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- PDB-5ad0: COMPLEX OF A B21 CHICKEN MHC CLASS I MOLECULE AND A 11MER CHICKEN... -

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Basic information

Entry
Database: PDB / ID: 5ad0
TitleCOMPLEX OF A B21 CHICKEN MHC CLASS I MOLECULE AND A 11MER CHICKEN PEPTIDE
Components
  • 11MER PEPTIDE
  • BETA-2-MICROGLOBULIN
  • MHC CLASS I ALPHA CHAIN 2
KeywordsIMMUNE SYSTEM / CHICKEN / B21
Function / homology
Function and homology information


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 / 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 ...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 / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / 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 / 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 / external side of plasma membrane / signaling receptor binding / 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...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: 2.84 Å
AuthorsChappell, P.E. / Roversi, P. / Harrison, M.C. / Kaufman, J.F. / Lea, S.M.
CitationJournal: To be Published
Title: Complex of a B21 Chicken Mhc Class I Molecule and a 11mer Chicken Peptide
Authors: Chappell, P.E. / Roversi, P. / Harrison, M.C. / Kaufman, J.F. / Lea, S.M.
History
DepositionAug 19, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionSep 28, 2016ID: 2YF1
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: 11MER PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2526
Polymers49,0883
Non-polymers1643
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-25.7 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.861, 72.329, 73.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC CLASS I ALPHA CHAIN 2


Mass: 36862.012 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 1-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Strain: B21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA / References: UniProt: Q95601
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11062.404 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Strain: B21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA / References: UniProt: P21611

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide 11MER PEPTIDE


Mass: 1163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GALLUS GALLUS (chicken)

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Non-polymers , 3 types, 35 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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 Å3/Da / Density % sol: 38.52 % / Description: NONE
Crystal growpH: 8
Details: 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1M TRIS, PH 8.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.84→73.78 Å / Num. obs: 9390 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 65.71 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 11
Reflection shellResolution: 2.84→2.99 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 87.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BEV

3bev


Resolution: 2.84→52.11 Å / Cor.coef. Fo:Fc: 0.8687 / Cor.coef. Fo:Fc free: 0.8023 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.445
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 449 4.8 %RANDOM
Rwork0.2362 ---
obs0.2378 9355 96.07 %-
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.3239 Å20 Å20 Å2
2---1.1821 Å20 Å2
3---4.506 Å2
Refinement stepCycle: LAST / Resolution: 2.84→52.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 9 32 3063
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073116HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.834213HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1043SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes455HARMONIC5
X-RAY DIFFRACTIONt_it3116HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.44
X-RAY DIFFRACTIONt_other_torsion20.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion382SEMIHARMONIC5
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_contact3132SEMIHARMONIC4
LS refinement shellResolution: 2.84→3.17 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2712 105 4.42 %
Rwork0.2564 2268 -
all0.2571 2373 -
obs--87.66 %
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)
11.57020.1733-0.89782.2488-0.56754.422-0.038-0.13380.01230.03240.16040.059-0.00990.0318-0.1224-0.0920.0549-0.0275-0.1026-0.0057-0.0731-15.244126.5272-2.4126
22.06830.8555-0.13650.6363-0.49032.23080.0064-0.021-0.02240.03590.0128-0.03490.0186-0.015-0.0192-0.042-0.0291-0.01820.0129-0.0202-0.06151.6985-3.87927.3802
31.10380.28831.53612.1544-0.50040.34830.00620.0049-0.0235-0.09680.00070.0568-0.0364-0.037-0.00680.0169-0.00850.0203-0.03-0.0130.017-13.6214-0.5845-6.1618
40.24230.11180.130600.27210.0309-0.00020.0004-0.0045-0.00230.0006-0.0059-0.00010.0041-0.00040.0055-0.0015-0.00520.00960.01310.0125-18.659233.2394-3.6658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|2 - A|175}
2X-RAY DIFFRACTION2{A|176 - A|269}
3X-RAY DIFFRACTION3{B|1 - B|98}
4X-RAY DIFFRACTION4{C|1 - C|11}

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