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

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Basic information

Entry
Database: PDB / ID: 5npz
TitlePorcine (Sus scrofa) Major Histocompatibility Complex, class I, presenting EFEDLTFLA
Components
  • Beta-2-microglobulin
  • GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC / CD8+ / SLA / swine / 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 / cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome ...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 / cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Transport of Ribonucleoproteins into the Host Nucleus / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / NEP/NS2 Interacts with the Cellular Export Machinery / vRNP Assembly / Viral Messenger RNA Synthesis / helical viral capsid / Viral mRNA Translation / 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 / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / viral penetration into host nucleus / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / host cell / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / host cell nucleus / structural molecule activity / RNA binding / extracellular space / extracellular region / identical protein binding / plasma membrane
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / MHC class I antigen / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesSus scrofa (pig)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 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 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 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

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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: GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,02311
Polymers44,4223
Non-polymers6018
Water8,935496
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-1 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.034, 128.290, 46.794
Angle α, β, γ (deg.)90.000, 101.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31775.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SLA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: B1PJV3
#2: Protein Beta-2-microglobulin / Lactollin


Mass: 11563.115 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 GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA


Mass: 1084.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus / References: UniProt: P03466*PLUS

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Non-polymers , 4 types, 504 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: TOPS screen, condition B02: 20% PEG 4000, 15% Glycerol, 0.1 M Sodium Cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.43→42.75 Å / Num. obs: 89178 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.035 / Rrim(I) all: 0.068 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1 / % possible all: 99.7

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all
1.43-1.473.10.8810.5680.5621.049
6.4-42.7540.0210.9990.0120.025

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.43 Å41.13 Å
Translation1.43 Å41.13 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER2.6.1phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHASER

Resolution: 1.43→41.17 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.206 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0634 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.067
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 4301 4.8 %RANDOM
Rwork0.1841 ---
obs0.1855 84448 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.93 Å2 / Biso mean: 19.018 Å2 / Biso min: 7.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0.05 Å2
2---0.5 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 1.43→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3130 0 39 496 3665
Biso mean--34.78 30.97 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193475
X-RAY DIFFRACTIONr_bond_other_d0.0030.023123
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.944741
X-RAY DIFFRACTIONr_angle_other_deg1.04637213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6145431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80423.967184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38915559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1451527
X-RAY DIFFRACTIONr_chiral_restr0.1180.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214110
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02865
LS refinement shellResolution: 1.429→1.466 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 290 -
Rwork0.362 6118 -
all-6408 -
obs--97 %
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)
11.5707-0.1297-0.47030.63340.22271.32710.04390.0480.0554-0.0436-0.02710.0544-0.0102-0.0573-0.01670.0045-0.0032-0.0040.06840.00770.0204-10.43873.2562-8.2784
21.65620.1010.15016.0583-1.66891.75490.0327-0.1022-0.14780.0624-0.01510.38630.1249-0.067-0.01760.0809-0.00450.01950.0853-0.02260.1277-0.4491-30.65290.2216
33.1411-1.4750.44812.2293-0.06961.3479-0.0586-0.2216-0.11990.12550.083-0.09190.14350.0533-0.02440.0282-0.0073-0.00620.10510.01150.02357.9149-11.03956.6841
400000000000000-00.1618000.161800.1618000
500000000000000-00.1618000.161800.1618000
64.13681.6243-1.01430.96680.04840.87010.07340.00730.16060.07390.1157-0.10850.07710.1265-0.18910.04460.0242-0.00060.2047-0.00580.26955.3149-4.0457-2.9067
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D0 - 180
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99

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