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- PDB-8d5j: The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen ... -

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Basic information

Entry
Database: PDB / ID: 8d5j
TitleThe complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd
Components
  • Beta-2-microglobulin
  • MHC class I heavy chain maturation peptide H-2K(D)
  • Pre-mRNA-processing factor 19
KeywordsIMMUNE SYSTEM / Complex / MHC
Function / homology
Function and homology information


Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / mRNA Splicing - Major Pathway / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication factor A complex / positive regulation of astrocyte differentiation / Prp19 complex / U2-type catalytic step 1 spliceosome / U2-type catalytic step 2 spliceosome / Endosomal/Vacuolar pathway ...Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / mRNA Splicing - Major Pathway / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication factor A complex / positive regulation of astrocyte differentiation / Prp19 complex / U2-type catalytic step 1 spliceosome / U2-type catalytic step 2 spliceosome / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of mRNA splicing, via spliceosome / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / ubiquitin-ubiquitin ligase activity / lipid biosynthetic process / spliceosomal complex assembly / protein K63-linked ubiquitination / spliceosomal tri-snRNP complex assembly / cellular defense response / proteasomal protein catabolic process / Neutrophil degranulation / lipid droplet / DNA damage checkpoint signaling / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / spliceosomal complex / 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 / RING-type E3 ubiquitin transferase / 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 / mRNA splicing, via spliceosome / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / double-strand break repair via nonhomologous end joining / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / spindle / positive regulation of T cell mediated cytotoxicity / protein polyubiquitination / ubiquitin-protein transferase activity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / ubiquitin protein ligase activity / positive regulation of T cell activation / sensory perception of smell / protein localization / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / site of double-strand break / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / nuclear speck / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / 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 / Zinc finger, RING/FYVE/PHD-type / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I heavy chain maturation peptide H-2K(D) / Pre-mRNA-processing factor 19
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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: The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd
Authors: Custodio, J.M.F. / Baker, B.M.
History
DepositionJun 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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 I heavy chain maturation peptide H-2K(D)
B: Beta-2-microglobulin
C: Pre-mRNA-processing factor 19


Theoretical massNumber of molelcules
Total (without water)45,1283
Polymers45,1283
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-19 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.440, 66.570, 56.960
Angle α, β, γ (deg.)90.000, 92.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-379-

HOH

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Components

#1: Protein MHC class I heavy chain maturation peptide H-2K(D)


Mass: 32245.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6RJ37
#2: Protein Beta-2-microglobulin


Mass: 11835.555 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 BL21(DE3) (bacteria) / References: UniProt: P01887
#3: Protein/peptide Pre-mRNA-processing factor 19 / Nuclear matrix protein 200 / PRP19/PSO4 homolog / RING-type E3 ubiquitin transferase PRP19 / ...Nuclear matrix protein 200 / PRP19/PSO4 homolog / RING-type E3 ubiquitin transferase PRP19 / Senescence evasion factor


Mass: 1046.219 Da / Num. of mol.: 1 / Fragment: UNP residues 206-214 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
References: UniProt: Q99KP6, RING-type E3 ubiquitin transferase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.4336634 Å3/Da / Density % sol: 49.490311 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% w/v PEG3000, 100 mM HEPES, 200 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→40.902 Å / Num. obs: 30593 / % possible obs: 97.1 % / Redundancy: 4.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.103 / Rrim(I) all: 0.173 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.94-40.876.30.06821990.9950.0440.081
1.95-240.7485770.6820.5940.954

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
REFMAC5.8.0350refinement
SCALEPACKdata scaling
PHASERphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VGK

1vgk


Resolution: 1.95→40.902 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.201 / SU B: 8.752 / SU ML: 0.117 / Average fsc free: 0.9598 / Average fsc work: 0.9734 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.155 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2297 1561 5.102 %
Rwork0.186 29032 -
all0.188 --
obs-30593 96.868 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.061 Å2
Baniso -1Baniso -2Baniso -3
1--0.596 Å20 Å20.062 Å2
2--0.595 Å20 Å2
3----0.003 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 0 123 3274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0113249
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.6544421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.5671027
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18410516
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.76110170
X-RAY DIFFRACTIONr_chiral_restr0.1110.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022537
X-RAY DIFFRACTIONr_nbd_refined0.2250.21196
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22193
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2163
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2530.26
X-RAY DIFFRACTIONr_mcbond_it2.6662.8561533
X-RAY DIFFRACTIONr_mcangle_it3.9074.2641911
X-RAY DIFFRACTIONr_scbond_it4.0273.2221716
X-RAY DIFFRACTIONr_scangle_it6.1374.6522510
X-RAY DIFFRACTIONr_lrange_it8.41941.9224739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.95-20.2761220.23221180.23423110.9520.96496.92770.223
2-2.0550.2651200.22220600.22422360.9460.96897.49550.213
2.055-2.1150.2731020.22620720.22822110.9530.96798.32660.211
2.115-2.1790.2711180.21519760.21821430.960.97297.71350.206
2.179-2.2510.2771140.21818850.22120510.9520.96997.46470.207
2.251-2.3290.2641120.22218000.22420090.9580.96895.17170.212
2.329-2.4170.298780.22918320.23219340.9370.96898.7590.224
2.417-2.5150.2531040.21917370.22118670.960.97298.60740.216
2.515-2.6270.235810.20216780.20317870.9610.97698.43310.2
2.627-2.7550.242870.20716170.20917240.9650.97598.83990.212
2.755-2.9030.286600.21315290.21516280.9560.97397.60440.225
2.903-3.0780.329500.21314350.21615360.9410.97196.67970.229
3.078-3.2890.258750.19712680.214600.9640.97691.98630.215
3.289-3.5510.219640.18911940.19113570.9720.97892.70450.207
3.551-3.8870.202760.16111090.16312400.9760.98595.56450.19
3.887-4.3410.185490.1510310.15211450.9850.98794.32310.178
4.341-5.0030.154380.1329110.13210020.9840.99194.71060.166
5.003-6.1040.193540.167850.1628590.9790.98697.67170.198
6.104-8.5380.182360.1756170.1766720.9790.98597.17260.217
8.538-40.9020.211210.1423780.1454010.9760.98799.50120.178
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)
10.43680.13410.39610.26720.14230.38530.0040.0853-0.0336-0.00270.0253-0.0093-0.05190.0671-0.02940.1217-0.00410.00260.0995-0.00070.003120.63625.655914.6311
20.53820.62920.43850.95870.76151.30950.1277-0.03250.01670.0803-0.11720.0647-0.04080.0439-0.01050.1116-0.04090.00230.1102-0.030.024919.184728.151133.6841
30.32680.7559-0.355.53820.49590.84130.04180.08250.0266-0.0370.0224-0.0061-0.0646-0.1121-0.06420.07090.0366-0.02790.1310.00090.0365.490121.40143.6313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 180
2X-RAY DIFFRACTION1ALLA181 - 274

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