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- PDB-9c6w: Crystal Structure of a single chain trimer composed of HLA-B*39:0... -

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Basic information

Entry
Database: PDB / ID: 9c6w
TitleCrystal Structure of a single chain trimer composed of HLA-B*39:06 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2 (2 molecules/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 / 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 / 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 / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / regulation of inflammatory response / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / inflammatory response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / intracellular membrane-bounded organelle / apoptotic process / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / 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 / NACHT nucleoside triphosphatase / NACHT domain / DAPIN domain profile. / NACHT-NTPase domain profile. ...: / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / NACHT nucleoside triphosphatase / NACHT domain / DAPIN domain profile. / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Death-like domain superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Leucine-rich repeat / 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
3,6,9,12,15-PENTAOXAHEPTADECANE / DI(HYDROXYETHYL)ETHER / 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 1.2Nov 6, 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
B: NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,94740
Polymers93,8252
Non-polymers3,12238
Water7,548419
1
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)48,29418
Polymers46,9131
Non-polymers1,38117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,65322
Polymers46,9131
Non-polymers1,74021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.244, 84.237, 149.204
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
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

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Non-polymers , 7 types, 457 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O5
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M Ammonuim sulfate,0.2 M Lithium sulfate, 0.1 M HEPES

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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: 1.67→19.73 Å / Num. obs: 110321 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Rrim(I) all: 0.04 / Χ2: 0.92 / Net I/σ(I): 22.8 / Num. measured all: 711734
Reflection shellResolution: 1.67→1.7 Å / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.509 / Num. measured all: 35993 / Num. unique obs: 5380 / CC1/2: 0.911 / Rpim(I) all: 0.213 / Rrim(I) all: 0.553 / Χ2: 0.72 / Net I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156)refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.73 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 5340 5.11 %
Rwork0.1866 --
obs0.1881 104543 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6299 0 182 419 6900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.8
X-RAY DIFFRACTIONf_dihedral_angle_d18.7462531
X-RAY DIFFRACTIONf_chiral_restr0.054937
X-RAY DIFFRACTIONf_plane_restr0.0071201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.26332000.22793261X-RAY DIFFRACTION100
1.72-1.740.23561760.21953287X-RAY DIFFRACTION100
1.74-1.760.24571660.21113288X-RAY DIFFRACTION100
1.76-1.780.22281730.20133270X-RAY DIFFRACTION100
1.78-1.810.22261670.20113240X-RAY DIFFRACTION100
1.81-1.830.24891910.19593293X-RAY DIFFRACTION100
1.83-1.860.20991760.19373257X-RAY DIFFRACTION100
1.86-1.890.24181750.19473306X-RAY DIFFRACTION100
1.89-1.910.24231830.19973272X-RAY DIFFRACTION100
1.91-1.950.23251560.19323301X-RAY DIFFRACTION100
1.95-1.980.21561720.1973280X-RAY DIFFRACTION100
1.98-2.020.24471960.19713265X-RAY DIFFRACTION100
2.02-2.050.21081870.17313271X-RAY DIFFRACTION100
2.05-2.10.19221650.1873306X-RAY DIFFRACTION100
2.1-2.140.22531850.18333255X-RAY DIFFRACTION100
2.14-2.190.25271750.19333261X-RAY DIFFRACTION100
2.19-2.250.22461590.18943318X-RAY DIFFRACTION100
2.25-2.310.23141780.19323307X-RAY DIFFRACTION100
2.31-2.370.2091710.19333310X-RAY DIFFRACTION100
2.37-2.450.22471750.18843300X-RAY DIFFRACTION100
2.45-2.540.21071880.19343299X-RAY DIFFRACTION100
2.54-2.640.2721870.20453302X-RAY DIFFRACTION100
2.64-2.760.21071570.20473311X-RAY DIFFRACTION99
2.76-2.90.25111660.21133357X-RAY DIFFRACTION100
2.9-3.090.22911760.20333320X-RAY DIFFRACTION100
3.09-3.320.20371790.19923339X-RAY DIFFRACTION100
3.32-3.660.22161900.17533364X-RAY DIFFRACTION100
3.66-4.180.2041850.15833358X-RAY DIFFRACTION99
4.18-5.250.18422060.14643373X-RAY DIFFRACTION100
5.25-19.730.19461800.19463532X-RAY DIFFRACTION99

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