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- PDB-2x4t: Crystal structure of MHC CLass I HLA-A2.1 bound to a Peiodate- cl... -

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Basic information

Entry
Database: PDB / ID: 2x4t
TitleCrystal structure of MHC CLass I HLA-A2.1 bound to a Peiodate- cleavable peptide
Components
  • 65 KDA PHOSPHOPROTEIN
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
KeywordsIMMUNE SYSTEM / MHC CLASS I / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / GLYCATION / AMYLOIDOSIS / AMYLOID / PHOTOCLEAVABLE PEPTIDE / IMMUNE RESPONSE
Function / homology
Function and homology information


viral tegument / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...viral tegument / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / 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 / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / antibacterial humoral response / MHC class II protein complex binding / E3 ubiquitin ligases ubiquitinate target proteins / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / signaling receptor binding / focal adhesion / virus-mediated perturbation of host defense response / Neutrophil degranulation / endoplasmic reticulum membrane / host cell nucleus
Similarity search - Function
Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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 ...Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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 / 65 kDa phosphoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN HERPESVIRUS 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRodenko, B. / Toebes, M. / Celie, P.H.N. / Perrakis, A. / Schumacher, T.N.M. / Ovaa, H.
Citation
Journal: J.Am.Chem.Soc. / Year: 2009
Title: Class I Major Histocompatibility Complexes Loaded by a Periodate Trigger.
Authors: Rodenko, B. / Toebes, M. / Celie, P.H.N. / Perrakis, A. / Schumacher, T.N.M. / Ovaa, H.
#1: Journal: J.Am.Chem.Soc. / Year: 2009
Title: Uv-Induced Ligand Exchange in Mhc Class I Protein Crystals.
Authors: Celie, P.H.N. / Toebes, M. / Rodenko, B. / Ovaa, H. / Perrakis, A. / Schumacher, T.N.M.
History
DepositionFeb 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_site
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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-2.1
B: BETA-2-MICROGLOBULIN
C: 65 KDA PHOSPHOPROTEIN
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
E: BETA-2-MICROGLOBULIN
F: 65 KDA PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,24811
Polymers89,5816
Non-polymers6675
Water4,125229
1
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
E: BETA-2-MICROGLOBULIN
F: 65 KDA PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1706
Polymers44,7903
Non-polymers3793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-19 kcal/mol
Surface area18530 Å2
MethodPISA
2
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
B: BETA-2-MICROGLOBULIN
C: 65 KDA PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0785
Polymers44,7903
Non-polymers2872
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-17.5 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.391, 85.516, 80.394
Angle α, β, γ (deg.)90.00, 90.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1 / HLA CLASS I HISTOCOMPATIBILITY ANTIGEN / A-2 ALPHA CHAIN


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN / BETA-2-MICROGLOBULIN FORM PI 5.3


Mass: 11973.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XLI BLUE / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide 65 KDA PHOSPHOPROTEIN / LOWER MATRIX PROTEIN PP65 / 64 KDA MATRIX PHOSPHOPROTEIN


Mass: 963.149 Da / Num. of mol.: 2 / Fragment: EPITOPE, RESIDUES 495-503 / Source method: obtained synthetically / Source: (synth.) HUMAN HERPESVIRUS 5 / References: UniProt: P06725

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Non-polymers , 3 types, 234 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsINITIALIZING METHIONINE (B0 AND E0) ADDED TO SEQUENCE. PRW REPLACES PRO IN CHAINS C AND F.

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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: 2.4 Å3/Da / Density % sol: 48.77 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES PH 6.5, 22% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9779
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2007 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.107
ReflectionResolution: 2.2→37.5 Å / Num. obs: 37003 / % possible obs: 98.1 % / Observed criterion σ(I): -3.7 / Redundancy: 3.1 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.4 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EEY

1eey


Resolution: 2.3→19.83 Å / σ(F): 1.38 / Phase error: 35.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2357 1855 5 %
Rwork0.1839 --
obs0.1858 36785 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.477 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 66.92 Å2
Baniso -1Baniso -2Baniso -3
1--2.906 Å20 Å2-0.1416 Å2
2--5.5356 Å20 Å2
3----2.6296 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 42 229 6571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086550
X-RAY DIFFRACTIONf_angle_d1.3348866
X-RAY DIFFRACTIONf_dihedral_angle_d20.5572360
X-RAY DIFFRACTIONf_chiral_restr0.125907
X-RAY DIFFRACTIONf_plane_restr0.0041149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3004-2.36250.32321230.30762685X-RAY DIFFRACTION94
2.3625-2.43190.35911270.28782658X-RAY DIFFRACTION93
2.4319-2.51020.29461570.27242661X-RAY DIFFRACTION92
2.5102-2.59970.3331400.27552677X-RAY DIFFRACTION93
2.5997-2.70350.32691410.25492629X-RAY DIFFRACTION93
2.7035-2.82620.35451360.24872688X-RAY DIFFRACTION93
2.8262-2.97470.28561370.23542669X-RAY DIFFRACTION92
2.9747-3.16020.28661520.21242660X-RAY DIFFRACTION92
3.1602-3.40290.29771440.19982689X-RAY DIFFRACTION94
3.4029-3.7430.21831330.18522691X-RAY DIFFRACTION94
3.743-4.27910.21721390.15272732X-RAY DIFFRACTION94
4.2791-5.37050.15551330.13142758X-RAY DIFFRACTION94
5.3705-18.87590.21151680.1442731X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1769-0.5305-0.63550.5948-0.05611.14740.1138-0.64070.02640.1970.14990.6563-0.0734-0.2022-0.00030.42790.01720.05720.46250.17730.55575.03753.005819.5794
20.84710.23040.44340.6505-0.25790.47060.16490.21210.34020.0507-0.2455-0.1263-0.24420.2430.00030.35010.03470.03560.22070.09110.271236.40636.83893.7278
30.34890.3505-0.17070.56060.24361.99940.1286-0.2877-0.6814-0.05650.08830.06690.1180.380.61590.36030.034-0.0556-0.15130.17890.45326.1994-11.373811.4556
41.3433-0.61980.68590.6123-0.00990.9661-0.0496-0.3577-0.13030.12520.0447-0.3854-0.07120.1727-00.3602-0.02640.03960.498-0.09260.390925.758738.498335.6223
50.50310.0336-0.35180.46010.06050.31080.06010.2926-0.23-0.1099-0.11930.52560.164-0.401-0.00010.362-0.07-0.02150.5486-0.14590.4978-5.627334.077219.7843
60.47360.09780.36870.6234-0.2090.42710.04920.0080.18040.0304-0.00880.0253-0.2522-0.1462-0.00010.413-0.0410.08670.4019-0.08690.32465.212152.532826.4701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID :180)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 181:275)
3X-RAY DIFFRACTION3CHAIN B
4X-RAY DIFFRACTION4(CHAIN D AND RESID :180)
5X-RAY DIFFRACTION5(CHAIN D AND RESID 181:275)
6X-RAY DIFFRACTION6CHAIN E

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