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- PDB-3bev: 11mer Structure of an MHC class I molecule from B21 chickens illu... -

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Basic information

Entry
Database: PDB / ID: 3bev
Title11mer Structure of an MHC class I molecule from B21 chickens illustrate promiscuous peptide binding
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Hemoglobin subunit alpha-A
  • Major histocompatibility complex class I glycoprotein haplotype B21
KeywordsIMMUNE SYSTEM / MHC class I / chicken / B21 / BF21 / 11mer / bulge / water cushion / Immune response / Immunoglobulin domain / MHC I / Polymorphism / Secreted / Heme / Iron / Metal-binding / Oxygen transport / Transport
Function / homology
Function and homology information


Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Post-translational modification: synthesis of GPI-anchored proteins / Transferrin endocytosis and recycling / 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 ...Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Post-translational modification: synthesis of GPI-anchored proteins / Transferrin endocytosis and recycling / 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 / cellular oxidant detoxification / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / hydrogen peroxide catabolic process / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / oxygen carrier activity / 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 / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / oxygen binding / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / iron ion binding / lysosomal membrane / external side of plasma membrane / signaling receptor binding / heme binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Globin/Protoglobin / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Globin domain profile. / Globin / Globin / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...Hemoglobin, pi / Hemoglobin, alpha-type / Globin/Protoglobin / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Globin domain profile. / Globin / Globin / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / Globin-like superfamily / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemoglobin subunit alpha-A / Beta-2-microglobulin / MHC class I alpha chain 2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoch, M. / Kaufman, J. / Jones, Y.
CitationJournal: Immunity / Year: 2007
Title: Structures of an MHC class I molecule from b21 chickens illustrate promiscuous Peptide binding
Authors: Koch, M. / Camp, S. / Collen, T. / Avila, D. / Salomonsen, J. / Wallny, H.-J. / van Hateren, A. / Hunt, L. / Jacob, J.P. / Johnston, F. / Marston, D.A. / Shaw, I. / Dunbar, P.R. / Cerundolo, ...Authors: Koch, M. / Camp, S. / Collen, T. / Avila, D. / Salomonsen, J. / Wallny, H.-J. / van Hateren, A. / Hunt, L. / Jacob, J.P. / Johnston, F. / Marston, D.A. / Shaw, I. / Dunbar, P.R. / Cerundolo, V. / Jones, E.Y. / Kaufman, J.
History
DepositionNov 20, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major histocompatibility complex class I glycoprotein haplotype B21
B: Beta-2-microglobulin
C: Hemoglobin subunit alpha-A


Theoretical massNumber of molelcules
Total (without water)43,5023
Polymers43,5023
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.306, 72.199, 72.711
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Major histocompatibility complex class I glycoprotein haplotype B21 / MHC class I molecule precursor / MHC class I alpha chain 2 / MHC class I antigen / MHC class I glycoprotein


Mass: 31131.588 Da / Num. of mol.: 1 / Fragment: UNP residues 1-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Strain: B21 / Gene: BFIV21, B-FIV, BF2 / Plasmid: pET22(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q95601
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11193.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Strain: B21 / Gene: B2M / Plasmid: pET22(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21611
#3: Protein/peptide Hemoglobin subunit alpha-A / / Hemoglobin alpha-A chain / Alpha-A-globin


Mass: 1177.198 Da / Num. of mol.: 1 / Fragment: UNP residues 20-30 / Source method: obtained synthetically
Details: This sequence occurs naturally in B21 chickens. The peptide was synthesized by solid-phase synthesis.
References: UniProt: P01994
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 27% PEG 3350, 0.1M HEPES pH7.0, 0.1M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97904 Å
DetectorType: MACSCIENCE / Detector: CCD / Date: Nov 7, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 22499 / Num. obs: 22499 / Rmerge(I) obs: 0.143 / Rsym value: 0.143 / Net I/σ(I): 17.1
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1160 / Rsym value: 0.65

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGT

1ogt


Resolution: 2.1→19.95 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.876 / SU B: 6.428 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.307 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1135 5 %RANDOM
Rwork0.23 ---
obs0.233 21363 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.165 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2---1 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 0 193 3259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213154
X-RAY DIFFRACTIONr_angle_refined_deg2.3271.9344287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6535381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04223.354161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8715492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9011526
X-RAY DIFFRACTIONr_chiral_restr0.0790.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022500
X-RAY DIFFRACTIONr_nbd_refined0.1480.21383
X-RAY DIFFRACTIONr_nbtor_refined0.260.22035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.217
X-RAY DIFFRACTIONr_mcbond_it2.262.51996
X-RAY DIFFRACTIONr_mcangle_it3.0713.53056
X-RAY DIFFRACTIONr_scbond_it3.1763.51411
X-RAY DIFFRACTIONr_scangle_it4.5134.91231
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 82 -
Rwork0.242 1548 -
all-1630 -
obs--100 %

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