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

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Basic information

Entry
Database: PDB / ID: 4pge
TitleMHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGNYPAW
Components
  • Beta-2-microglobulinBeta-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


TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / helical viral capsid / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / inner ear development / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / viral nucleocapsid / cellular response to lipopolysaccharide / intracellular iron ion homeostasis
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 / MHC class I-like antigen recognition-like ...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 / Immunoglobulins / Immunoglobulin-like fold / 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 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
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.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)48,60411
Polymers47,8153
Non-polymers7898
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-50 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.933, 136.665, 45.231
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is the same as asymmetric unit

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Components

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Protein , 2 types, 2 molecules AB

#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 / 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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Sendai virus nucleoprotein


Mass: 1022.112 Da / Num. of mol.: 1 / Fragment: peptide 324-332 / Mutation: L332W / Source method: obtained synthetically / Details: Solid Phase Peptide Synthesis / Source: (synth.) Sendai virus / References: UniProt: O57286*PLUS

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Non-polymers , 3 types, 112 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.72 %
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→73.948 Å / Num. all: 37692 / Num. obs: 37692 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 34.17 Å2 / Rpim(I) all: 0.061 / Rrim(I) all: 0.123 / Rsym value: 0.106 / Net I/av σ(I): 6.584 / Net I/σ(I): 9.1 / Num. measured all: 144680
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.113.90.6231.22091954080.3610.6232.3100
2.11-2.243.90.4351.71986751290.2520.4353.1100
2.24-2.393.90.3262.31878148620.1880.3264.1100
2.39-2.583.90.2433.11751045160.140.2435.2100
2.58-2.833.90.164.71619541940.0920.167.3100
2.83-3.163.90.1047.11453237660.060.10410.799.9
3.16-3.653.80.06610.41289833700.0380.06616.699.9
3.65-4.473.70.04613.91068528740.0270.04622.499.8
4.47-6.323.80.03517.5859722680.0210.03523.299.8
6.32-42.943.60.02818.3469613050.0170.02821.198.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
XDSdata scaling
REFMACrefmac_5.7.0032refinement
Cootmodel building
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vab

2vab


Resolution: 2→42.98 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / Matrix type: sparse / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.183 / SU B: 7.807 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 1885 5 %RANDOM
Rwork0.2009 35766 --
obs0.2026 37651 99.82 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 83.42 Å2 / Biso mean: 28.105 Å2 / Biso min: 14.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 2→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 52 104 3282
Biso mean--43.18 27.95 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193305
X-RAY DIFFRACTIONr_bond_other_d0.0010.023039
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.9534489
X-RAY DIFFRACTIONr_angle_other_deg0.6813.0026994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8815389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57823.353170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3415537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6221527
X-RAY DIFFRACTIONr_chiral_restr0.0680.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02799
X-RAY DIFFRACTIONr_mcbond_it1.5222.0641535
X-RAY DIFFRACTIONr_mcbond_other1.5222.0641534
X-RAY DIFFRACTIONr_mcangle_it2.4433.0851916
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2-2.0520.2831290.267261327421000.259
2.052-2.1080.291170.253254226591000.24
2.108-2.1690.2811540.248245026041000.234
2.169-2.2360.2431290.227238925181000.211
2.236-2.3090.2921230.22233624591000.202
2.309-2.390.2851200.232228524051000.21
2.39-2.480.231100.2162176228799.9560.195
2.48-2.5810.2621150.222096221299.9550.195
2.581-2.6960.2151090.207201321221000.182
2.696-2.8270.2461080.21196620741000.189
2.827-2.980.2581020.211807191099.9480.187
2.98-3.1610.198930.1941753185099.7840.175
3.161-3.3780.204950.1981654175299.8290.181
3.378-3.6480.2241010.1891514161699.9380.174
3.648-3.9960.232660.1751444151399.8020.168
3.996-4.4660.196600.1521303137099.4890.15
4.466-5.1530.193340.1531195123199.8380.151
5.153-6.3040.246450.19998105199.2390.184
6.304-8.8830.201570.19576883598.8020.189
8.883-73.9480.227180.22646450894.8820.241
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)
10.51750.1131-0.14580.2925-0.06370.0813-0.02440.0303-0.069-0.0173-0.00910.029-0.01850.00670.03350.0501-0.0034-0.00490.0238-0.01330.045942.152918.5756-0.4018
21.2975-0.4759-0.88820.3878-0.02041.2258-0.08280.02210.05010.03480.0507-0.03060.0509-0.07650.03220.01620.0046-0.00890.050.00310.061929.461729.44337.0325
30.44140.5347-0.95720.9621-1.57532.6261-0.08660.009-0.0611-0.017-0.1733-0.17030.07420.22470.25990.0694-0.0434-0.01120.1110.05630.038458.243925.4264-5.4092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 274
2X-RAY DIFFRACTION2B1 - 99
3X-RAY DIFFRACTION3C1 - 9

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