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- PDB-4cw1: COMPLEX OF A B14 CHICKEN MHC CLASS I MOLECULE AND A 9MER CHICKEN ... -

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Basic information

Entry
Database: PDB / ID: 4cw1
TitleCOMPLEX OF A B14 CHICKEN MHC CLASS I MOLECULE AND A 9MER CHICKEN PEPTIDE
Components
  • BETA-2-MICROGLOBULIN
  • MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B14
  • PEPTIDE
KeywordsIMMUNE SYSTEM / MHC / B14
Function / homology
Function and homology information


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 / peptide antigen assembly with MHC class II protein complex / negative regulation of forebrain neuron differentiation ...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 / peptide antigen assembly with MHC class II protein complex / negative regulation of forebrain neuron differentiation / MHC class II protein complex / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / peptide antigen binding / positive regulation of T cell activation / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / positive regulation of cellular senescence / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I molecule / Beta-2-microglobulin
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 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.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, 2014Deposition site: PDBE / Processing site: PDBE
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 1.2Dec 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
Revision 1.3Nov 20, 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: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B14
B: BETA-2-MICROGLOBULIN
C: PEPTIDE
D: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B14
E: BETA-2-MICROGLOBULIN
F: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)94,9256
Polymers94,9256
Non-polymers00
Water1,38777
1
A: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B14
B: BETA-2-MICROGLOBULIN
F: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)47,4633
Polymers47,4633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-19.2 kcal/mol
Surface area18770 Å2
MethodPISA
2
C: PEPTIDE
D: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B14
E: BETA-2-MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)47,4633
Polymers47,4633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-21.4 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.200, 90.580, 144.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99999, 0.00415, -0.00101), (0.00416, 0.99981, -0.01889), (0.00093, -0.0189, -0.99982)62.20206, -0.15564, 4.66718
2given(-1, 0.00144, -0.00272), (0.00148, 0.99988, -0.01552), (0.0027, -0.01552, -0.99988)62.13829, -0.012, 4.65622

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Components

#1: Protein MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B14


Mass: 35188.766 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 24-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Description: B14 HAPLOTYPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA CELLS / References: UniProt: A0ZXM3
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11062.404 Da / Num. of mol.: 2 / 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) / Variant (production host): PLYSS ROSETTA CELLS / References: UniProt: P21611
#3: Protein/peptide PEPTIDE


Mass: 1211.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SELF-PEPTIDE / Source: (synth.) GALLUS GALLUS (chicken)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.21 Å3/Da / Density % sol: 44.32 % / Description: NONE
Crystal growpH: 5 / Details: 0.1M MIB BUFFER, PH 5.0, 25% W/V PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97932
DetectorDate: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.58→72.38 Å / Num. obs: 26279 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 56.06 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.8
Reflection shellResolution: 2.58→2.65 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / % possible all: 98.4

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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 2YF6

2yf6
PDB Unreleased entry


Resolution: 2.58→72.38 Å / Cor.coef. Fo:Fc: 0.8741 / Cor.coef. Fo:Fc free: 0.8733 / SU R Cruickshank DPI: 1.378 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.446 / SU Rfree Blow DPI: 0.358 / SU Rfree Cruickshank DPI: 0.363
RfactorNum. reflection% reflectionSelection details
Rfree0.2909 1333 5.08 %RANDOM
Rwork0.2857 ---
obs0.286 26228 99.12 %-
Displacement parametersBiso mean: 39.91 Å2
Baniso -1Baniso -2Baniso -3
1-4.4774 Å20 Å20 Å2
2---15.0266 Å20 Å2
3---10.5492 Å2
Refine analyzeLuzzati coordinate error obs: 0.571 Å
Refinement stepCycle: LAST / Resolution: 2.58→72.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 0 77 6119
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076220HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.848463HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2077SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes164HARMONIC2
X-RAY DIFFRACTIONt_gen_planes905HARMONIC5
X-RAY DIFFRACTIONt_it6220HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.64
X-RAY DIFFRACTIONt_other_torsion18.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion767SEMIHARMONIC5
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_contact6472SEMIHARMONIC4
LS refinement shellResolution: 2.58→2.69 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3478 155 5.35 %
Rwork0.3343 2741 -
all0.335 2896 -
obs--99.12 %

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