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- PDB-4d0c: COMPLEX OF A B21 CHICKEN MHC CLASS I MOLECULE AND A 10MER CHICKEN... -

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Basic information

Entry
Database: PDB / ID: 4d0c
TitleCOMPLEX OF A B21 CHICKEN MHC CLASS I MOLECULE AND A 10MER CHICKEN PEPTIDE
Components
  • 10MER PEPTIDE
  • BETA-2-MICROGLOBULIN
  • MHC CLASS I ALPHA CHAIN 2
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


Transferrin endocytosis and recycling / Post-translational modification: synthesis of GPI-anchored proteins / 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 ...Transferrin endocytosis and recycling / Post-translational modification: synthesis of GPI-anchored proteins / 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 / external side of plasma membrane / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / cytosol
Similarity search - Function
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 / : ...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 / MHC class I alpha chain 2
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsChappell, P.E. / 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.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. ...Authors: Chappell, P. / Meziane, E.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
DepositionApr 25, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionMay 6, 2015ID: 2YF5
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 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 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation_author / pdbx_database_proc / Item: _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC CLASS I ALPHA CHAIN 2
B: BETA-2-MICROGLOBULIN
C: 10MER PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1124
Polymers49,0503
Non-polymers621
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-23 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.410, 68.790, 94.610
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 MHC CLASS I ALPHA CHAIN 2 / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B21


Mass: 36862.012 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 1-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Description: B21 HAPLOTYPE / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA CELLS / 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) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA CELLS / References: UniProt: P21611
#3: Protein/peptide 10MER PEPTIDE


Mass: 1125.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / Source: (synth.) GALLUS GALLUS (chicken)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.27 Å3/Da / Density % sol: 45.95 % / Description: NONE
Crystal growDetails: 0.05 M KH2PO4 AND 20% PEG 8000

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.81→68.79 Å / Num. obs: 9089 / % possible obs: 91.4 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 48.55 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.8
Reflection shellResolution: 2.81→2.88 Å / Redundancy: 2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.9 / % possible all: 78.5

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSTHROUGH XIA2data reduction
AimlessTHROUGH XIA2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BEV

3bev


Resolution: 2.81→50.92 Å / Cor.coef. Fo:Fc: 0.7661 / Cor.coef. Fo:Fc free: 0.7702 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.48
RfactorNum. reflection% reflectionSelection details
Rfree0.282 421 4.69 %RANDOM
Rwork0.275 ---
obs0.2753 8967 88.94 %-
Displacement parametersBiso mean: 34.02 Å2
Baniso -1Baniso -2Baniso -3
1-14.3503 Å20 Å20 Å2
2--18.9832 Å20 Å2
3----33.3335 Å2
Refine analyzeLuzzati coordinate error obs: 0.588 Å
Refinement stepCycle: LAST / Resolution: 2.81→50.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3057 0 4 31 3092
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073147HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.864275HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1059SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes461HARMONIC5
X-RAY DIFFRACTIONt_it3147HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.56
X-RAY DIFFRACTIONt_other_torsion18.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion385SEMIHARMONIC5
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_contact3275SEMIHARMONIC4
LS refinement shellResolution: 2.81→3.14 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3508 103 4.48 %
Rwork0.3312 2198 -
all0.332 2301 -
obs--88.94 %

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