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- PDB-2x4n: Crystal structure of MHC CLass I HLA-A2.1 bound to residual fragm... -

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Basic information

Entry
Database: PDB / ID: 2x4n
TitleCrystal structure of MHC CLass I HLA-A2.1 bound to residual fragments of a photocleavable peptide that is cleaved upon UV-light treatment
Components
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
  • HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE
KeywordsIMMUNE SYSTEM / GLYCOPROTEIN / TRANSMEMBRANE / DISEASE MUTATION / IMMUNOGLOBULIN DOMAIN / PHOSPHOPROTEIN / IMMUNE RESPONSE / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / GLYCATION / AMYLOIDOSIS
Function / homology
Function and homology information


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 / Golgi medial cisterna / CD8-positive, alpha-beta T cell activation / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent ...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 / Golgi medial cisterna / CD8-positive, alpha-beta T cell activation / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / Interferon gamma signaling / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / T cell receptor signaling pathway / late endosome membrane / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / immune response / defense response to Gram-positive bacterium / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding
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 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
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)
INFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsCelie, P.H.N. / Toebes, M. / Rodenko, B. / Ovaa, H. / Perrakis, A. / Schumacher, T.N.M.
CitationJournal: 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 2.0Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
E: BETA-2-MICROGLOBULIN
F: HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,07118
Polymers89,7606
Non-polymers1,31112
Water4,234235
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1566
Polymers44,8803
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-22.4 kcal/mol
Surface area18780 Å2
MethodPISA
2
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
E: BETA-2-MICROGLOBULIN
F: HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,91512
Polymers44,8803
Non-polymers1,0359
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-16.1 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.509, 86.523, 80.003
Angle α, β, γ (deg.)90.00, 90.34, 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 ALPHA CHAIN / MHC CLASS I ANTIGEN A*2


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


Mass: 11879.356 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 HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE


Mass: 1146.314 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: MODIFIED AT P5 (RESIDUE62) AND P8 (RESIDUE 65).(2-NITRO)PHENYL-PROPIONIC ACID AT P5 AND 3-AMINO-3-(2- NITRO)PHENYL-PROPIONIC ACID AT P8. CRYSTAL WAS EXPOSED TO UV LIGHT TO CLEAVE PEPTIDE AT ...Details: MODIFIED AT P5 (RESIDUE62) AND P8 (RESIDUE 65).(2-NITRO)PHENYL-PROPIONIC ACID AT P5 AND 3-AMINO-3-(2- NITRO)PHENYL-PROPIONIC ACID AT P8. CRYSTAL WAS EXPOSED TO UV LIGHT TO CLEAVE PEPTIDE AT PRV AND PRQ RESIDUES, RESULTING IN REMOVAL OF RESIDUES 62-64 FROM THE STRUCTURE.
Source: (synth.) INFLUENZA A VIRUS

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Non-polymers , 3 types, 247 molecules

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


Mass: 92.094 Da / Num. of mol.: 10 / 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.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsINITIALIZING METHIONINE (B0 AND E0) ADDED TO SEQUENCE. ORIGINAL SEQUENCE IS GILGFVFTL. G AT P1 IS ...INITIALIZING METHIONINE (B0 AND E0) ADDED TO SEQUENCE. ORIGINAL SEQUENCE IS GILGFVFTL. G AT P1 IS REPLACED BY K

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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: 49 % / Description: NONE
Crystal growpH: 6.5
Details: 100 MM MES PH 5.5, 20% PEG 1500. CRYSTALS WERE FROZEN IN 100 MM MES, 30% PEG 1500, 10% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 6, 2007 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.34→80.06 Å / Num. obs: 33198 / % possible obs: 92.4 % / Observed criterion σ(I): -3.7 / Redundancy: 1.88 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.02
Reflection shellResolution: 2.34→2.47 Å / Redundancy: 1.82 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.47 / % possible all: 92.7

