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- PDB-2ckb: STRUCTURE OF THE 2C/KB/DEV8 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2ckb
TitleSTRUCTURE OF THE 2C/KB/DEV8 COMPLEX
Components
  • (ALPHA, BETA T CELL ...) x 2
  • BETA-2 MICROGLOBULIN
  • DEV8 PEPTIDE
  • MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B)
KeywordsMAJOR HISTOCOMPATIBILITY COMPLEX / T CELL ANTIGEN RECEPTOR
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport / respiratory chain complex IV / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling ...Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport / respiratory chain complex IV / 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 / T cell receptor complex / 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 / respiratory chain complex I / 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 / peptide antigen binding / 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 / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / mitochondrial inner membrane / defense response to bacterium / external side of plasma membrane / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / cytosol
Similarity search - Function
NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / : / 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 / Immunoglobulin V-Type ...NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / : / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
: / : / T-cell receptor alpha chain V region PHDS58 / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Cytochrome c oxidase subunit NDUFA4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGarcia, K.C. / Degano, M. / Wilson, I.A.
Citation
Journal: Science / Year: 1998
Title: Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen.
Authors: Garcia, K.C. / Degano, M. / Pease, L.R. / Huang, M. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
#1: Journal: Science / Year: 1996
Title: An Alphabeta T Cell Receptor Structure at 2.5 A and its Orientation in the Tcr-Mhc Complex
Authors: Garcia, K.C. / Degano, M. / Stanfield, R.L. / Brunmark, A. / Jackson, M.R. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
History
DepositionJan 14, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_sheet
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_sheet.number_strands
Revision 1.4Oct 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

Downloads & links

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Assembly

Deposited unit
A: ALPHA, BETA T CELL RECEPTOR
B: ALPHA, BETA T CELL RECEPTOR
H: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B)
P: DEV8 PEPTIDE
L: BETA-2 MICROGLOBULIN
C: ALPHA, BETA T CELL RECEPTOR
D: ALPHA, BETA T CELL RECEPTOR
I: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B)
Q: DEV8 PEPTIDE
M: BETA-2 MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)186,00010
Polymers186,00010
Non-polymers00
Water1086
1
A: ALPHA, BETA T CELL RECEPTOR
B: ALPHA, BETA T CELL RECEPTOR
H: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B)
P: DEV8 PEPTIDE
L: BETA-2 MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)93,0005
Polymers93,0005
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ALPHA, BETA T CELL RECEPTOR
D: ALPHA, BETA T CELL RECEPTOR
I: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B)
Q: DEV8 PEPTIDE
M: BETA-2 MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)93,0005
Polymers93,0005
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)295.660, 89.960, 84.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.961149, 0.275631, -0.014864), (-0.275712, 0.961233, -0.003698), (0.013268, 0.007653, 0.999883)-202.06081, 47.5935, -48.5005
2given(0.963537, 0.266972, -0.017951), (-0.267279, 0.963457, -0.017688), (0.012572, 0.021841, 0.999682)-201.83701, 46.7915, -49.1706
3given(0.959949, 0.279146, -0.023998), (-0.279589, 0.959959, -0.017589), (0.018127, 0.023594, 0.999557)-201.18221, 50.1028, -50.9724
4given(0.966869, 0.253587, -0.029307), (-0.254435, 0.96662, -0.030144), (0.020684, 0.036602, 0.999116)-200.733, 44.0797, -52.3646
5given(0.947092, 0.320962, -0.000891), (-0.320963, 0.947085, -0.003616), (-0.000316, 0.003711, 0.999993)-202.0744, 61.4576, -44.2977
6given(0.948063, 0.318082, -0.000309), (-0.31807, 0.948034, 0.007925), (0.002813, -0.007415, 0.999969)-202.2825, 60.2545, -44.4623

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Components

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ALPHA, BETA T CELL ... , 2 types, 4 molecules ACBD

#1: Protein ALPHA, BETA T CELL RECEPTOR / T CELL ANTIGEN RECEPTOR


Mass: 22298.889 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Details: VB8.2DB2JB2.4CB2\;VA3JA58CA / Source: (gene. exp.) Mus musculus (house mouse) / Cell: T-LYMPHOCYTES / Cellular location: EXTRACELLULAR / Production host: Drosophila melanogaster (fruit fly) / References: EMBL: X01134, UniProt: P01738*PLUS
#2: Protein ALPHA, BETA T CELL RECEPTOR / T CELL ANTIGEN RECEPTOR


Mass: 26284.180 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Details: VB8.2DB2JB2.4CB2\;VA3JA58CA / Source: (gene. exp.) Mus musculus (house mouse) / Cell: T-LYMPHOCYTES / Cellular location: EXTRACELLULAR / Production host: Drosophila melanogaster (fruit fly) / References: GenBank: 1791255

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Protein , 2 types, 4 molecules HILM

#3: Protein MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE K(B) / MHC CLASS I


Mass: 31648.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ANTIGEN PRESENTING MOLECULE / Source: (gene. exp.) Mus musculus (house mouse) / Cell: NUCLEATED CELLS / Cellular location: EXTRACELLULAR / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01901
#5: Protein BETA-2 MICROGLOBULIN / BETA2M / B2M


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: NUCLEATED CELLS / Cellular location: EXTRACELLULAR / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887

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Protein/peptide / Non-polymers , 2 types, 8 molecules PQ

#4: Protein/peptide DEV8 PEPTIDE / DEV8


Mass: 1064.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PEPTIDE DERIVED FROM A MITOCHONDRIAL PROTEIN / References: UniProt: Q62425*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.11 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.2
Details: PROTEIN WAS CRYSTALLIZED FROM 0.2 M TRIS ACETATE PH 7.2 0.1 M SODIUM CHLORIDE 12 % PEG 4000 AND TRANSFERRED IN ETHYLENE GLYCOL CONTAINING PRECIPITANT SOLUTION, FROM 4% TO 22%, BEFORE DATA COLLECTION.
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mphosphate1reservoir
21.0 %methylpentanediol1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 314268 / % possible obs: 83.3 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.088 / Net I/σ(I): 9.2
Reflection shellResolution: 3→3.12 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.328 / % possible all: 70.1
Reflection
*PLUS
Num. obs: 37960 / Num. measured all: 314268 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 70.1 % / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1TCR, 1VAC

1tcr

1vac


Resolution: 3→25 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.322 1435 4 %SPHERES
Rwork0.221 ---
obs0.221 34092 78.7 %-
Displacement parametersBiso mean: 43.2 Å2
Baniso -1Baniso -2Baniso -3
1-14.6 Å20 Å20 Å2
2---11 Å20 Å2
3---14.9 Å2
Refine analyzeLuzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13104 0 0 6 13110
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.78
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it9.941.5
X-RAY DIFFRACTIONx_mcangle_it14.72
X-RAY DIFFRACTIONx_scbond_it15.62
X-RAY DIFFRACTIONx_scangle_it20.62.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11RESTRAINED8.530.042300
2214.20.064150
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.38 143 -
Rwork0.322 3499 -
obs--67.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.TOP
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.38

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