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- PDB-4uq2: Crystal structure of HLA-A1101 in complex with an azobenzene- con... -

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Basic information

Entry
Database: PDB / ID: 4uq2
TitleCrystal structure of HLA-A1101 in complex with an azobenzene- containing peptide
Components
  • AZOBENZENE-CONTAINING PEPTIDE
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-11 ALPHA CHAIN
KeywordsIMMUNE SYSTEM / AZOBENZENE / HLA-A / SYNTHETIC PEPTIDE
Function / homology
Function and homology information


T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / CD8 receptor binding ...T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum
Similarity search - Function
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 ...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 / Immunoglobulins / Immunoglobulin-like fold / 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 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsThong, S.Y. / Yap, J.W. / Lim, P.Y. / Verhelst, S.H. / Lescar, J. / Meijers, R. / Grotenbreg, G.M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Bioorthogonal Cleavage and Exchange of Major Histocompatibility Complex Ligands by Employing Azobenzene-Containing Peptides.
Authors: Choo, J.A.L. / Thong, S.Y. / Yap, J. / Van Esch, W.J.E. / Raida, M. / Meijers, R. / Lescar, J. / Verhelst, S.H.L. / Grotenbreg, G.M.
History
DepositionJun 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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-11 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-11 ALPHA CHAIN
D: BETA-2-MICROGLOBULIN
E: AZOBENZENE-CONTAINING PEPTIDE
G: AZOBENZENE-CONTAINING PEPTIDE


Theoretical massNumber of molelcules
Total (without water)89,1876
Polymers89,1876
Non-polymers00
Water4,486249
1
C: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-11 ALPHA CHAIN
D: BETA-2-MICROGLOBULIN
E: AZOBENZENE-CONTAINING PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,5933
Polymers44,5933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-15 kcal/mol
Surface area19930 Å2
MethodPISA
2
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-11 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
G: AZOBENZENE-CONTAINING PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,5933
Polymers44,5933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-13.6 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.140, 71.460, 75.430
Angle α, β, γ (deg.)106.74, 96.74, 105.28
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUAA1 - 2751 - 275
21GLYGLYGLUGLUCC1 - 2751 - 275
12ILEILEMETMETBB1 - 991 - 99
22ILEILEMETMETDD1 - 991 - 99

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.87768, -0.47891, 0.01799), (-0.47913, 0.87768, -0.01078), (-0.01063, -0.01808, -0.99978)42.17059, 11.64744, 91.41589
2given(-0.86852, -0.49556, 0.00905), (-0.49565, 0.86834, -0.01779), (0.00095, -0.01994, -0.9998)41.62122, 11.75023, 91.13715
3given(1), (1), (1)
4given(-0.878923, -0.476829, -0.011376), (-0.476571, 0.878916, -0.019656), (0.019371, -0.011855, -0.999742)43.71459, 11.66632, 90.67875
5given(-0.870139, -0.492806, -0.001055), (-0.492667, 0.869941, -0.021977), (0.011748, -0.018603, -0.999758)42.17533, 12.36281, 90.82258

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-11 ALPHA CHAIN / MHC CLASS I ANTIGEN A*11 / HLA CLASS I HISTOCOMPATIBILITY AN ANTIGEN / A-11 / ALPHA CHAIN


Mass: 31855.051 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13746, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide AZOBENZENE-CONTAINING PEPTIDE


Mass: 990.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.42 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM SULFATE, 15% W/V PEG4000, 0.1M TRI-SODIUM CITRATE PH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV++ / Detector: IMAGE PLATE / Date: Sep 19, 2012 / Details: MIRROR
RadiationMonochromator: CU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→29.93 Å / Num. obs: 35112 / % possible obs: 94.7 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.4
Reflection shellResolution: 2.43→2.56 Å / Redundancy: 4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6.8 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HN7

2hn7


Resolution: 2.43→29.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.72 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 1740 5 %RANDOM
Rwork0.18653 ---
obs0.18976 33278 94.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.344 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.43→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 0 0 249 6537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196707
X-RAY DIFFRACTIONr_bond_other_d0.0010.026015
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.9769111
X-RAY DIFFRACTIONr_angle_other_deg0.843.00213828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9395764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31523.408358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.585151057
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6471562
X-RAY DIFFRACTIONr_chiral_restr0.0980.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021676
X-RAY DIFFRACTIONr_nbd_refined0.2370.21500
X-RAY DIFFRACTIONr_nbd_other0.230.25545
X-RAY DIFFRACTIONr_nbtor_refined0.1930.23056
X-RAY DIFFRACTIONr_nbtor_other0.1110.23622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2209
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0440.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2040.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Dom-ID: 2 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C4237medium positional0.370.5
2D1587medium positional0.390.5
1C4237medium thermal3.262
2D1587medium thermal3.32
LS refinement shellResolution: 2.431→2.494 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 119 -
Rwork0.267 2260 -
obs--87.98 %

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