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- PDB-8d5k: The complex of Pre-mRNA-Processing Factor 19 (Prpf19) peptide KYL... -

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Basic information

Entry
Database: PDB / ID: 8d5k
TitleThe complex of Pre-mRNA-Processing Factor 19 (Prpf19) peptide KYLQVASHV Presented by H2-Kd
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-D alpha chain
  • 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 / positive regulation of mRNA splicing, via spliceosome / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...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 / positive regulation of mRNA splicing, via spliceosome / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / U2-type catalytic step 2 spliceosome / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / inner cell mass cell proliferation / ubiquitin-ubiquitin ligase activity / lipid biosynthetic process / antigen processing and presentation of exogenous peptide antigen via MHC class I / spliceosomal complex assembly / MHC class I protein binding / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / spliceosomal tri-snRNP complex assembly / Prp19 complex / protein K63-linked ubiquitination / negative regulation of neuron differentiation / cellular defense response / proteasomal protein catabolic process / lipid droplet / Neutrophil degranulation / positive regulation of neuron differentiation / DNA damage checkpoint signaling / 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 / 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 / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / peptide antigen binding / negative regulation of neurogenesis / double-strand break repair via nonhomologous end joining / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / spindle / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / protein polyubiquitination / negative regulation of epithelial cell proliferation / ubiquitin protein ligase activity / sensory perception of smell / intracellular protein localization / site of double-strand break / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / nuclear speck / defense response to bacterium / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
U-box domain / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain profile. / Modified RING finger domain / U-box domain / 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 ...U-box domain / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain profile. / Modified RING finger domain / U-box domain / 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 / Zinc finger, RING/FYVE/PHD-type / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Ig-like domain profile. / Immunoglobulin-like domain / Trp-Asp (WD) repeats circular profile. / Immunoglobulin-like domain superfamily / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing 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, K-D alpha chain / Pre-mRNA-processing factor 19
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.066 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: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes.
Authors: Custodio, J.M. / Ayres, C.M. / Rosales, T.J. / Brambley, C.A. / Arbuiso, A.G. / Landau, L.M. / Keller, G.L.J. / Srivastava, P.K. / Baker, B.M.
History
DepositionJun 5, 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 1.2Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: H-2 class I histocompatibility antigen, K-D alpha chain
B: Beta-2-microglobulin
C: Pre-mRNA-processing factor 19


Theoretical massNumber of molelcules
Total (without water)45,0403
Polymers45,0403
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-20 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.370, 66.200, 56.790
Angle α, β, γ (deg.)90.000, 92.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 32114.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01902
#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 / Plasmid: pGMT7 / 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: 1090.255 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.: 55 / 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: 2.4348 Å3/Da / Density % sol: 49.5142 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 10% w/v PEG8000, 200 mM magnesium 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: Jun 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→41.349 Å / Num. obs: 23784 / % possible obs: 90.4 % / Redundancy: 2.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.067 / Rrim(I) all: 0.096 / Net I/σ(I): 14.6
Reflection shellResolution: 1.95→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.281 / Num. unique obs: 8577 / CC1/2: 0.899 / Rpim(I) all: 0.278 / Rrim(I) all: 0.396 / % possible all: 97

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Processing

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

1vgk


Resolution: 2.066→41.349 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.527 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.191 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2335 1254 5.272 %
Rwork0.2027 22530 -
all0.204 --
obs-23784 90.245 %
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: 46.908 Å2
Baniso -1Baniso -2Baniso -3
1--0.426 Å20 Å20.163 Å2
2--3.235 Å20 Å2
3----2.812 Å2
Refinement stepCycle: LAST / Resolution: 2.066→41.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 0 55 3194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0113236
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.6544402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6775378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.7141028
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06710510
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.38810173
X-RAY DIFFRACTIONr_chiral_restr0.120.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022537
X-RAY DIFFRACTIONr_nbd_refined0.2250.21368
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2169
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5010.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3260.29
X-RAY DIFFRACTIONr_mcbond_it3.0643.6681524
X-RAY DIFFRACTIONr_mcangle_it4.1885.4741898
X-RAY DIFFRACTIONr_scbond_it4.2483.9991712
X-RAY DIFFRACTIONr_scangle_it5.8055.8562504
X-RAY DIFFRACTIONr_lrange_it8.0872.07113089
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
2.066-2.1190.322810.26411800.26819560.920.9564.46830.236
2.119-2.1770.2831040.2316260.23318820.9520.96491.92350.207
2.177-2.240.257950.22215580.22417990.9510.96791.88440.203
2.24-2.3090.28860.23215450.23418170.9430.96589.76330.211
2.309-2.3850.275650.21314270.21517080.9570.97187.35360.186
2.385-2.4680.283720.22514880.22816930.950.96992.14410.206
2.468-2.5610.257860.23714520.23815930.9590.96696.54740.22
2.561-2.6650.308830.22414020.22915520.9480.9795.6830.209
2.665-2.7830.251610.20713690.20914900.9610.97495.97320.197
2.783-2.9180.307440.23412980.23714170.9450.96594.70710.231
2.918-3.0750.289600.23912070.24113640.9490.96492.88860.24
3.075-3.260.32550.22511060.22912810.9280.96890.63230.231
3.26-3.4840.238590.2119690.21212300.9650.97483.57720.227
3.484-3.7610.237380.2049950.20611230.9650.97891.98570.221
3.761-4.1160.239490.2039260.20510390.9670.97693.84020.233
4.116-4.5970.201550.168150.1639500.9720.98691.57890.193
4.597-5.2970.162500.167290.168370.9830.98693.07050.201
5.297-6.4610.231540.1876280.1917190.9720.9894.8540.222
6.461-9.0280.169260.185030.1795590.9870.98394.63330.224
9.028-41.3490.165310.1673070.1673430.9870.98398.54230.201
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)
10.8750.18910.79860.46750.17430.8428-0.00450.1485-0.0223-0.0240.0357-0.0217-0.12510.1183-0.03120.1250.01360.01590.0314-0.00160.003120.559725.89814.5167
21.25630.75610.81292.24551.28032.15580.1423-0.05630.06130.1642-0.06430.0911-0.08330.0517-0.0780.089-0.04280.03190.0208-0.01450.020218.910628.359533.4409
32.46230.77120.56371.72061.61691.57230.04780.47540.0995-0.12910.0294-0.0752-0.1584-0.0956-0.07720.11570.0594-0.03060.25280.05380.04215.5122.00313.2152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 180
2X-RAY DIFFRACTION1ALLA181 - 274

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