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- PDB-2clr: THREE DIMENSIONAL STRUCTURE OF A PEPTIDE EXTENDING OUT ONE END OF... -

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Entry
Database: PDB / ID: 2clr
TitleTHREE DIMENSIONAL STRUCTURE OF A PEPTIDE EXTENDING OUT ONE END OF A CLASS I MHC BINDING SITE
Components
  • BETA 2-MICROGLOBULIN
  • CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) (ALPHA CHAIN)
  • DECAMERIC PEPTIDE FROM CALRETICULIN
KeywordsHISTOCOMPATIBILITY ANTIGEN
Function / homology
Function and homology information


response to biphenyl / Calnexin/calreticulin cycle / cytolytic granule / positive regulation of dendritic cell chemotaxis / nuclear receptor-mediated glucocorticoid signaling pathway / Assembly of Viral Components at the Budding Site / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of trophoblast cell migration / cortical granule / cellular response to electrical stimulus ...response to biphenyl / Calnexin/calreticulin cycle / cytolytic granule / positive regulation of dendritic cell chemotaxis / nuclear receptor-mediated glucocorticoid signaling pathway / Assembly of Viral Components at the Budding Site / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of trophoblast cell migration / cortical granule / cellular response to electrical stimulus / response to peptide / regulation of meiotic nuclear division / complement component C1q complex binding / sequestering of calcium ion / negative regulation of retinoic acid receptor signaling pathway / endoplasmic reticulum quality control compartment / protein folding in endoplasmic reticulum / sarcoplasmic reticulum lumen / negative regulation of intracellular steroid hormone receptor signaling pathway / nuclear export signal receptor activity / cardiac muscle cell differentiation / cortical actin cytoskeleton organization / response to glycoside / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Scavenging by Class A Receptors / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / nuclear androgen receptor binding / Scavenging by Class F Receptors / cellular response to lithium ion / negative regulation of neuron differentiation / CD8 receptor binding / response to testosterone / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / smooth endoplasmic reticulum / hormone binding / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / molecular sequestering activity / 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 / protein localization to nucleus / detection of bacterium / T cell receptor binding / positive regulation of cell cycle / ERAD pathway / endocytic vesicle lumen / endoplasmic reticulum-Golgi intermediate compartment membrane / protein folding chaperone / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / peptide binding / acrosomal vesicle / protein export from nucleus / positive regulation of phagocytosis / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / protein maturation / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / positive regulation of non-canonical NF-kappaB signal transduction / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / cellular response to virus / 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 / specific granule lumen
Similarity search - Function
Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / MHC class I, alpha chain, C-terminal ...Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / 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 / Concanavalin A-like lectin/glucanase 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Calreticulin / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsCollins, E.J. / Garboczi, D.N. / Wiley, D.C.
Citation
Journal: Nature / Year: 1994
Title: Three-dimensional structure of a peptide extending from one end of a class I MHC binding site.
Authors: Collins, E.J. / Garboczi, D.N. / Wiley, D.C.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Five Viral Peptide-Hla-A2 Co-Crystals: Simultaneous Space Group Determination and X-Ray Data Collection
Authors: Garboczi, D.N. / Madden, D.R. / Wiley, D.C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Comparison of the P2 Specificity Pocket in Three Human Histocompatibility Antigens: Hla-A(Asterisk)6801, Hla-A(Asterisk)0201, and Hla-B(Asterisk)2705
Authors: Guo, H.-C. / Madden, D.R. / Silver, M.L. / Jardetzky, T.S. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: The Antigenic Identity of Peptide-Mhc Complexes a Comparison of the Conformations of Five Viral Peptides Presented by Hla-A2
Authors: Madden, D.R. / Garboczi, D.N. / Wiley, D.C.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Hla-A2-Peptide Complexes: Refolding and Crystallization of Molecules Expressed in Escherichia Coli and Complexed with Single Antigenic Peptides
Authors: Garboczi, D.N. / Hung, D.T. / Wiley, D.C.
#5: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution
Authors: Saper, M.A. / Bjorkman, P.J. / Wiley, D.C.
#6: Journal: Nature / Year: 1987
Title: Structure of the Human Class I Histocompatibility Antigen, Hla-A2
Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C.
#7: Journal: Nature / Year: 1987
Title: The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens
Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C.
#8: Journal: J.Mol.Biol. / Year: 1985
Title: Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes
Authors: Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C.
History
DepositionAug 1, 1994Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 16, 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: CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) (ALPHA CHAIN)
B: BETA 2-MICROGLOBULIN
C: DECAMERIC PEPTIDE FROM CALRETICULIN
D: CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) (ALPHA CHAIN)
E: BETA 2-MICROGLOBULIN
F: DECAMERIC PEPTIDE FROM CALRETICULIN


