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- PDB-4pgd: MHC Class I in complex with modified Sendai virus nucleoprotein p... -

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Basic information

Entry
Database: PDB / ID: 4pgd
TitleMHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGNYPAF
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • Sendai virus nucleoprotein
KeywordsIMMUNE SYSTEM/PEPTIDE / IMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / IMMUNE RESPONSE / IMMUNE SYSTEM-PEPTIDE complex
Function / homology
Function and homology information


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 / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent ...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 / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / 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 / peptide antigen binding / 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 / viral nucleocapsid / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / defense response to bacterium / ribonucleoprotein complex / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / cytosol
Similarity search - Function
Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / 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 / : ...Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / 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
Nucleoprotein / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Sendai virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCelie, P. / Joosten, R.P. / Perrakis, A. / Neefjes, J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: The first step of peptide selection in antigen presentation by MHC class I molecules.
Authors: Garstka, M.A. / Fish, A. / Celie, P.H. / Joosten, R.P. / Janssen, G.M. / Berlin, I. / Hoppes, R. / Stadnik, M. / Janssen, L. / Ovaa, H. / van Veelen, P.A. / Perrakis, A. / Neefjes, J.
History
DepositionMay 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Feb 11, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.7Oct 23, 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-B alpha chain
B: Beta-2-microglobulin
C: Sendai virus nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8684
Polymers47,7763
Non-polymers921
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-27 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.047, 137.027, 45.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is the same as asymmetric unit

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Components

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


Mass: 34956.996 Da / Num. of mol.: 1 / Fragment: heavy chain, UNP residues 22-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01887
#3: Protein/peptide Sendai virus nucleoprotein


Mass: 983.076 Da / Num. of mol.: 1 / Fragment: peptide 324-332 / Mutation: L332F / Source method: obtained synthetically / Details: Solid Phase Peptide Synthesis / Source: (synth.) Sendai virus / References: UniProt: O57286*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium/potassium phosphate buffer 1.9M, MPD 1%, glycerol (cryoprotection)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→74.074 Å / Num. all: 15630 / Num. obs: 15630 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 39.42 Å2 / Rpim(I) all: 0.082 / Rrim(I) all: 0.162 / Rsym value: 0.139 / Net I/av σ(I): 4.688 / Net I/σ(I): 10.6 / Num. measured all: 58928
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.7-2.853.90.551.3868722450.3210.553.899.6
2.85-3.023.80.4151.7815921250.2440.4154.799.9
3.02-3.233.80.2712.6761019900.1590.2716.399.8
3.23-3.493.80.1763.9711918620.1020.1768.599.7
3.49-3.823.70.1126.3648317320.0660.11211.899.8
3.82-4.273.70.0789571315590.0470.07814.899.8
4.27-4.933.70.05711.9524514080.0330.05718.499.7
4.93-6.043.80.05612.2449811940.0330.05616.899.6
6.04-8.543.70.04615.235009430.0280.04617.599.3
8.54-45.6763.30.046.819145720.0280.0421.898.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SCALA3.3.20data scaling
XDSdata scaling
Cootmodel building
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VAB

2vab


Resolution: 2.7→45.22 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.885 / SU B: 25.246 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.683 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.259 773 5 %RANDOM
Rwork0.21 ---
obs0.213 15605 99.5 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.5 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--0.97 Å20 Å2
3----0.43 Å2
Refinement stepCycle: final / Resolution: 2.7→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 6 15 3144
Biso mean--57.08 16.57 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193222
X-RAY DIFFRACTIONr_bond_other_d0.0010.022938
X-RAY DIFFRACTIONr_angle_refined_deg0.9261.9434377
X-RAY DIFFRACTIONr_angle_other_deg0.6623.0026764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3855379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40123.515165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52115525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6141524
X-RAY DIFFRACTIONr_chiral_restr0.0570.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213649
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02781
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7141.9931525
X-RAY DIFFRACTIONr_mcbond_other1.7121.9931524
X-RAY DIFFRACTIONr_mcangle_it3.0282.9781901
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 47 -
Rwork0.248 1076 -
obs--99.29 %
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)
10.56420.2156-0.33550.60330.01880.3662-0.00320.0208-0.0595-0.0142-0.04880.08230.03780.05690.0520.04730.0169-0.00930.0699-0.01460.059142.093618.6245-0.2458
22.3266-0.7899-2.08040.61460.0843.2896-0.11670.02290.0270.0489-0.0035-0.02370.0144-0.04040.12020.03270.0188-0.03270.0349-0.02160.084528.706129.12667.2
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 274
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2B1 - 99

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