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Processing

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

1eey


Resolution: 2.34→19.806 Å / SU ML: 0.42 / σ(F): 1.37 / Phase error: 28.79 / Stereochemistry target values: ML
Details: THIS ENTRY IS RELATED TO PDB ENTRY 2X4M WHERE THE PHOTOCLEAVABLE MOIETIES PRQ AND PRV ARE DESCRBED (PRQ WA FIRST DESCRIBED IN 2VE6)
RfactorNum. reflection% reflection
Rfree0.2739 2013 6.1 %
Rwork0.1957 --
obs0.2004 33140 92.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.527 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso mean: 50.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.6263 Å20 Å21.1234 Å2
2--5.0402 Å20 Å2
3----3.4139 Å2
Refinement stepCycle: LAST / Resolution: 2.34→19.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6243 0 84 235 6562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086548
X-RAY DIFFRACTIONf_angle_d1.3178860
X-RAY DIFFRACTIONf_dihedral_angle_d19.6582381
X-RAY DIFFRACTIONf_chiral_restr0.129896
X-RAY DIFFRACTIONf_plane_restr0.0041149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3401-2.39850.33491560.28932168X-RAY DIFFRACTION92
2.3985-2.46330.36761450.27872230X-RAY DIFFRACTION93
2.4633-2.53560.39441310.27762268X-RAY DIFFRACTION94
2.5356-2.61730.32121550.25942251X-RAY DIFFRACTION93
2.6173-2.71060.32321510.22872238X-RAY DIFFRACTION94
2.7106-2.81880.28771460.20842276X-RAY DIFFRACTION94
2.8188-2.94670.30221490.20662225X-RAY DIFFRACTION93
2.9467-3.10160.29851580.20962262X-RAY DIFFRACTION94
3.1016-3.2950.28551270.20052269X-RAY DIFFRACTION93
3.295-3.54810.27361510.18622209X-RAY DIFFRACTION92
3.5481-3.90270.24611280.16092250X-RAY DIFFRACTION92
3.9027-4.46180.22441470.14822198X-RAY DIFFRACTION91
4.4618-5.60030.21641360.14462140X-RAY DIFFRACTION88
5.6003-19.80670.23531330.1882143X-RAY DIFFRACTION86
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)
13.748-0.1587-0.5141.4367-0.59022.6533-0.0504-0.0954-0.06740.04210.0538-0.3782-0.01720.227-0.00020.1762-0.0121-0.03530.2484-0.06880.236226.037-3.613-4.6171
21.77150.43050.07712.09020.40691.63080.13770.2812-0.0995-0.2673-0.03960.39430.1876-0.68660.00010.2166-0.0895-0.02340.4229-0.09790.2588-5.4704-8.1168-20.4181
32.64140.81290.21041.1932-0.18141.23620.03890.1820.376-0.0568-0.00160.1165-0.2715-0.1089-0.00010.2594-0.00950.03270.2554-0.01980.1674.988110.4482-13.3116
42.68310.10031.11431.4298-0.19313.32490.17120.3760.0757-0.00890.0482-0.3761-0.14290.3329-0.00020.1694-0.02560.05660.1905-0.08930.233757.18553.823820.5947
52.6485-0.84-0.08081.55651.11161.84140.1282-0.29330.22040.1445-0.06480.1612-0.0154-0.2370.00210.1871-0.0710.04780.1937-0.08750.153525.84287.738236.317
62.7239-0.8264-0.56832.72150.18761.42180.0944-0.0165-0.71030.1880.03890.03370.2344-0.14390.00120.256-0.0352-0.04660.0698-0.04140.224735.9844-10.587128.507
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 DIFFRACTION3(CHAIN B AND RESID 0:)
4X-RAY DIFFRACTION4(CHAIN D AND RESID :180)
5X-RAY DIFFRACTION5(CHAIN D AND RESID 181:275)
6X-RAY DIFFRACTION6(CHAIN E AND RESID 0:)

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