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- PDB-5nq1: Porcine (Sus scrofa) Major Histocompatibility Complex, class I, w... -

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Basic information

Entry
Database: PDB / ID: 5nq1
TitlePorcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro globulin, presenting DFEREGYSL
Components
  • ASP-PHE-GLU-ARG-GLU-GLY-TYR-SER-LEU
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / SLA / MHC / swine / influenza virus / Porcine Leukocyte Antigen
Function / homology
Function and homology information


helical viral capsid / antigen processing and presentation of peptide antigen via MHC class I / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion ...helical viral capsid / antigen processing and presentation of peptide antigen via MHC class I / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / 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 / 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 / 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 / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / viral penetration into host nucleus / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / host cell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / symbiont entry into host cell / ribonucleoprotein complex / 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 / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
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)
Homo sapiens (human)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 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 1.3Nov 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
D: MHC class I antigen
E: Beta-2-microglobulin
F: ASP-PHE-GLU-ARG-GLU-GLY-TYR-SER-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,81812
Polymers89,3476
Non-polymers4706
Water6,413356
1
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)44,7985
Polymers44,6743
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-15 kcal/mol
Surface area19150 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: ASP-PHE-GLU-ARG-GLU-GLY-TYR-SER-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0207
Polymers44,6743
Non-polymers3464
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-55 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.388, 60.288, 65.645
Angle α, β, γ (deg.)81.240, 67.590, 67.940
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 ASP-PHE-GLU-ARG-GLU-GLY-TYR-SER-LEU


Mass: 1116.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus / References: UniProt: Q9Q0U8*PLUS

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Non-polymers , 4 types, 362 molecules

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


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: PACT screen, condition D02: 0.1M MMT Buffer, pH 5.0, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.14→55.87 Å / Num. obs: 41686 / % possible obs: 96.9 % / Redundancy: 1.9 % / CC1/2: 0.979 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.115 / Rrim(I) all: 0.172 / Net I/σ(I): 3.4 / Num. measured all: 79873 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.14-2.21.90.669562330240.5220.6140.911.796
9.57-55.872.10.03810234760.9950.0310.055.799.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.16 Å60.48 Å
Translation5.16 Å60.48 Å

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
DIALS2.6.1data reduction
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ3

3qq3


Resolution: 2.14→55.87 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.865 / SU B: 21.839 / SU ML: 0.265 / SU R Cruickshank DPI: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.257
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2021 4.8 %RANDOM
Rwork0.2195 ---
obs0.2226 39657 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.95 Å2 / Biso mean: 28.043 Å2 / Biso min: 8.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å2-0.23 Å2-0.32 Å2
2--0.01 Å20.29 Å2
3---0.88 Å2
Refinement stepCycle: final / Resolution: 2.14→55.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6294 0 28 356 6678
Biso mean--48.81 30.85 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196570
X-RAY DIFFRACTIONr_bond_other_d0.0020.025711
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.9378918
X-RAY DIFFRACTIONr_angle_other_deg1.115313266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2895778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25823.465355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.145151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3011558
X-RAY DIFFRACTIONr_chiral_restr0.1250.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217416
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021454
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A17822
12D17822
21B6294
22E6294
LS refinement shellResolution: 2.14→2.196 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 157 -
Rwork0.37 2860 -
all-3017 -
obs--96.02 %
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)
13.8995-0.6623-0.73581.4876-0.38142.41280.0532-0.24670.03110.18570.01520.0152-0.0608-0.1154-0.06840.0778-0.04250.00440.09480.02530.016238.032539.696338.7049
21.36250.0693-0.58823.94433.11656.7534-0.05590.0143-0.31220.2684-0.0303-0.0120.461-0.07520.08620.043-0.02510.00310.17920.08170.112922.455625.065410.5319
34.7936-2.0253.38092.3824-1.16294.28090.03630.48060.1152-0.2854-0.0647-0.0691-0.30720.20610.02840.1481-0.03380.03940.16140.04160.050734.375644.52512.1873
41.84460.52690.89794.85991.36222.5298-0.0910.2848-0.0634-0.44530.17610.0941-0.02320.1448-0.08510.0869-0.04010.00860.19050.04650.048351.144120.275-1.4832
53.4209-0.8553-3.11372.771.98196.89330.01680.09530.08680.0705-0.17320.3168-0.1437-0.37720.15640.1034-0.0313-0.00540.11110.05650.127231.877410.673326.5886
60.88980.2382-0.40395.6337-3.11593.96050.027-0.2569-0.00020.48340.0217-0.1224-0.04930.2721-0.04870.0895-0.0004-0.00330.20030.02180.051554.136614.327125.0455
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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