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- PDB-1bz9: CRYSTAL STRUCTURE OF MURINE CLASS I MHC H2-DB COMPLEXED WITH A SY... -

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Basic information

Entry
Database: PDB / ID: 1bz9
TitleCRYSTAL STRUCTURE OF MURINE CLASS I MHC H2-DB COMPLEXED WITH A SYNTHETIC PEPTIDE P1027
Components
  • (PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN)) x 2
  • PROTEIN (PEPTIDE P1027 (FAPGVFPYM))
KeywordsMURINE CLASS I MHC/PEPTIDE COMPLEX / MURINE CLASS I MHC-PEPTIDE COMPLEX / MURINE CLASS I MHC-PEPTIDE COMPLEX complex
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 endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane ...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 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 / 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 / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / 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, D-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhao, R. / Collins, E.J.
CitationJournal: J.Exp.Med. / Year: 1999
Title: Structural evidence of T cell xeno-reactivity in the absence of molecular mimicry.
Authors: Zhao, R. / Loftus, D.J. / Appella, E. / Collins, E.J.
History
DepositionNov 6, 1998Processing site: RCSB
SupersessionMay 24, 1999ID: 1A9D
Revision 1.0May 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 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: PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN)
B: PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN)
C: PROTEIN (PEPTIDE P1027 (FAPGVFPYM))


Theoretical massNumber of molelcules
Total (without water)45,2703
Polymers45,2703
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-25 kcal/mol
Surface area19430 Å2
MethodPISA
2
A: PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN)
B: PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN)
C: PROTEIN (PEPTIDE P1027 (FAPGVFPYM))

A: PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN)
B: PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN)
C: PROTEIN (PEPTIDE P1027 (FAPGVFPYM))


Theoretical massNumber of molelcules
Total (without water)90,5406
Polymers90,5406
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area10320 Å2
ΔGint-62 kcal/mol
Surface area36910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.350, 109.190, 57.780
Angle α, β, γ (deg.)90.00, 122.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN)


Mass: 32406.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: FOLDED WITH SYNTHETIC PEPTIDE IN VITRO / Cellular location: CELL SURFACE / Plasmid: PLM1 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P01899
#2: Protein PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN)


Mass: 11835.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: FOLDED WITH SYNTHETIC PEPTIDE IN VITRO / Cellular location: CELL SURFACE / Plasmid: PLM1 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P01887
#3: Protein/peptide PROTEIN (PEPTIDE P1027 (FAPGVFPYM))


Mass: 1028.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.7 Å3/Da / Density % sol: 54.02 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 %PEG80001reservoir
2150 mM1reservoirNaCl
30.8 MGly1reservoir
46 %DMSO1reservoir
525 mMMES1reservoir
610 mg/mlprotein1drop
70.8 MGly1drop
825 mMMES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 11820 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 20.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 5.9 / % possible all: 100
Reflection
*PLUS
Num. measured all: 62278
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREIN CCP4phasing
REFMACrefinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HOC

1hoc


Resolution: 2.8→30 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.48
RfactorNum. reflection% reflectionSelection details
Rfree0.319 559 5 %RANDOM
Rwork0.252 ---
obs0.266 11759 99 %-
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.466 Å20 Å28.675 Å2
2---11 Å20 Å2
3---10.55 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 0 5 3152
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.05
X-RAY DIFFRACTIONp_mcbond_it2.372
X-RAY DIFFRACTIONp_mcangle_it4.1013
X-RAY DIFFRACTIONp_scbond_it3.1572
X-RAY DIFFRACTIONp_scangle_it5.2363
X-RAY DIFFRACTIONp_plane_restr0.01490.03
X-RAY DIFFRACTIONp_chiral_restr0.1160.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2750.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1520.3
X-RAY DIFFRACTIONp_planar_tor27
X-RAY DIFFRACTIONp_staggered_tor21.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.620
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_dihedral_angle_d25.55
X-RAY DIFFRACTIONp_improper_angle_d1.307
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_chiral_restr0.15
X-RAY DIFFRACTIONp_mcbond_it22.37
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it3

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