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- PDB-2clv: MHC Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With bet... -

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Basic information

Entry
Database: PDB / ID: 2clv
TitleMHC Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With beta-2 Microglobulin and pBM8 peptide
Components
  • BETA-2 MICROGLOBULIN
  • H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN
  • RBM5 PROTEIN
KeywordsIMMUNE SYSTEM / IMMUNE RESPONSE / IMMUNOGLOBULIN DOMAIN / GLYCOPROTEIN / TRANSMEMBRANE / ALLOREACTIVITY / MHC I / H-2KBM8 / MEMBRANE / CLASS I MHC / POLYMORPHISM
Function / homology
Function and homology information


mRNA Splicing - Major Pathway / 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 / regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / antigen processing and presentation of exogenous peptide antigen via MHC class I ...mRNA Splicing - Major Pathway / 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 / regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / 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 / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / spliceosomal complex / peptide binding / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / mRNA splicing, via spliceosome / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to bacterium / immune response / positive regulation of apoptotic process / external side of plasma membrane / lysosomal membrane / signaling receptor binding / mRNA binding / protein-containing complex binding / apoptotic process / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others ...RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger C2H2 type domain profile. / 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 / Zinc finger C2H2-type / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / RNA-binding domain 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 / Nucleotide-binding alpha-beta plait domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / 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 / RNA-binding protein 5 / RNA-binding protein 5
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMazza, C. / Auphan-Anezin, N. / Guimezanes, A. / Barrett-Wilt, G.A. / Montero-Julian, F. / Roussel, A. / Hunt, D.F. / Schmitt-Verhulst, A.M. / Malissen, B.
Citation
Journal: Eur. J. Immunol. / Year: 2006
Title: Distinct orientation of the alloreactive monoclonal CD8 T cell activation program by three different peptide/MHC complexes.
Authors: Auphan-Anezin, N. / Mazza, C. / Guimezanes, A. / Barrett-Wilt, G.A. / Montero-Julian, F. / Roussel, A. / Hunt, D.F. / Malissen, B. / Schmitt-Verhulst, A.M.
#1: Journal: Nat.Immunol. / Year: 2003
Title: Cdr3 Loop Flexibility Contributes to the Degeneracy of Tcr Recognition
Authors: Reiser, J.B. / Darnault, C. / Gregoire, C. / Mosser, T. / Mazza, G. / Kearney, A. / Van Der Merwe, P.A. / Fontecilla-Camps, J.C. / Housset, D. / Malissen, B.
History
DepositionMay 2, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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: RBM5 PROTEIN
H: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN
M: RBM5 PROTEIN
P: BETA-2 MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)89,6406
Polymers89,6406
Non-polymers00
Water11,602644
1
A: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN
B: BETA-2 MICROGLOBULIN
C: RBM5 PROTEIN


Theoretical massNumber of molelcules
Total (without water)44,8203
Polymers44,8203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
H: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN
M: RBM5 PROTEIN
P: BETA-2 MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)44,8203
Polymers44,8203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.146, 90.461, 89.032
Angle α, β, γ (deg.)90.00, 111.02, 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-2K(B)


Mass: 32078.799 Da / Num. of mol.: 2
Fragment: EXTRACELLULAR DOMAINS (ALPHA1, ALPHA2, ALPHA3), RESIDUES 22-300
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET3A / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01901
#2: Protein BETA-2 MICROGLOBULIN


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET3A / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01887
#3: Protein/peptide RBM5 PROTEIN


Mass: 1037.082 Da / Num. of mol.: 2 / Fragment: RESIDUES 189-196 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q99KV9, UniProt: Q91YE7*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 22 TO PHE ENGINEERED RESIDUE IN CHAIN A, MET 23 TO ILE ...ENGINEERED RESIDUE IN CHAIN A, TYR 22 TO PHE ENGINEERED RESIDUE IN CHAIN A, MET 23 TO ILE ENGINEERED RESIDUE IN CHAIN A, GLU 24 TO SER ENGINEERED RESIDUE IN CHAIN A, ASP 30 TO ASN ENGINEERED RESIDUE IN CHAIN H, TYR 22 TO PHE ENGINEERED RESIDUE IN CHAIN H, MET 23 TO ILE ENGINEERED RESIDUE IN CHAIN H, GLU 24 TO SER ENGINEERED RESIDUE IN CHAIN H, ASP 30 TO ASN
Sequence detailsTHE Y22F, M23I, E24S, D30N QUADRUPLE MUTANT IS CALLED BM8, A NATURALLY OCCURING MUTANT IN MICE

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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: 54.8 %
Crystal growpH: 6.3 / Details: 14% PEG 10000, 100 MM MES PH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.009
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 78205 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NAN

1nan


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.36 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3930 5 %RANDOM
Rwork0.21 ---
obs0.212 74179 100 %-
Solvent computationVDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-0.52 Å2
2--2.16 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6306 0 0 644 6950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226496
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.9448834
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8595764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00223.554332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.946151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3651548
X-RAY DIFFRACTIONr_chiral_restr0.0830.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025098
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.22959
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.24361
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2638
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6451.53979
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11726234
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47332968
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3864.52600
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 282
Rwork0.269 5400

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