Theoretical massNumber of molelcules
Total (without water)89,5786
Polymers89,5786
Non-polymers00
Water00
1
A: CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) (ALPHA CHAIN)
B: BETA 2-MICROGLOBULIN
C: DECAMERIC PEPTIDE FROM CALRETICULIN


Theoretical massNumber of molelcules
Total (without water)44,7893
Polymers44,7893
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-22 kcal/mol
Surface area18480 Å2
MethodPISA
2
D: CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) (ALPHA CHAIN)
E: BETA 2-MICROGLOBULIN
F: DECAMERIC PEPTIDE FROM CALRETICULIN


Theoretical massNumber of molelcules
Total (without water)44,7893
Polymers44,7893
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-20 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.410, 62.909, 74.810
Angle α, β, γ (deg.)81.99, 76.43, 78.06
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO A 210 / 2: CIS PROLINE - PRO B 32 / 3: CIS PROLINE - PRO D 210 / 4: CIS PROLINE - PRO E 32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.924892, 0.380207, 0.004274), (0.38021, 0.9249, -0.000132), (-0.004004, 0.001503, -0.999991)25.91708, -47.34475, 32.12666
2given(-0.906251, 0.42183, 0.027723), (0.421773, 0.906665, -0.00816), (-0.028578, 0.004298, -0.999582)22.78743, -47.91862, 32.41289
3given(-0.912356, 0.409396, 0.000786), (0.409388, 0.912323, 0.008246), (0.002658, 0.007845, -0.999966)24.03463, -48.32787, 31.44072
DetailsTHE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES AS FOLLOWS: MTRIX 1: APPLIED TO CHAIN D RESIDUES 1 - 183, APPROXIMATELY GENERATES CHAIN A RESIDUES 1 - 183 MTRIX 1: APPLIED TO CHAIN F RESIDUES 1 - 10, APPROXIMATELY GENERATES CHAIN C RESIDUES 1 - 10 MTRIX 2: APPLIED TO CHAIN D RESIDUES 184 - 275, APPROXIMATELY GENERATES CHAIN A RESIDUES 184 - 275 MTRIX 3: APPLIED TO CHAIN E RESIDUES 1 - 99, APPROXIMATELY GENERATES CHAIN B RESIDUES 1 - 99

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Components

#1: Protein CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) (ALPHA CHAIN)


Mass: 31854.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BETA-2-MICROGLOBULIN / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA 2-MICROGLOBULIN


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BETA-2-MICROGLOBULIN / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide DECAMERIC PEPTIDE FROM CALRETICULIN


Mass: 1055.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P27797
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 6.5 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
225 mM2-(N-morpholino)ethanesulfonic acid1dropor 100mM imidazole
315 %(w/v)PEG60001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 2.07 Å / Lowest resolution: 2.16 Å / Rmerge(I) obs: 0.205

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.236 -
obs0.236 42669
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6308 0 0 0 6308
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg2.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor Rfree: 0.299
Solvent computation
*PLUS
Displacement parameters
*PLUS

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