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- PDB-9eb4: Chicken YF1.7*1 presenting N-palmitoylated glycine -

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Basic information

Entry
Database: PDB / ID: 9eb4
TitleChicken YF1.7*1 presenting N-palmitoylated glycine
Components
  • Beta-2-microglobulin
  • MHC Rfp-Y class I alpha chain
KeywordsIMMUNE SYSTEM / Chicken / Antigen presentation / lipopeptide / MHC-like
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / cellular response to iron ion / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / cellular response to iron ion / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / 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 / cellular response to nicotine / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular region / cytosol
Similarity search - Function
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. ...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
Similarity search - Domain/homology
N-PALMITOYLGLYCINE / TRIETHYLENE GLYCOL / Beta-2-microglobulin / MHC Rfp-Y class I alpha chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKhandokar, Y. / Wang, C.J. / Rossjohn, J. / Le Nours, J.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2008616 Australia
Monash University/ARC Centre of Excellence in Advanced Molecular Imaging AllianceCE140100011 Australia
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Molecular basis for presentation of N-myristoylated peptides by the chicken YF1∗7.1 molecule.
Authors: Khandokar, Y. / Cheng, T.Y. / Wang, C.J.H. / Cao, T.P. / Nagampalli, R.S.K. / Sivaraman, K.K. / Van Rhijn, I. / Rossjohn, J. / Moody, D.B. / Nours, J.L.
History
DepositionNov 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC Rfp-Y class I alpha chain
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,08211
Polymers42,0992
Non-polymers9839
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-21 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.669, 55.390, 133.456
Angle α, β, γ (deg.)90.00, 100.98, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-542-

HOH

21A-544-

HOH

31B-271-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC Rfp-Y class I alpha chain


Mass: 31036.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: YFV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BCW3
#2: Protein Beta-2-microglobulin


Mass: 11062.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21611

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Non-polymers , 6 types, 235 molecules

#3: Chemical ChemComp-140 / N-PALMITOYLGLYCINE / N-HEXADECANOYLGLYCINE


Mass: 313.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H35NO3
#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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% w/v PEG 4000 200 mM magnesium sulfate 10% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 2.2→51.02 Å / Num. obs: 20758 / % possible obs: 99.69 % / Redundancy: 1.9 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.04 / Rrim(I) all: 0.056 / Net I/σ(I): 12.74
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.098 / Num. unique obs: 2036 / CC1/2: 0.952 / CC star: 0.988 / Rpim(I) all: 0.098 / Rrim(I) all: 0.14 / % possible all: 98.93

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Processing

Software
NameVersionClassification
PHASERphasing
MOSFLMdata reduction
Aimlessdata scaling
REFMAC5.0.32refinement
PHENIX1.21.2-5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→51.02 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 1045 5.04 %
Rwork0.1574 --
obs0.1606 20754 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→51.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2831 0 64 226 3121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083038
X-RAY DIFFRACTIONf_angle_d0.914138
X-RAY DIFFRACTIONf_dihedral_angle_d19.857455
X-RAY DIFFRACTIONf_chiral_restr0.053432
X-RAY DIFFRACTIONf_plane_restr0.006534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.32221570.19222740X-RAY DIFFRACTION99
2.32-2.460.28551520.1812800X-RAY DIFFRACTION100
2.46-2.650.2241310.17852838X-RAY DIFFRACTION100
2.65-2.920.23541320.1752822X-RAY DIFFRACTION100
2.92-3.340.22361390.16432839X-RAY DIFFRACTION100
3.34-4.210.18591620.13472790X-RAY DIFFRACTION100
4.21-51.020.20071720.1432880X-RAY DIFFRACTION100
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)
13.39850.62041.18411.98420.77024.19860.04170.21420.214-0.1842-0.0642-0.0486-0.50540.21470.04160.25080.00290.01860.1457-0.01340.184313.74680.371723.0076
24.90920.09392.2793.0340.90546.96930.2234-0.41880.05230.4945-0.0016-0.1740.09680.3884-0.25930.2218-0.00050.01180.1808-0.0110.174914.5596-4.776137.7999
31.7811-0.44520.01840.72150.15384.5920.013-0.0495-0.07160.07910.03990.2122-0.2627-0.3038-0.05040.18970.02560.0090.1279-0.00530.24152.1821-6.456832.9427
40.8703-2.12970.58187.0883-0.96255.23840.140.2632-0.0407-0.1865-0.2015-0.39620.25020.22680.06880.1687-0.06490.01360.1941-0.04570.189822.5705-22.68747.151
52.9245-0.82460.70046.3825-0.47944.45720.12840.1417-0.4199-0.0318-0.1247-0.24760.75940.1781-0.00560.255-0.00360.04990.2333-0.03210.232322.999-30.157511.3544
65.32740.3067-2.75974.43451.98427.7851-0.3595-0.4793-0.29010.47740.0909-0.00250.935-0.05180.21560.16520.02630.01130.19290.03860.182429.6009-18.377524.4068
72.1091-0.6192-1.74950.7317-0.14912.1083-0.0363-0.22720.05460.09880.088-0.1862-0.0160.5342-0.07180.1301-0.0287-0.00650.2469-0.00570.196331.9118-12.757617.2988
83.9656-4.87980.07376.2029-0.65782.863-0.01060.7490.3730.3274-0.2582-0.0023-0.42560.24550.24040.1769-0.1164-0.03530.3018-0.04560.25638.5005-6.660514.9983
95.64564.5137-5.48633.7448-3.81837.8586-0.48560.4463-0.1128-0.7580.1376-0.45210.2380.02340.25490.22690.0370.00190.25240.02490.210418.94-10.807327.917
105.2618-0.2274-3.28610.4440.38257.6555-0.2496-0.1279-0.4709-0.04820.0933-0.05070.28050.59550.0990.1427-0.01940.00810.2383-0.02750.230933.8952-12.040514.0496
113.73550.25694.25972.1476-0.7895.410.1716-0.95860.20160.4450.5306-0.2204-0.21920.9199-0.52050.2370.004-0.03160.4649-0.05030.238637.4423-13.023427.8442
121.98892.17812.16076.10762.26883.2843-0.1568-0.0121-0.4815-0.08320.8532-0.78641.48630.6746-0.53220.37150.01470.02570.3816-0.04450.299937.7486-21.023115.6445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 100 )
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 171 )
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 193 )
5X-RAY DIFFRACTION5chain 'A' and (resid 194 through 270 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 11 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 41 )
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 61 )
10X-RAY DIFFRACTION10chain 'B' and (resid 62 through 77 )
11X-RAY DIFFRACTION11chain 'B' and (resid 78 through 90 )
12X-RAY DIFFRACTION12chain 'B' and (resid 91 through 99 )

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