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

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Basic information

Entry
Database: PDB / ID: 4pgc
TitleMHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGN(3,5-diiodotyrosine)PAL
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • Sendai virus nucleoprotein
  • Unknown helical fragment
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 / 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 / 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 / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / 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)
Escherichia coli (E. coli)
Sendai virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / entity_src_nat / pdbx_entity_src_syn / 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 / _entity_src_nat.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.7Nov 6, 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
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: Sendai virus nucleoprotein
H: Unknown helical fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,75413
Polymers97,2017
Non-polymers5536
Water1,02757
1
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)48,3627
Polymers47,9933
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-17 kcal/mol
Surface area20010 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: Sendai virus nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1785
Polymers47,9933
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-15 kcal/mol
Surface area20150 Å2
MethodPISA
3
H: Unknown helical fragment


Theoretical massNumber of molelcules
Total (without water)1,2141
Polymers1,2141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.179, 90.303, 89.370
Angle α, β, γ (deg.)90.000, 111.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 27827 - 304
21GLYGLYPROPRODD1 - 27827 - 304
12ILEILEMETMETBB1 - 992 - 100
22ILEILEMETMETEE1 - 992 - 100

NCS ensembles :
ID
1
2
DetailsThere are 2 biological units in the asymmetric unit (chains A, B, and C and chains D, E, and F). Chain H is an unknown helical fragment that is not part of the biological unit.

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Components

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Protein , 2 types, 4 molecules ADBE

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


Mass: 34956.996 Da / Num. of mol.: 2 / 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.: 2 / 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 , 2 types, 3 molecules CFH

#3: Protein/peptide Sendai virus nucleoprotein


Mass: 1200.853 Da / Num. of mol.: 2 / Fragment: peptide 324-332 / Mutation: Y329(TYI) / Source method: obtained synthetically / Details: Solid Phase Peptide Synthesis / Source: (synth.) Sendai virus / References: UniProt: O57286*PLUS
#4: Protein/peptide Unknown helical fragment


Mass: 1214.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Author are quite sure that the fragment is not from H-2Kb or beta2 macroglobulin. Because E-coli was the expression system, this was the most likely source.
Source: (natural) Escherichia coli (E. coli) / Strain: BL21(DE3)pLysS

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Non-polymers , 2 types, 63 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.85 %
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: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.3→83.108 Å / Num. all: 43356 / Num. obs: 43356 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.091 / Rsym value: 0.077 / Net I/av σ(I): 8.909 / Net I/σ(I): 12 / Num. measured all: 152881
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
2.3-2.423.50.5291.52228163070.3290.5292.299.4
2.42-2.573.50.37722107759460.2340.3773.199.5
2.57-2.753.50.25331991056140.1570.2534.599.4
2.75-2.973.50.164.81857352350.10.166.999.6
2.97-3.253.50.0947.91703648060.0580.09411.199.6
3.25-3.643.50.05712.61543243710.0360.05717.499.6
3.64-4.23.50.04115.81356538550.0260.04123.999.6
4.2-5.143.50.035181146332790.0220.03528.899.6
5.14-7.273.50.03618882625300.0220.03625.899.5
7.27-50.793.30.02919471814130.0180.02932.298.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefmac_5.8.0071refinement
SCALA3.3.16data scaling
XDSdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rjz

1rjz


Resolution: 2.3→83.108 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / Matrix type: sparse / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.195 / SU B: 17.453 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 2178 5 %RANDOM
Rwork0.212 41159 --
obs0.2135 43337 99.45 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.17 Å2 / Biso mean: 39.719 Å2 / Biso min: 18.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å2-1.41 Å2
2--2.38 Å2-0 Å2
3----1.07 Å2
Refinement stepCycle: final / Resolution: 2.3→83.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6381 0 36 57 6474
Biso mean--50.26 29.27 -
Num. residues----785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196611
X-RAY DIFFRACTIONr_bond_other_d0.0020.026012
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9568984
X-RAY DIFFRACTIONr_angle_other_deg0.737313867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5923.587329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.097151063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1941548
X-RAY DIFFRACTIONr_chiral_restr0.0710.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217455
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021567
X-RAY DIFFRACTIONr_mcbond_it2.6542.6213135
X-RAY DIFFRACTIONr_mcbond_other2.6542.6213134
X-RAY DIFFRACTIONr_mcangle_it4.2223.9183907
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A160540.05
12D160540.05
21B58240.04
22E58240.04
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
2.3-2.360.3591470.3123069323799.3510.297
2.36-2.4240.3071500.3052935310099.5160.287
2.424-2.4950.3111620.2782871305599.280.258
2.495-2.5710.31650.2542748292499.6240.229
2.571-2.6560.3161280.2642730287699.3740.232
2.656-2.7490.2811480.2532598276299.4210.223
2.749-2.8520.2571360.2372504265199.5850.209
2.852-2.9690.2611310.2132457260099.5380.186
2.969-3.10.2731160.2122373249899.640.187
3.1-3.2520.2361060.2092212232899.570.191
3.252-3.4270.2611020.2162150226499.470.2
3.427-3.6350.216970.1972020212299.7640.186
3.635-3.8850.198930.1811908201099.5520.172
3.885-4.1960.2011010.1731751186099.570.169
4.196-4.5950.179880.1551616171199.5910.157
4.595-5.1350.198930.161478157699.6830.162
5.135-5.9260.279710.1981303138499.2770.197
5.926-7.2480.255600.2341098116599.3990.23
7.248-10.2120.171510.1885892198.6970.193
10.212-83.1080.305330.27448053396.2480.296
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)
11.1145-0.28170.01170.2870.12880.12740.0049-0.1657-0.07520.02520.01510.0327-0.00970.029-0.020.0359-0.0240.02470.24780.03250.0371-16.10223.631-15.1843
20.8775-0.7084-0.73811.15590.48931.05020.02880.08580.0389-0.0303-0.00580.02570.0355-0.01-0.0230.0196-0.03110.00950.27710.02170.0299-11.461921.3686-34.4771
30.85730.074-0.38850.03490.0150.3933-0.07020.08-0.0235-0.02960.0479-0.0151-0.0239-0.090.02230.0284-0.01630.0130.2409-0.02120.02841.685922.642814.8935
41.02730.7436-1.1261.0046-0.98531.63010.0526-0.11380.0286-0.0134-0.071-0.04440.0014-0.03030.01850.01660.00550.01030.3355-0.02720.0123-2.959820.809634.2061
51.5359-1.70621.8271.9043-2.03642.18070.0801-0.049-0.0919-0.10640.04850.10720.1135-0.0599-0.12860.1237-0.07140.0220.0824-0.02240.1732-11.73461.5724-34.0073
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 278
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2B1 - 99
4X-RAY DIFFRACTION3D1 - 278
5X-RAY DIFFRACTION3F1 - 9
6X-RAY DIFFRACTION4E1 - 99
7X-RAY DIFFRACTION5H4 - 16

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