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- PDB-4g42: Structure of the Chicken MHC Class I Molecule BF2*0401 complexed ... -

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Basic information

Entry
Database: PDB / ID: 4g42
TitleStructure of the Chicken MHC Class I Molecule BF2*0401 complexed to pepitde P8D
Components
  • 8-MERIC PEPTIDE P8D
  • Beta-2 microglobulin
  • MHC class I alpha chain 2
KeywordsIMMUNE SYSTEM / MHC I complex / narrow binding groove
Function / homology
Function and homology information


MHC class I protein binding, via antigen binding groove / 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 / lumenal side of endoplasmic reticulum membrane ...MHC class I protein binding, via antigen binding groove / 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 / lumenal side of endoplasmic reticulum membrane / 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 / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / regulation of DNA-templated transcription / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular region / nucleus / metal ion binding / cytosol
Similarity search - Function
TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains ...TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / RNA-binding 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 / Nucleotide-binding alpha-beta plait domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I alpha chain 2 / Beta-2-microglobulin / FUS/TLS
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.294 Å
AuthorsZhang, J. / Chen, Y. / Qi, J. / Gao, F. / Liu, J. / Kaufman, J. / Xia, C. / Gao, G.F.
CitationJournal: J.Immunol. / Year: 2012
Title: Narrow Groove and Restricted Anchors of MHC Class I Molecule BF2*0401 Plus Peptide Transporter Restriction Can Explain Disease Susceptibility of B4 Chickens.
Authors: Zhang, J. / Chen, Y. / Qi, J. / Gao, F. / Liu, Y. / Liu, J. / Zhou, X. / Kaufman, J. / Xia, C. / Gao, G.F.
History
DepositionJul 16, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I alpha chain 2
B: Beta-2 microglobulin
D: MHC class I alpha chain 2
E: Beta-2 microglobulin
C: 8-MERIC PEPTIDE P8D
F: 8-MERIC PEPTIDE P8D


Theoretical massNumber of molelcules
Total (without water)88,6396
Polymers88,6396
Non-polymers00
Water9,656536
1
A: MHC class I alpha chain 2
B: Beta-2 microglobulin
C: 8-MERIC PEPTIDE P8D


Theoretical massNumber of molelcules
Total (without water)44,3193
Polymers44,3193
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-9 kcal/mol
Surface area17930 Å2
MethodPISA
2
D: MHC class I alpha chain 2
E: Beta-2 microglobulin
F: 8-MERIC PEPTIDE P8D


Theoretical massNumber of molelcules
Total (without water)44,3193
Polymers44,3193
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-9 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.832, 40.108, 130.952
Angle α, β, γ (deg.)90.00, 119.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-487-

HOH

21D-463-

HOH

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Components

#1: Protein MHC class I alpha chain 2 / MHC class I glycoprotein / MHC class I molecule


Mass: 31853.465 Da / Num. of mol.: 2 / Fragment: UNP residues 22-291 / Mutation: D244E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: O46790
#2: Protein Beta-2 microglobulin


Mass: 11469.888 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P21611
#3: Protein/peptide 8-MERIC PEPTIDE P8D


Mass: 996.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in Gallus. / Source: (synth.) Gallus gallus (chicken) / References: UniProt: Q6J4Y8*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% MPD, 20% PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 3, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.294→40.627 Å / Num. all: 45028 / Num. obs: 33771 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 7.5 / Num. unique all: 44078 / Rsym value: 0.279 / % possible all: 75

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.294→40.627 Å / SU ML: 0.34 / σ(F): 1.35 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1712 5.07 %0.254
Rwork0.196 ---
all0.254 44078 --
obs0.199 33771 98.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.371 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.3547 Å20 Å2-1.1629 Å2
2--10.1679 Å20 Å2
3----5.8132 Å2
Refinement stepCycle: LAST / Resolution: 2.294→40.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 0 536 6644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056292
X-RAY DIFFRACTIONf_angle_d0.9428541
X-RAY DIFFRACTIONf_dihedral_angle_d17.8842259
X-RAY DIFFRACTIONf_chiral_restr0.068860
X-RAY DIFFRACTIONf_plane_restr0.0041123
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2937-2.36120.30571200.2322257894
2.3612-2.43740.32231240.2275261398
2.4374-2.52450.34141610.2276259898
2.5245-2.62550.30361520.2225262798
2.6255-2.7450.27841560.2108261699
2.745-2.88970.2821230.2057268999
2.8897-3.07070.25421200.1928271399
3.0707-3.30770.23231530.1813266499
3.3077-3.64030.19071170.1696272899
3.6403-4.16660.23511610.15962664100
4.1666-5.24770.19921640.15842742100
5.2477-40.63350.25931610.2129282799

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