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- PDB-9eb6: Chicken YF1.7*1 presenting myristoylated peptide derived from teg... -

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Basic information

Entry
Database: PDB / ID: 9eb6
TitleChicken YF1.7*1 presenting myristoylated peptide derived from tegument protein CIRC
Components
  • Beta-2-microglobulin
  • MHC Rfp-Y class I alpha chain
  • Peptide derived from tegument protein CIRC
KeywordsIMMUNE SYSTEM / Chicken / Antigen presentation / lipopeptide / MHC-like / tegument / Marek's Disease Virus / MDV
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
MYRISTIC ACID / TRIETHYLENE GLYCOL / Beta-2-microglobulin / MHC Rfp-Y class I alpha chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
Marek's disease herpesvirus type 1 strain MD5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKhandokar, Y. / Wang, C.J.H. / 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
C: Peptide derived from tegument protein CIRC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,25811
Polymers42,6353
Non-polymers6238
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-54 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.289, 55.410, 137.904
Angle α, β, γ (deg.)90.00, 97.92, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-549-

HOH

21B-196-

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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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Peptide derived from tegument protein CIRC


Mass: 535.634 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Marek's disease herpesvirus type 1 strain MD5

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Non-polymers , 6 types, 309 molecules

#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 18% w/v PEG 4000, Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→38.95 Å / Num. obs: 32495 / % possible obs: 99.18 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.032 / Rrim(I) all: 0.045 / Net I/σ(I): 13.88
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 2 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 3219 / CC1/2: 0.798 / CC star: 0.942 / Rpim(I) all: 0.319 / Rrim(I) all: 0.451 / % possible all: 98.65

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.0.32refinement
PHENIX1.21.2-5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38.95 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 1635 5.03 %
Rwork0.1713 --
obs0.1738 32493 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 36 301 3180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083044
X-RAY DIFFRACTIONf_angle_d1.1084151
X-RAY DIFFRACTIONf_dihedral_angle_d7.237448
X-RAY DIFFRACTIONf_chiral_restr0.065439
X-RAY DIFFRACTIONf_plane_restr0.007539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.30841470.25952509X-RAY DIFFRACTION99
1.96-2.020.26721340.22372547X-RAY DIFFRACTION99
2.02-2.090.28831400.19722537X-RAY DIFFRACTION99
2.09-2.170.24391290.18872580X-RAY DIFFRACTION99
2.17-2.270.24831390.17942532X-RAY DIFFRACTION99
2.27-2.390.23231390.18572553X-RAY DIFFRACTION99
2.39-2.540.22891150.18132586X-RAY DIFFRACTION99
2.54-2.740.22481330.18632574X-RAY DIFFRACTION100
2.74-3.020.22031400.18112577X-RAY DIFFRACTION99
3.02-3.450.23251480.16492605X-RAY DIFFRACTION100
3.45-4.350.16981370.13792585X-RAY DIFFRACTION99
4.35-38.950.20311340.15752673X-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)
13.0770.00430.17962.4686-0.17552.80610.00070.00940.11440.0204-0.0019-0.0508-0.3670.1268-0.00010.2551-0.00390.00960.112-0.03410.14713.8485-2.078327.3167
21.1444-0.4231-0.42881.60510.8052.7947-0.13040.0835-0.19150.1350.04340.06980.29990.04630.0830.1666-0.05450.00230.08240.01260.199715.0614-19.682320.7469
33.2716-0.761-2.21022.23211.30451.9278-0.1111-0.0872-0.07990.14810.0877-0.09710.40930.14630.03510.1086-0.0231-0.00510.1676-0.00890.161430.5798-16.886815.8027
47.74430.6149-4.91561.7299-0.87723.28930.2211-0.26410.28790.15810.182-0.2966-0.26770.9973-0.40050.1773-0.0665-0.03760.4029-0.02970.263237.3109-9.879722.2632
53.6583.473-0.3486.9943-4.08813.8923-0.36760.38410.0137-0.31590.3487-0.20160.0021-0.27180.04880.2206-0.0236-0.0180.1813-0.02980.170324.0026-9.11524.6152
61.8098-0.07990.21881.3562-0.01022.51010.0548-0.2704-0.01580.0360.1072-0.2325-0.13530.8374-0.13490.1607-0.043-0.00680.3832-0.03320.205136.1091-13.279719.3224
75.6297-0.9104-3.12423.71521.55562.4702-0.1058-0.1872-0.5637-0.0199-0.084-0.55681.0414-0.00070.12970.29870.06860.06350.31420.00880.30737.5933-21.428214.957
82.8108-3.53783.74794.9554-5.49276.19431.011-0.6022-0.61940.58790.2875-0.03911.0414-0.3038-1.20411.3328-0.1147-0.1150.57690.01350.664612.18331.057544.191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 114 )
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 270 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 30 )
4X-RAY DIFFRACTION4chain 'B' and (resid 31 through 46 )
5X-RAY DIFFRACTION5chain 'B' and (resid 47 through 61 )
6X-RAY DIFFRACTION6chain 'B' and (resid 62 through 90 )
7X-RAY DIFFRACTION7chain 'B' and (resid 91 through 99 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 5 )

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