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- PDB-4e0r: Structure of the chicken MHC class I molecule BF2*0401 -

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Basic information

Entry
Database: PDB / ID: 4e0r
TitleStructure of the chicken MHC class I molecule BF2*0401
Components
  • 8-MERIC PEPTIDE (FUS/TLS)
  • 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 / 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 / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell activation / cellular response to nicotine / phagocytic vesicle membrane / 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 / 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 superfamily / Zinc finger RanBP2-type signature. / 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 superfamily / Zinc finger RanBP2-type signature. / 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 / Immunoglobulin-like fold / Immunoglobulins / 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: 2.26 Å
AuthorsZhang, J. / Chen, Y. / Qi, J. / Gao, F. / 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
DepositionMar 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: 8-MERIC PEPTIDE (FUS/TLS)
D: MHC class I alpha chain 2
E: Beta-2 microglobulin
F: 8-MERIC PEPTIDE (FUS/TLS)


Theoretical massNumber of molelcules
Total (without water)88,6676
Polymers88,6676
Non-polymers00
Water9,314517
1
A: MHC class I alpha chain 2
B: Beta-2 microglobulin
C: 8-MERIC PEPTIDE (FUS/TLS)


Theoretical massNumber of molelcules
Total (without water)44,3333
Polymers44,3333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-8 kcal/mol
Surface area18220 Å2
MethodPISA
2
D: MHC class I alpha chain 2
E: Beta-2 microglobulin
F: 8-MERIC PEPTIDE (FUS/TLS)


Theoretical massNumber of molelcules
Total (without water)44,3333
Polymers44,3333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-9 kcal/mol
Surface area18090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.196, 40.286, 131.585
Angle α, β, γ (deg.)90.00, 119.71, 90.00
Int Tables number5
Space group name H-MC121

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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) / Gene: B-FIV, BF2 / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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) / Gene: B-F-S-b2m02 / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21611
#3: Protein/peptide 8-MERIC PEPTIDE (FUS/TLS)


Mass: 1010.078 Da / Num. of mol.: 2 / Fragment: UNP residues 319-326 / Source method: obtained synthetically / Details: chemical synthesis from Fus proto-onc gene / Source: (synth.) Gallus gallus (chicken) / References: UniProt: Q6J4Y8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES BUFFER (PH 7.0), 5% MPD, 20% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 6, 2008
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.259→50 Å / Num. all: 36222 / Num. obs: 34950 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 19.6
Reflection shellResolution: 2.26→2.36 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 6.8 / Rsym value: 0.196 / % possible all: 94

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
PHENIX(PHENIX.REFINE: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BEV

3bev


Resolution: 2.26→43.83 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 26.83 / Stereochemistry target values: ML / Details: REFMAC WAS ALSO USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1747 5 %Random
Rwork0.197 ---
all0.2 ---
obs0.2 34927 96.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.95 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 28.05 Å2
Baniso -1Baniso -2Baniso -3
1--3.8572 Å20 Å2-1.2064 Å2
2--10.0476 Å20 Å2
3----6.1904 Å2
Refinement stepCycle: LAST / Resolution: 2.26→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6118 0 0 517 6635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036302
X-RAY DIFFRACTIONf_angle_d0.7718554
X-RAY DIFFRACTIONf_dihedral_angle_d17.1382264
X-RAY DIFFRACTIONf_chiral_restr0.058862
X-RAY DIFFRACTIONf_plane_restr0.0031124
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 (%)
2.2593-2.32570.31031200.2211263193
2.3257-2.40080.33691280.2028272496
2.4008-2.48660.28761310.2071270195
2.4866-2.58620.27611410.2067274897
2.5862-2.70380.24931340.2129271395
2.7038-2.84640.33371370.2179277597
2.8464-3.02470.29111480.2205277698
3.0247-3.25810.25321530.2056276997
3.2581-3.58590.27031420.1829279597
3.5859-4.10440.22611710.1663279397
4.1044-5.16980.17881620.1514284399
5.1698-43.83970.22841800.1969291297

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