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

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Basic information

Entry
Database: PDB / ID: 2clz
TitleMhc Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With beta-2 Microglobulin and pBM1 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 / MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling ...mRNA Splicing - Major Pathway / MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / ER-Phagosome pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / regulation of alternative mRNA splicing, via spliceosome / Golgi medial cisterna / inner ear development / CD8 receptor binding / spliceosomal complex assembly / beta-2-microglobulin binding / endoplasmic reticulum exit site / MHC class I protein binding / TAP binding / positive regulation of phosphorylation / cellular defense response / 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 / T cell receptor binding / Neutrophil degranulation / 14-3-3 protein binding / spliceosomal complex / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / iron ion transport / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / mRNA splicing, via spliceosome / 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 / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / T cell differentiation in thymus / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome membrane / negative regulation of neuron projection development / antibacterial humoral response / protein-folding chaperone binding / protein refolding / cellular response to lipopolysaccharide / early endosome membrane / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / learning or memory / early endosome / defense response to bacterium / defense response to Gram-positive bacterium / immune response / positive regulation of apoptotic process / receptor ligand activity / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane / mRNA binding / apoptotic process / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
Similarity search - Function
BTBD10/KCTD20, BTB/POZ domain / BTBD10/KCTD20 / BTB/POZ domain / 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 ...BTBD10/KCTD20, BTB/POZ domain / BTBD10/KCTD20 / BTB/POZ domain / 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 superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 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 / SKP1/BTB/POZ domain superfamily / 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 / 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 / BTB/POZ domain-containing protein KCTD20 / 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. / Kearnay, A. / Van Der Merwe, P.A. / Fontecilla-Camps, J.C. / Housset, D. / Malissen, B.
History
DepositionMay 3, 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 1.3Dec 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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)89,5326
Polymers89,5326
Non-polymers00
Water11,548641
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)44,7663
Polymers44,7663
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)44,7663
Polymers44,7663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.588, 90.759, 89.248
Angle α, β, γ (deg.)90.00, 111.35, 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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / 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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01887
#3: Protein/peptide RBM5 PROTEIN


Mass: 983.076 Da / Num. of mol.: 2 / Fragment: RESIDUES 136-143 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE IS NATURALLY FOUND IN MUS MUCULUS (MOUSE)
Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q99KV9, UniProt: Q8CDD8*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 43 TO PHE ENGINEERED RESIDUE IN CHAIN A, MET 44 TO ILE ...ENGINEERED RESIDUE IN CHAIN A, TYR 43 TO PHE ENGINEERED RESIDUE IN CHAIN A, MET 44 TO ILE ENGINEERED RESIDUE IN CHAIN A, GLU 45 TO SER ENGINEERED RESIDUE IN CHAIN A, ASP 51 TO ASN ENGINEERED RESIDUE IN CHAIN H, TYR 43 TO PHE ENGINEERED RESIDUE IN CHAIN H, MET 44 TO ILE ENGINEERED RESIDUE IN CHAIN H, GLU 45 TO SER ENGINEERED RESIDUE IN CHAIN H, ASP 51 TO ASN
Has protein modificationY
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: 54.6 % / Description: STARTING FROM PDB 1CLV
Crystal growpH: 6.3 / Details: 14% PEG 6000 ; 100 MM MES PH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→51.23 Å / Num. obs: 75377 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.3 / % possible all: 86.8

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Processing

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

1clv


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.905 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3777 5 %RANDOM
Rwork0.206 ---
obs0.208 71423 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-0.45 Å2
2--1.58 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6298 0 0 641 6939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226486
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9438820
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6095764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80723.614332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.452151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0861548
X-RAY DIFFRACTIONr_chiral_restr0.0790.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025086
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.22864
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24329
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2626
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6781.53970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15626240
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.53432949
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4844.52580
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
Rfree0.299 208
Rwork0.259 4180

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