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- PDB-9c6v: Crystal Structure of a single chain trimer composed of HLA-B*39:0... -

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Basic information

Entry
Database: PDB / ID: 9c6v
TitleCrystal Structure of a single chain trimer composed of HLA-B*39:06 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2 (1 molecule/asymmetric unit)
ComponentsNACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA CLASS I HISTOCOMPATIBILITY ANTIGEN / B-39 ALPHA CHAIN / BETA-2-MICROGLOBULIN / NLRP2
Function / homology
Function and homology information


Pyrin domain binding / negative regulation of non-canonical NF-kappaB signal transduction / 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 ...Pyrin domain binding / negative regulation of non-canonical NF-kappaB signal transduction / 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 / positive regulation of interleukin-1 beta production / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle 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 / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / regulation of inflammatory response / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / inflammatory response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / intracellular membrane-bounded organelle / innate immune response / focal adhesion / apoptotic process / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase ...: / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Death-like domain superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Leucine-rich repeat / 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 / Leucine-rich repeat domain 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin / NACHT, LRR and PYD domains-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSharma, R. / Amdare, N.P. / Celikgil, A. / Garforth, S.J. / DiLorenzo, T.P. / Almo, S.C. / Ghosh, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI123730 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA013330 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural and biochemical analysis of highly similar HLA-B allotypes differentially associated with type 1 diabetes.
Authors: Sharma, R. / Amdare, N.P. / Ghosh, A. / Schloss, J. / Sidney, J. / Garforth, S.J. / Lopez, Y. / Celikgil, A. / Sette, A. / Almo, S.C. / DiLorenzo, T.P.
History
DepositionJun 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1024
Polymers46,9131
Non-polymers1903
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.954, 83.450, 148.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen / Nucleotide-binding site protein 1 / PYRIN domain and NACHT domain-containing protein 1 / PYRIN- ...Nucleotide-binding site protein 1 / PYRIN domain and NACHT domain-containing protein 1 / PYRIN-containing APAF1-like protein 2 / Major histocompatibility complex


Mass: 46912.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: NLRP2, NALP2, NBS1, PAN1, PYPAF2, B2M, CDABP0092, HDCMA22P, HLA-B, HLA-B39
Plasmid: pIRES-acGFP / Cell line (production host): Human Embryonic Kidney / Production host: Homo sapiens (human)
References: UniProt: Q9NX02, UniProt: P61769, UniProt: I3ZN83
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M Potassium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.68→24.77 Å / Num. obs: 52030 / % possible obs: 97.7 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Χ2: 0.72 / Net I/σ(I): 16 / Num. measured all: 291767
Reflection shellResolution: 1.68→1.71 Å / % possible obs: 98.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.585 / Num. measured all: 14117 / Num. unique obs: 2698 / CC1/2: 0.837 / Rpim(I) all: 0.274 / Rrim(I) all: 0.649 / Χ2: 0.27 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.77 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 2576 5.14 %
Rwork0.1959 --
obs0.1971 50132 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 11 158 3338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.856
X-RAY DIFFRACTIONf_dihedral_angle_d18.831231
X-RAY DIFFRACTIONf_chiral_restr0.054459
X-RAY DIFFRACTIONf_plane_restr0.008595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.27691420.2762615X-RAY DIFFRACTION99
1.73-1.770.29521300.26522660X-RAY DIFFRACTION99
1.77-1.810.24051460.242664X-RAY DIFFRACTION99
1.81-1.850.27471480.22692600X-RAY DIFFRACTION98
1.85-1.890.251260.22382641X-RAY DIFFRACTION97
1.89-1.950.22931520.20772614X-RAY DIFFRACTION98
1.95-20.22851500.21512673X-RAY DIFFRACTION98
2-2.070.22151380.21742646X-RAY DIFFRACTION98
2.07-2.140.24981530.20562654X-RAY DIFFRACTION98
2.14-2.230.23751410.20632599X-RAY DIFFRACTION97
2.23-2.330.23951370.19972569X-RAY DIFFRACTION94
2.33-2.450.19641520.192637X-RAY DIFFRACTION98
2.45-2.60.24031590.21672624X-RAY DIFFRACTION98
2.6-2.810.25571300.22262666X-RAY DIFFRACTION97
2.81-3.090.23281160.21392577X-RAY DIFFRACTION94
3.09-3.530.23171590.19612664X-RAY DIFFRACTION97
3.53-4.450.19071420.15922625X-RAY DIFFRACTION95
4.45-24.770.18731550.1732828X-RAY DIFFRACTION98

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