral_restr0.1330.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024920
X-RAY DIFFRACTIONr_nbd_refined0.2140.22513
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24214
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2284
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.27
X-RAY DIFFRACTIONr_mcbond_it2.4442.1492995
X-RAY DIFFRACTIONr_mcangle_it3.4533.8453728
X-RAY DIFFRACTIONr_scbond_it4.1752.5583321
X-RAY DIFFRACTIONr_scangle_it6.1544.4614849
X-RAY DIFFRACTIONr_lrange_it7.83327.27625159
X-RAY DIFFRACTIONr_ncsr_local_group_10.140.058104
X-RAY DIFFRACTIONr_ncsr_local_group_20.1310.052844
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.139610.05007
12AX-RAY DIFFRACTIONLocal ncs0.139610.05007
23AX-RAY DIFFRACTIONLocal ncs0.131150.05008
24AX-RAY DIFFRACTIONLocal ncs0.131150.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.898-1.9530.291150.2461970X-RAY DIFFRACTION32.0375
1.953-2.0130.2811380.2322542X-RAY DIFFRACTION42.3047
2.013-2.0790.2771520.253214X-RAY DIFFRACTION55.099
2.079-2.1510.3092090.2544119X-RAY DIFFRACTION73.1452
2.151-2.2330.2812590.2414646X-RAY DIFFRACTION85.3637
2.233-2.3240.312760.2534949X-RAY DIFFRACTION94.5017
2.324-2.4270.3432230.2375049X-RAY DIFFRACTION99.1164
2.427-2.5450.2592400.224822X-RAY DIFFRACTION99.6457
2.545-2.6820.2772460.2194589X-RAY DIFFRACTION99.9173
2.682-2.8440.2742530.2344356X-RAY DIFFRACTION99.9783
2.844-3.040.2422050.2124099X-RAY DIFFRACTION99.9072
3.04-3.2820.282180.2113832X-RAY DIFFRACTION99.4597
3.282-3.5940.2191920.1963511X-RAY DIFFRACTION99.8113
3.594-4.0160.2071630.1813242X-RAY DIFFRACTION99.7364
4.016-4.6320.1741610.1562853X-RAY DIFFRACTION99.8344
4.632-5.6610.21340.1682447X-RAY DIFFRACTION99.4988
5.661-7.9540.271980.1941936X-RAY DIFFRACTION99.5595
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)
10.1172-0.17730.13170.4126-0.24660.3625-0.0669-0.01660.00880.07550.0528-0.0358-0.0795-0.01010.01410.0465-0.0071-0.01230.0270.01170.0228-22.168450.7259-5.8246
21.4790.0478-0.32862.039-0.22581.62040.0466-0.04540.1065-0.1686-0.0158-0.151-0.22140.3033-0.03070.0573-0.0480.01560.0594-0.00440.022-17.419461.6568-21.9128
30.6591.01820.27981.67160.70820.8939-0.06010.0518-0.1192-0.11470.0667-0.169-0.0662-0.0337-0.00660.0131-0.0159-0.00010.04660.01580.0439-17.802231.3882-4.4138
40.2208-0.31620.31430.484-0.38810.66560.11960.006-0.0206-0.1833-0.0460.0070.2032-0.0589-0.07360.0918-0.0005-0.0070.03710.02240.0188-0.992119.3782-38.7635
50.8275-0.20830.36980.3651-0.25441.55670.0484-0.00860.0073-0.1235-0.1073-0.04270.0087-0.20130.05890.09060.0289-0.00140.09550.01350.0111-11.998835.5742-38.9901
62.67941.74141.18863.05371.6620.9425-0.1993-0.0005-0.0057-0.22340.15670.0581-0.12430.06850.04260.0742-0.0278-0.00580.02810.02070.02735.404710.861-22.7174
Refinement TLS groupSelection: ALL

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