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- PDB-5nq0: Porcine (Sus scrofa) Major Histocompatibility Complex, class I, p... -

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Basic information

Entry
Database: PDB / ID: 5nq0
TitlePorcine (Sus scrofa) Major Histocompatibility Complex, class I, presenting DFEREGYSL
Components
  • ASP-PHE-GLU-ARG-GLU-GLY-TYR-SER-LEU
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC / CD8+ / SLA / Swine
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 / lumenal side of endoplasmic reticulum membrane ...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 / 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 / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / viral penetration into host nucleus / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / host cell / viral nucleocapsid / immune response / ribonucleoprotein complex / lysosomal membrane / symbiont entry into host cell / host cell nucleus / structural molecule activity / 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 / Resolution: 1.1 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 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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: MHC class I antigen
B: Beta-2-microglobulin
C: ASP-PHE-GLU-ARG-GLU-GLY-TYR-SER-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,56720
Polymers44,2263
Non-polymers1,34117
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-66 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.616, 46.340, 66.735
Angle α, β, γ (deg.)104.36, 101.21, 102.20
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31546.902 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 ASP-PHE-GLU-ARG-GLU-GLY-TYR-SER-LEU


Mass: 1116.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus / References: UniProt: Q9Q0U8*PLUS

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Non-polymers , 4 types, 555 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: PACT screen, condition A09: 0.2 M LiCl, 0.1 M Sodium Acetate, pH 5.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.1→39.28 Å / Num. obs: 170825 / % possible obs: 92.3 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 6
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 11419 / CC1/2: 0.596 / % possible all: 83.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ3

3qq3


Resolution: 1.1→39.27 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.688 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20852 8412 5 %RANDOM
Rwork0.18903 ---
obs0.18999 161372 91.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.308 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å2-0.25 Å2-0.14 Å2
2--0.06 Å20.02 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.1→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 82 538 3737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193599
X-RAY DIFFRACTIONr_bond_other_d0.0070.023156
X-RAY DIFFRACTIONr_angle_refined_deg2.1271.9494896
X-RAY DIFFRACTIONr_angle_other_deg1.06437365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14523.598189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64615596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8231532
X-RAY DIFFRACTIONr_chiral_restr0.1180.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02786
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_it0.6450.6581694
X-RAY DIFFRACTIONr_mcbond_other0.6450.6581693
X-RAY DIFFRACTIONr_mcangle_it1.0760.9812163
X-RAY DIFFRACTIONr_mcangle_other1.0750.9812164
X-RAY DIFFRACTIONr_scbond_it1.0450.7981905
X-RAY DIFFRACTIONr_scbond_other1.040.7951889
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5951.1462710
X-RAY DIFFRACTIONr_long_range_B_refined6.82310.2464152
X-RAY DIFFRACTIONr_long_range_B_other6.5768.7713997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 576 -
Rwork0.387 10484 -
obs--80.34 %
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)
11.2097-0.3444-0.23581.02450.02270.58860.04180.03010.0364-0.0275-0.0388-0.0118-0.0370.0274-0.0030.0043-0.0021-0.00720.00730.01730.07216.903747.823122.2385
20.69250.1160.3281.9694-1.67213.76260.0278-0.1615-0.02060.3059-0.0891-0.1227-0.13070.17680.06120.1384-0.0309-0.00210.12570.02040.1135-2.78239.526155.9477
32.64240.2602-0.86190.9664-0.1631.4620.0045-0.1526-0.10760.1278-0.03080.06960.0514-0.07920.02620.0233-0.0119-0.00420.02580.01890.0936-11.144933.12236.431
40.584-0.07160.2770.0153-0.03940.1464-0.01390.19070.10220.0365-0.0305-0.0435-0.06440.06130.04440.35280.00720.0160.2210.01620.3927-4.210937.35828.6063
500000000000000-00.1091000.109100.1091000
60.81340.9409-0.09951.3168-0.57351.456-0.0150.0199-0.00790.02550.01820.06750.06320.0727-0.00320.1240.0121-0.02340.10850.00030.1579-6.79340.425329.3844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B1 - 99
5X-RAY DIFFRACTION4D1 - 6
6X-RAY DIFFRACTION4F1 - 6
7X-RAY DIFFRACTION6E1 - 8

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