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- PDB-5nq3: 'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, ... -

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Basic information

Entry
Database: PDB / ID: 5nq3
Title'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro globulin, presenting EFEDLTFLA
Components
  • Beta-2-microglobulin
  • GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC / CD8+ / influenza / swine / SLA
Function / homology
Function and homology information


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 / vRNA Synthesis ...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 / vRNA Synthesis / Viral RNP Complexes in the Host Cell Nucleus / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral Messenger RNA Synthesis / vRNP Assembly / helical viral capsid / antigen processing and presentation of peptide antigen via MHC class I / Viral mRNA Translation / : / : / negative regulation of receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / 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 / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / positive regulation of protein binding / specific granule lumen / viral penetration into host nucleus / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / host cell / negative regulation of neuron projection development / iron ion transport / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / ribonucleoprotein complex / symbiont entry into host cell / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome
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 / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 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 / 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 1.3Oct 16, 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: GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA
D: MHC class I antigen
E: Beta-2-microglobulin
F: GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,81812
Polymers89,2836
Non-polymers5346
Water14,322795
1
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)44,8345
Polymers44,6423
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-63 kcal/mol
Surface area19050 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9847
Polymers44,6423
Non-polymers3424
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-39 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.301, 59.696, 66.443
Angle α, β, γ (deg.)81.48, 67.62, 68.60
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA1 - 2761 - 276
21ASPASPDD1 - 2761 - 276
12METMETBB0 - 991 - 100
22METMETEE0 - 991 - 100

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein MHC class I antigen


Mass: 31678.094 Da / Num. of mol.: 2
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


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide GLU-PHE-GLU-ASP-LEU-THR-PHE-LEU-ALA


Mass: 1084.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus / References: UniProt: P03466*PLUS

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Non-polymers , 4 types, 801 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 795 / 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: 45.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: JBS screen, condition A07: 30% MPD, 100 mM Na Citrate, pH 5.6, 200 mM Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.57→61.44 Å / Num. obs: 105240 / % possible obs: 96 % / Redundancy: 1.9 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.7
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.665 / % possible all: 93.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.36 Å60.78 Å
Translation2.36 Å60.78 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.26data scaling
xia22.6.1data reduction
PDB_EXTRACT3.22data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5QQ3

5qq3


Resolution: 1.57→61.44 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.374 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26232 5113 4.9 %RANDOM
Rwork0.21772 ---
obs0.21989 99669 95.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.823 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20.07 Å20.14 Å2
2--0.17 Å20.44 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.57→61.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6290 0 31 795 7116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196672
X-RAY DIFFRACTIONr_bond_other_d0.0020.025794
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9389070
X-RAY DIFFRACTIONr_angle_other_deg1.058313476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6795799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50123.611360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.436151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.821558
X-RAY DIFFRACTIONr_chiral_restr0.120.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217568
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021474
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_it0.9691.5113166
X-RAY DIFFRACTIONr_mcbond_other0.9691.5113165
X-RAY DIFFRACTIONr_mcangle_it1.542.2583975
X-RAY DIFFRACTIONr_mcangle_other1.542.2583976
X-RAY DIFFRACTIONr_scbond_it1.4741.733506
X-RAY DIFFRACTIONr_scbond_other1.471.733506
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2672.5195096
X-RAY DIFFRACTIONr_long_range_B_refined6.04319.367745
X-RAY DIFFRACTIONr_long_range_B_other5.88518.3617540
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A183080.07
12D183080.07
21B66560.04
22E66560.04
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 353 -
Rwork0.394 7133 -
obs--92.29 %
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)
13.0542-0.6545-1.06160.8792-0.0361.4812-0.0254-0.1516-0.08570.07980.0095-0.0074-0.0101-0.02110.01590.0324-0.0201-0.02620.02860.02490.027436.702840.276739.2885
21.2453-0.1372-0.17743.28552.47163.8522-0.033-0.0113-0.16810.31010.00270.00140.43450.02690.03030.0566-0.0151-0.01830.05550.05630.105421.39625.808410.9199
33.0995-1.01281.97451.147-0.84882.3726-0.00160.28160.114-0.1281-0.0039-0.0275-0.12850.11770.00550.0619-0.0162-0.01220.04030.02310.031633.002645.431512.7405
40.9524-0.28120.31222.57410.30661.95640.03030.0653-0.0619-0.17050.00260.03740.0999-0.0008-0.03290.0222-0.0094-0.01320.02710.01960.029350.101221.0034-1.3764
52.8041-0.5034-2.04411.48880.76314.75330.07750.10270.20410.0681-0.10840.1861-0.2793-0.410.03090.081-0.0099-0.02250.07010.01980.105530.718611.508926.9672
60.6171-0.22240.01893.9988-2.43762.67160.0221-0.16620.010.3445-0.0045-0.0771-0.06630.1484-0.01760.0536-0.0019-0.02080.07420.01430.033153.117815.48725.3189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 180
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99

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