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- PDB-2jcc: AH3 recognition of mutant HLA-A2 W167A -

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Basic information

Entry
Database: PDB / ID: 2jcc
TitleAH3 recognition of mutant HLA-A2 W167A
Components
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
  • P1049
  • TCR ALPHA
  • TCR BETA
KeywordsIMMUNE SYSTEM / GLYCOPROTEIN / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / MHC I / MEMBRANE / RECEPTOR / POLYMORPHISM / PYRROLIDONE CARBOXYLIC ACID / IMUNOREGULATORY COMPLEX / CLASS I MHC-TCR CO-CRYSTAL / UBL CONJUGATION / IMMUNE RESPONSE / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / EMC complex / Co-inhibition by PD-1 / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / Generation of second messenger molecules / tail-anchored membrane protein insertion into ER membrane / Downstream TCR signaling / alpha-beta T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / EMC complex / Co-inhibition by PD-1 / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / Generation of second messenger molecules / tail-anchored membrane protein insertion into ER membrane / Downstream TCR signaling / alpha-beta T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / T cell lineage commitment / 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 / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / endoplasmic reticulum exit site / TAP binding / beta-2-microglobulin binding / detection of bacterium / 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 / response to bacterium / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / T cell mediated cytotoxicity / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / 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 / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / MHC class II protein complex binding / T cell differentiation in thymus / DAP12 signaling / T cell receptor signaling pathway / late endosome membrane / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / carbohydrate binding / protein refolding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane
Similarity search - Function
ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / Carbohydrate-binding-like fold / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 ...ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / Carbohydrate-binding-like fold / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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
T-cell receptor alpha chain constant / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Endoplasmic reticulum membrane protein complex subunit 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMiller, P. / Benhar, Y.P. / Biddison, W. / Collins, E.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Single Mhc Mutation Eliminates Enthalpy Associated with T Cell Receptor Binding.
Authors: Miller, P. / Pazy, Y. / Conti, B. / Riddle, D. / Appella, E. / Collins, E.J.
History
DepositionDec 21, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 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: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: P1049
E: TCR ALPHA
F: TCR BETA
H: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
I: BETA-2-MICROGLOBULIN
J: P1049
L: TCR ALPHA
M: TCR BETA


Theoretical massNumber of molelcules
Total (without water)186,43010
Polymers186,43010
Non-polymers00
Water97354
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: P1049
E: TCR ALPHA
F: TCR BETA


Theoretical massNumber of molelcules
Total (without water)93,2155
Polymers93,2155
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
I: BETA-2-MICROGLOBULIN
J: P1049
L: TCR ALPHA
M: TCR BETA


Theoretical massNumber of molelcules
Total (without water)93,2155
Polymers93,2155
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.280, 84.346, 122.470
Angle α, β, γ (deg.)90.00, 92.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules AHBIELFM

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN / MHC CLASS I ANTIGEN A*2 / HLA-A2


Mass: 31739.070 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 25-299 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 RIL / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN / B2M


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 RIL / References: UniProt: P61769
#4: Protein TCR ALPHA


Mass: 21656.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: C57/BL6 / Cell: T-LYMPHOCYTE / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 RIL / References: UniProt: P01849*PLUS
#5: Protein TCR BETA


Mass: 26890.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: C57/BL6 / Cell: T-LYMPHOCYTE / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 RIL

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Protein/peptide / Non-polymers , 2 types, 56 molecules CJ

#3: Protein/peptide P1049


Mass: 1049.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9NPA0*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TRP 191 TO ALA ENGINEERED RESIDUE IN CHAIN H, TRP 191 TO ALA
Has protein modificationY
Sequence detailsMUTATION W167A

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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: 2.64 Å3/Da / Density % sol: 40.7 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 152000 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.67 Å / Redundancy: 2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LP9

1lp9


Resolution: 2.5→122.17 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9 / SU B: 31.854 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R: 0.88 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS IN THE TCR VALPHA CHAINS 50-60 ARE GIVEN ZERO OCCUPANCIES. THERE ARE TWO COMPLEXES IN THE AU. A,B,C,E,F ARE DUPLICATED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS IN THE TCR VALPHA CHAINS 50-60 ARE GIVEN ZERO OCCUPANCIES. THERE ARE TWO COMPLEXES IN THE AU. A,B,C,E,F ARE DUPLICATED AS H,I,J,L,M RESPECTIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 3099 5 %RANDOM
Rwork0.242 ---
obs0.244 58670 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å21.17 Å2
2---0.17 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.5→122.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13126 0 0 54 13180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02113314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9318089
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08251598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45423.659656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.816152143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1241582
X-RAY DIFFRACTIONr_chiral_restr0.0850.21906
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210332
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.25049
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.28764
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2362
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.2106
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8551.58292
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.999212963
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.64235894
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3114.55126
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: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.4 164
Rwork0.337 2960

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