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- PDB-1zt1: crystal structure of class I MHC H-2Kk in complex with an octapeptide -

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Basic information

Entry
Database: PDB / ID: 1zt1
Titlecrystal structure of class I MHC H-2Kk in complex with an octapeptide
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-K alpha chain
  • Influenza virus epitope, FEANGNLI
KeywordsIMMUNE SYSTEM / peptide binding groove
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-K alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKellenberger, C. / Roussel, A. / Malissen, B.
Citation
Journal: J Immunol. / Year: 2005
Title: The H-2Kk MHC peptide-binding groove anchors the backbone of an octameric antigenic peptide in an unprecedented mode.
Authors: Kellenberger, C. / Roussel, A. / Malissen, B.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Expression, refolding, crystallization and preliminary crystallographic study of MHC H-2Kk complexed with octapeptides and nonapeptides
Authors: Kellenberger, C. / Porciero, S. / Roussel, A.
History
DepositionMay 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 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: H-2 class I histocompatibility antigen, K-K alpha chain
B: Beta-2-microglobulin
P: Influenza virus epitope, FEANGNLI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1095
Polymers45,0383
Non-polymers712
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-31 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.758, 111.758, 109.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein H-2 class I histocompatibility antigen, K-K alpha chain / class I mouse MHC H-2Kk heavy chain / H- 2KK


Mass: 32325.137 Da / Num. of mol.: 1 / Fragment: residues 0-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04223
#2: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01887
#3: Protein/peptide Influenza virus epitope, FEANGNLI


Mass: 876.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 4.38 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NaCl, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2003
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. all: 27538 / Num. obs: 27403 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.069 / Net I/σ(I): 8.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3935 / Rsym value: 0.338 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LEG

1leg


Resolution: 2.5→14.87 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.325 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25141 1344 4.9 %RANDOM
Rwork0.21 ---
all0.21202 ---
obs0.21202 26053 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.161 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20.9 Å20 Å2
2--1.8 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 2.5→14.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 2 180 3314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213226
X-RAY DIFFRACTIONr_bond_other_d0.0020.022770
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9274381
X-RAY DIFFRACTIONr_angle_other_deg0.77736452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023596
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02699
X-RAY DIFFRACTIONr_nbd_refined0.1780.2572
X-RAY DIFFRACTIONr_nbd_other0.2240.23110
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.21906
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0870.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5161.51894
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99823063
X-RAY DIFFRACTIONr_scbond_it1.34231332
X-RAY DIFFRACTIONr_scangle_it2.3474.51318
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.358 99
Rwork0.245 1863

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