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- PDB-1rjy: Mhc Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With bet... -

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Basic information

Entry
Database: PDB / ID: 1rjy
TitleMhc Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With beta-2 Microglobulin and Herpes Simplex Virus Glycoprotein B Peptide
Components
  • Beta-2-microglobulin
  • Glycoprotein B
  • H-2 class I histocompatibility antigen, K-B alpha chain
KeywordsIMMUNE SYSTEM / MHC / class I / TCR
Function / homology
Function and homology information


TAP2 binding / TAP1 binding / natural killer cell lectin-like receptor binding / MHC class Ib protein complex / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...TAP2 binding / TAP1 binding / natural killer cell lectin-like receptor binding / MHC class Ib protein complex / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / DAP12 signaling / cellular response to iron(III) ion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to molecule of bacterial origin / regulation of erythrocyte differentiation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / inner ear development / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / multicellular organismal-level iron ion homeostasis / regulation of membrane depolarization / CD8 receptor binding / host cell Golgi membrane / endoplasmic reticulum exit site / TAP binding / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / beta-2-microglobulin binding / cellular defense response / T cell receptor binding / Neutrophil degranulation / 14-3-3 protein binding / T cell differentiation in thymus / positive regulation of T cell mediated cytotoxicity / host cell endosome membrane / negative regulation of neuron projection development / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / 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 assembly with MHC class II protein complex / protein refolding / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / late endosome membrane / cellular response to lipopolysaccharide / protein-folding chaperone binding / antimicrobial humoral immune response mediated by antimicrobial peptide / early endosome membrane / antibacterial humoral response / defense response to Gram-negative bacterium / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / early endosome / learning or memory / defense response to bacterium / defense response to Gram-positive bacterium / immune response / receptor ligand activity / external side of plasma membrane / Golgi membrane / signaling receptor binding / innate immune response / lysosomal membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / : / identical protein binding
Similarity search - Function
: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / 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-B alpha chain / Envelope glycoprotein B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Herpes simplex virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMiley, M.J. / Messaoudi, I. / Nikolich-Zugich, J. / Fremont, D.H.
CitationJournal: J.Exp.Med. / Year: 2004
Title: Structural Basis for the Restoration of TCR Recognition of an MHC Allelic Variant by Peptide Secondary Anchor Substitution
Authors: Miley, M.J. / Messaoudi, I. / Metzner, B.M. / Wu, Y. / Nikolich-Zugich, J. / Fremont, D.H.
History
DepositionNov 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: pdbx_entity_src_syn / pdbx_struct_assembly ...pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / struct_keywords / struct_ref_seq_dif
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_keywords.text / _struct_ref_seq_dif.details
Revision 1.4Oct 27, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
P: Glycoprotein B
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
Q: Glycoprotein B


Theoretical massNumber of molelcules
Total (without water)89,8776
Polymers89,8776
Non-polymers00
Water8,251458
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
P: Glycoprotein B


Theoretical massNumber of molelcules
Total (without water)44,9393
Polymers44,9393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-16 kcal/mol
Surface area19630 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
Q: Glycoprotein B


Theoretical massNumber of molelcules
Total (without water)44,9393
Polymers44,9393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-16 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.562, 90.137, 89.077
Angle α, β, γ (deg.)90.00, 111.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2KB


Mass: 32179.900 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide Glycoprotein B


Mass: 923.046 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: naturally occuring sequence in herpes simplex virus
Source: (synth.) Herpes simplex virus / References: UniProt: P06436
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, ca Acetate, sodium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 6, 2002
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 72537 / Num. obs: 72537 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.67 % / Biso Wilson estimate: 26.1 Å2 / Rsym value: 0.076 / Net I/σ(I): 19.9
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 3.09 / Rsym value: 0.36 / % possible all: 77.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 428892.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3425 5.1 %RANDOM
Rwork0.229 ---
all0.229 67588 --
obs0.229 67588 87.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.6886 Å2 / ksol: 0.358712 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1--6.71 Å20 Å2-2.28 Å2
2--15.31 Å20 Å2
3----8.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-20 Å
Luzzati sigma a0.33 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6302 0 0 458 6760
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.562
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.532.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 440 5.3 %
Rwork0.335 7793 -
obs--64.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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