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- PDB-2yez: COMPLEX OF A B21 CHICKEN MHC CLASS I MOLECULE AND A 10MER CHICKEN... -

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Basic information

Entry
Database: PDB / ID: 2yez
TitleCOMPLEX OF A B21 CHICKEN MHC CLASS I MOLECULE AND A 10MER CHICKEN PEPTIDE
Components
  • 14-3-3 PROTEIN THETA
  • BETA-2-MICROGLOBULIN
  • MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B21
KeywordsIMMUNE SYSTEM / BF21 / IMMUNE RESPONSE / IMMUNOGLOBULIN DOMAIN / MHC I
Function / homology
Function and homology information


TP53 Regulates Metabolic Genes / Regulation of localization of FOXO transcription factors / 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 / : ...TP53 Regulates Metabolic Genes / Regulation of localization of FOXO transcription factors / 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 / : / small GTPase-mediated signal transduction / protein targeting / Neutrophil degranulation / 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 / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / protein domain specific binding / lysosomal membrane / external side of plasma membrane / signaling receptor binding / negative regulation of DNA-templated transcription / structural molecule activity / Golgi apparatus / protein homodimerization activity / protein-containing complex / extracellular space / extracellular region / identical protein binding / cytoplasm / cytosol
Similarity search - Function
14-3-3 theta / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / MHC class I-like antigen recognition-like ...14-3-3 theta / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / 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 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / 14-3-3 protein theta / MHC class I alpha chain 2
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChappell, P. / Roversi, P. / Harrison, M.C. / Mears, L.E. / Kaufman, J.F. / Lea, S.M.
CitationJournal: Elife / Year: 2015
Title: Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding.
Authors: Chappell, P. / Meziane, e.l..K. / Harrison, M. / Magiera, L. / Hermann, C. / Mears, L. / Wrobel, A.G. / Durant, C. / Nielsen, L.L. / Buus, S. / Ternette, N. / Mwangi, W. / Butter, C. / Nair, ...Authors: Chappell, P. / Meziane, e.l..K. / Harrison, M. / Magiera, L. / Hermann, C. / Mears, L. / Wrobel, A.G. / Durant, C. / Nielsen, L.L. / Buus, S. / Ternette, N. / Mwangi, W. / Butter, C. / Nair, V. / Ahyee, T. / Duggleby, R. / Madrigal, A. / Roversi, P. / Lea, S.M. / Kaufman, J.
History
DepositionMar 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_status
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: 14-3-3 PROTEIN THETA


Theoretical massNumber of molelcules
Total (without water)49,1233
Polymers49,1233
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-23.7 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.570, 68.980, 94.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 ...MHC CLASS I MOLECULE PRECURSOR / MHC CLASS I ALPHA CHAIN 2 / MHC CLASS I ANTIGEN / MHC CLASS I GLYCOPROTEIN / MHC CLASS I MOLECULE / MHC CLASS I ALPHA CHAIN 2


Mass: 36862.012 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95601
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11062.404 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21611
#3: Protein/peptide 14-3-3 PROTEIN THETA


Mass: 1198.344 Da / Num. of mol.: 1 / Fragment: RESIDUES 110-119 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: Q5ZMD1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBIOTINYLATION TAG RSGGGLNDIFEAQKIEWHEN LINKER AND HIS-TAG SSSVDKLAAALEHHHHHH

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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: 2.29 Å3/Da / Density % sol: 46 %
Description: DATA PROCESSED WITH THE GLOBAL PHASING LTD. AUTOPROC SUITE
Crystal growpH: 4 / Details: 0.1 M MMT BUFFER PH 4.0, 25% PEG-1500

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0388
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0388 Å / Relative weight: 1
ReflectionResolution: 2.45→41.03 Å / Num. obs: 15146 / % possible obs: 85.9 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 51.62 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 1.5 / % possible all: 53

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Processing

Software
NameVersionClassification
BUSTER2.9.5refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BEV

3bev


Resolution: 2.9→41.03 Å / Cor.coef. Fo:Fc: 0.8057 / Cor.coef. Fo:Fc free: 0.7917 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.47
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 439 4.93 %RANDOM
Rwork0.251 ---
obs0.2521 8913 96.39 %-
Displacement parametersBiso mean: 31.99 Å2
Baniso -1Baniso -2Baniso -3
1-11.0333 Å20 Å20 Å2
2--11.4922 Å20 Å2
3----22.5255 Å2
Refine analyzeLuzzati coordinate error obs: 0.506 Å
Refinement stepCycle: LAST / Resolution: 2.9→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3071 0 0 30 3101
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073183HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.834308HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1074SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes468HARMONIC5
X-RAY DIFFRACTIONt_it3183HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.42
X-RAY DIFFRACTIONt_other_torsion19.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion389SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3357SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3137 131 5.23 %
Rwork0.2883 2375 -
all0.2896 2506 -
obs--96.39 %
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)
10.36070.1058-0.39760.5956-0.29830.45770.0489-0.07280.0021-0.0499-0.09960.0214-0.0331-0.02580.0508-0.01430.0107-0.0481-0.0201-0.01160.0686-32.802611.3391.2931
21.7273-0.6795-1.12661.35870.76890.14480.015-0.0265-0.009-0.05340.07280.02510.06370.0716-0.0877-0.05360.0229-0.0690.0913-0.01530.0185-4.0548-11.1538-0.6268
30.0059-0.22150.13760.4431-0.29050.5534-0.00780.0631-0.0298-0.1404-0.02870.0571-0.04120.04050.03650.02220.04370.03070.0461-0.0173-0.0132-18.074-5.3999-14.737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1-175)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 176-278)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 2-98)

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