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- PDB-9eb2: Chicken YF1*7.1 molecule presenting an endogenous N-myristoylated... -

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Basic information

Entry
Database: PDB / ID: 9eb2
TitleChicken YF1*7.1 molecule presenting an endogenous N-myristoylated amino acid
Components
  • Beta-2-microglobulin
  • MHC Rfp-Y class I alpha chain
KeywordsIMMUNE SYSTEM / Chicken / antigen presentation / Lipopeptide / MHC-like fold
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
: / 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0375
Polymers42,6242
Non-polymers4133
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-24 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.840, 61.340, 134.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC Rfp-Y class I alpha chain / YF1*7.1


Mass: 31490.312 Da / Num. of mol.: 1 / Fragment: residues 1-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: YFV / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q9BCW3
#2: Protein Beta-2-microglobulin


Mass: 11133.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B2M / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P21611

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Non-polymers , 4 types, 245 molecules

#3: Chemical ChemComp-BJU / N-tetradecanoylglycine


Mass: 285.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H31NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% w/v PEG3350, 200 mM ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→45.34 Å / Num. obs: 30861 / % possible obs: 99.88 % / Redundancy: 2 % / Biso Wilson estimate: 22.78 Å2 / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.025 / Rrim(I) all: 0.035 / Net I/σ(I): 14.04
Reflection shellResolution: 2→2.071 Å / Redundancy: 2 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 5.55 / Num. unique obs: 3014 / CC1/2: 0.955 / CC star: 0.988 / Rpim(I) all: 0.112 / Rrim(I) all: 0.158 / % possible all: 99.44

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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: 2→45.34 Å / SU ML: 0.1747 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.0867
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2094 1517 4.92 %
Rwork0.1623 29341 -
obs0.1646 30858 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.9 Å2
Refinement stepCycle: LAST / Resolution: 2→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 27 242 3153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663152
X-RAY DIFFRACTIONf_angle_d0.85114319
X-RAY DIFFRACTIONf_chiral_restr0.0559450
X-RAY DIFFRACTIONf_plane_restr0.0058571
X-RAY DIFFRACTIONf_dihedral_angle_d17.8238472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.25691200.18422599X-RAY DIFFRACTION99.41
2.06-2.140.23471300.17862622X-RAY DIFFRACTION99.82
2.14-2.220.25561300.16992628X-RAY DIFFRACTION99.93
2.22-2.330.24631320.16832646X-RAY DIFFRACTION100
2.33-2.450.21961490.17362642X-RAY DIFFRACTION100
2.45-2.60.2211450.17152617X-RAY DIFFRACTION100
2.6-2.80.20081340.17272686X-RAY DIFFRACTION99.96
2.8-3.080.21661430.16632659X-RAY DIFFRACTION100
3.08-3.530.20371520.15322672X-RAY DIFFRACTION100
3.53-4.450.17351320.13562727X-RAY DIFFRACTION100
4.45-45.340.20311500.1712843X-RAY DIFFRACTION99.73
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)
12.82410285096-0.6248759986610.02536432182374.34484017539-0.783841214962.42011245569-0.0746805042903-0.006100807739380.09758726063540.08612428530690.00968877033705-0.157799259069-0.07299299640080.1077205578810.06807739621820.103364296994-0.0163764668818-0.01485023870070.14218443859-0.003998262828670.08841978395411.39229072004-13.835904246910.8252250805
21.30413343686-0.5943567234660.2474642846870.713330331672-0.8536279240753.450107697970.1066743991260.241482214556-0.111808070139-0.225156700157-0.0860312760410.1677150477750.0966076707596-0.0286243138511-0.007058952089350.115018162507-0.00930758577782-0.02649563477110.184722799167-0.0204434527630.172472187701-5.41039154503-16.0421628155-2.0185765929
38.07088943715-4.96572250029-4.137758772464.543403193893.073222954293.5618857372-0.274388295072-0.58244381395-0.6098508263110.1034316924880.05322746283160.4228590924770.06044368361490.1003187635530.1984383139290.23325102353-0.0661548291176-0.0141107842550.1894894756150.03863262916970.196280323028-22.1637888828-20.673355378228.8192377524
44.319520802990.336324067267-0.09497692587592.10394466366-0.08069316898061.80292623286-0.0261091952277-0.147197988891-0.2147954741190.142627370925-0.006274173085450.04222753423910.00666384606641-0.1756958954610.03652648556390.176823206688-0.02143595122530.009520576781720.1303728764250.01332603545530.138651858348-31.175281033-18.378531301426.3684478375
54.203205180960.761924797574-1.932494367974.9620883492-0.2660370038716.889931160780.2207094771460.4944251332860.105846822101-0.6332534161340.2847307160310.531396622740.0538674889376-0.622294188485-0.4974841691260.162147869954-0.00629452049314-0.03463204411510.162833365425-0.008030922263270.15911521982-19.142360559-3.8502459486320.2035409912
61.63712881809-0.1265292156210.5366403891392.45363719051-1.058606526554.720112479930.0187270436594-0.187565966946-0.07465036061910.1557041044370.0323078515715-0.06029764914080.05712829456870.145564243691-0.04732924002460.1119269160630.0345842561851-0.01371928063110.12259971118-0.02214687012580.144161156161-11.4778692775-5.7011500979729.2782321786
75.22589858704-5.703165975195.07213064246.53431992053-5.3408298535.08524193559-0.307301651702-1.31479515356-0.1414847130420.05443103189360.0577638944012-0.07620323129610.709739083358-0.5016794390130.1748205193750.2554896309590.03008082225720.04380783827790.4109564258090.02765226865320.190470645667-10.6549821095-8.94676610911.0121747253
82.48653921002-0.422122093327-0.365810233413.94793743905-0.9201965959745.669745358380.041000208685-0.05700815586360.08043069570920.172051379653-0.0435433126723-0.0367200476285-0.477584650549-0.04771224727590.01132779705330.118900715906-0.0338097031324-0.02861334668970.101754126755-0.02327108978120.14080413612-12.9787020949-1.8222202373528.1198805525
94.72750175027-2.749109238322.247527442524.37083505032-4.078389417453.856014307110.160496602930.07739688983190.00108071536553-0.7612292589110.2018913580130.8185261516230.31072552378-0.795740357557-0.379059816670.2534597624480.00735591765274-0.04717290355220.123838121748-0.02740687242470.192884886082-20.0451914817-1.7109016932930.4634781167
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 82 )AA1 - 821 - 86
22chain 'A' and (resid 83 through 171 )AA83 - 17187 - 191
33chain 'A' and (resid 172 through 193 )AA172 - 193192 - 213
44chain 'A' and (resid 194 through 275 )AA194 - 275214 - 308
55chain 'B' and (resid 1 through 11 )BD1 - 111 - 13
66chain 'B' and (resid 12 through 51 )BD12 - 5114 - 58
77chain 'B' and (resid 52 through 61 )BD52 - 6159 - 70
88chain 'B' and (resid 62 through 90 )BD62 - 9071 - 101
99chain 'B' and (resid 91 through 99 )BD91 - 97102 - 108

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