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- PDB-4hs3: Crystal structure of H-2Kb with a disulfide stabilized F pocket i... -

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Basic information

Entry
Database: PDB / ID: 4hs3
TitleCrystal structure of H-2Kb with a disulfide stabilized F pocket in complex with the LCMV derived peptide GP34
Components
  • Beta-2-microglobulin
  • Envelope glycoprotein
  • H-2 class I histocompatibility antigen, K-B alpha chain
KeywordsIMMUNE SYSTEM / MHC class I / ANTIGEN PRESENTATION / ANTIGEN PROCESSING / PEPTIDE BINDING / IGG / MHC
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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / viral envelope / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / cytosol
Similarity search - Function
Arenavirus glycoprotein / Arenavirus glycoprotein / 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 / : ...Arenavirus glycoprotein / Arenavirus glycoprotein / 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
PHOSPHATE ION / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Envelope glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsUchtenhagen, H. / Boulanger, B. / Hein, Z. / Abualrous, E.T. / Zacharias, M. / Werner, J. / Elliott, T. / Springer, S. / Achour, A.
CitationJournal: J.Cell.Sci. / Year: 2014
Title: Peptide-independent stabilization of MHC class I molecules breaches cellular quality control.
Authors: Hein, Z. / Uchtenhagen, H. / Abualrous, E.T. / Saini, S.K. / Janen, L. / Van Hateren, A. / Wiek, C. / Hanenberg, H. / Momburg, F. / Achour, A. / Elliott, T. / Springer, S. / Boulanger, D.
History
DepositionOct 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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-B alpha chain
B: Beta-2-microglobulin
C: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6805
Polymers44,4673
Non-polymers2132
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-48 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.590, 90.570, 137.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 31846.582 Da / Num. of mol.: 1 / Fragment: UNP residues 22-297 / Mutation: A139C, Y84C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS / References: UniProt: P01887

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Envelope glycoprotein


Mass: 916.052 Da / Num. of mol.: 1 / Fragment: UNP residues 34-40 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: Q9WKU1

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Non-polymers , 3 types, 420 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystallization assays were performed in 24 well plates at 25 C using the vapor diffusion, hanging drop method. Best-diffracting crystals obtained from 7 mg/ml protein concentration in 2 M ...Details: Crystallization assays were performed in 24 well plates at 25 C using the vapor diffusion, hanging drop method. Best-diffracting crystals obtained from 7 mg/ml protein concentration in 2 M NaK phosphate pH 6.5 with 3% MPD, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 26, 2011
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.1→40.86 Å / Num. all: 32975 / Num. obs: 32975 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.76 Å2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S7S

1s7s


Resolution: 2.1→39.043 Å / SU ML: 0.69 / σ(F): 0 / Phase error: 23.11 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 1671 5.08 %Random
Rwork0.1872 ---
all0.1898 32908 --
obs0.1898 32908 96.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.151 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2119 Å2-0 Å20 Å2
2---3.4251 Å2-0 Å2
3---3.637 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 13 418 3559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083260
X-RAY DIFFRACTIONf_angle_d1.0654428
X-RAY DIFFRACTIONf_dihedral_angle_d14.1541210
X-RAY DIFFRACTIONf_chiral_restr0.072454
X-RAY DIFFRACTIONf_plane_restr0.004579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16180.29271230.22612610X-RAY DIFFRACTION97
2.1618-2.23160.30681470.22442522X-RAY DIFFRACTION97
2.2316-2.31130.27311450.24322561X-RAY DIFFRACTION97
2.3113-2.40380.29371200.22222619X-RAY DIFFRACTION97
2.4038-2.51320.27261380.21132572X-RAY DIFFRACTION97
2.5132-2.64570.27451470.20162556X-RAY DIFFRACTION97
2.6457-2.81140.28351430.20072582X-RAY DIFFRACTION97
2.8114-3.02840.25761410.18872574X-RAY DIFFRACTION96
3.0284-3.3330.21991300.16612562X-RAY DIFFRACTION95
3.333-3.8150.2021400.16512592X-RAY DIFFRACTION95
3.815-4.80510.16421510.14032602X-RAY DIFFRACTION95
4.8051-39.04930.25421460.1962885X-RAY DIFFRACTION99

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