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- PDB-5nq2: 'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, ... -

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Basic information

Entry
Database: PDB / ID: 5nq2
Title'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, presenting IAYERMCNI
Components
  • Beta-2-microglobulin
  • ILE-ALA-TYR-GLU-ARG-MET-CYS-ASN-ILE
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC / CD8+ / swine / influenza / Porcine Leukocyte Antigen
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / helical viral capsid / antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / helical viral capsid / antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / viral penetration into host nucleus / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / host cell / viral nucleocapsid / immune response / symbiont entry into host cell / ribonucleoprotein complex / external side of plasma membrane / signaling receptor binding / lysosomal membrane / host cell nucleus / structural molecule activity / extracellular space / RNA binding / extracellular region
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 / : ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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
MHC class I antigen / Beta-2-microglobulin / Nucleoprotein
Similarity search - Component
Biological speciesSus scrofa (pig)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsRizkallah, P.J. / Tungatt, K. / Sewell, A.K.
CitationJournal: Plos Pathog. / Year: 2018
Title: Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig.
Authors: Tungatt, K. / Dolton, G. / Morgan, S.B. / Attaf, M. / Fuller, A. / Whalley, T. / Hemmink, J.D. / Porter, E. / Szomolay, B. / Montoya, M. / Hammond, J.A. / Miles, J.J. / Cole, D.K. / ...Authors: Tungatt, K. / Dolton, G. / Morgan, S.B. / Attaf, M. / Fuller, A. / Whalley, T. / Hemmink, J.D. / Porter, E. / Szomolay, B. / Montoya, M. / Hammond, J.A. / Miles, J.J. / Cole, D.K. / Townsend, A. / Bailey, M. / Rizkallah, P.J. / Charleston, B. / Tchilian, E. / Sewell, A.K.
History
DepositionApr 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: ILE-ALA-TYR-GLU-ARG-MET-CYS-ASN-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8385
Polymers44,7363
Non-polymers1022
Water7,819434
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-24 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.478, 80.843, 61.964
Angle α, β, γ (deg.)90.000, 119.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31928.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SLA-2 / Production host: Escherichia coli (E. coli) / References: UniProt: B1A9P6
#2: Protein Beta-2-microglobulin / Lactollin


Mass: 11694.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q07717

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide ILE-ALA-TYR-GLU-ARG-MET-CYS-ASN-ILE


Mass: 1113.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus / References: UniProt: Q9Q0U8*PLUS

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Non-polymers , 3 types, 436 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: JBS Screen, condition F10: 10% Jeffamine M-600, 0.1 M Na Citrate, pH 5.6, 10 mM Ferric(III)Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.54→57.3 Å / Num. obs: 57504 / % possible obs: 97.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.54-1.623.90.660.7780.380.76497.2
4.87-57.33.60.0320.9970.0190.03793.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.61 Å57.3 Å
Translation5.61 Å57.3 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
xia22.7.17data reduction
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHASER

Resolution: 1.54→57.3 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.213 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.104
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 2921 5.1 %RANDOM
Rwork0.1914 ---
obs0.1945 54582 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.44 Å2 / Biso mean: 22.756 Å2 / Biso min: 7.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å2-0 Å2-0.81 Å2
2--1.78 Å20 Å2
3----1.14 Å2
Refinement stepCycle: final / Resolution: 1.54→57.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 5 434 3590
Biso mean--35.99 29.57 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193372
X-RAY DIFFRACTIONr_bond_other_d0.0020.022925
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9364602
X-RAY DIFFRACTIONr_angle_other_deg1.07136818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1025410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24623.799179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99615543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2131527
X-RAY DIFFRACTIONr_chiral_restr0.0560.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213860
X-RAY DIFFRACTIONr_gen_planes_other00.02735
X-RAY DIFFRACTIONr_rigid_bond_restr3.33133361
X-RAY DIFFRACTIONr_sphericity_free14.01451
X-RAY DIFFRACTIONr_sphericity_bonded5.35453259
LS refinement shellResolution: 1.541→1.581 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 215 -
Rwork0.294 3994 -
all-4209 -
obs--96.83 %
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)
11.3885-0.4141-0.34122.15140.17511.75190.04370.2339-0.0251-0.0794-0.10990.26590.1411-0.610.06620.0507-0.0670.02270.2446-0.03280.1105-31.0207-12.21928.3726
22.33830.50081.49751.06160.81995.06570.03430.07510.31110.015-0.0648-0.0961-0.46610.04530.03040.082-0.00680.0550.00990.01790.162-23.03258.24736.6167
32.3984-0.8385-2.41981.05231.06593.6274-0.18380.0768-0.09890.16210.04960.08580.282-0.22530.13420.0767-0.02320.03920.042-0.01040.0844-31.3877-12.443936.042
40.0402-0.258-0.35341.68042.29663.1399-0.0034-0.0110.01540.01370.0582-0.02820.0180.0797-0.05490.2015-0.0263-0.00860.2016-0.01270.2333-3.01835.748237.0071
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 277
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4E301 - 317

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