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- PDB-2x70: Crystal structure of MHC CLass I HLA-A2.1 bound to a photocleavab... -

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Basic information

Entry
Database: PDB / ID: 2x70
TitleCrystal structure of MHC CLass I HLA-A2.1 bound to a photocleavable peptide
Components
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
  • HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE
KeywordsIMMUNE SYSTEM / AMYLOID / IMMUNOGLOBULIN DOMAIN / IMMUNE RESPONSE / HOST-VIRUS INTERACTION
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 / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / 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 / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / 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 / 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 / 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 / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma 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 / extracellular exosome
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 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 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 3.0Nov 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_main_chain_plane / pdbx_validate_peptide_omega / 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 3.1Dec 20, 2023Group: 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-2.1
B: BETA-2-MICROGLOBULIN
C: HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
E: BETA-2-MICROGLOBULIN
F: HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,00115
Polymers89,7606
Non-polymers1,2419
Water13,890771
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
B: BETA-2-MICROGLOBULIN
C: HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2596
Polymers44,8803
Non-polymers3793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-19.7 kcal/mol
Surface area18660 Å2
MethodPISA
2
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
E: BETA-2-MICROGLOBULIN
F: HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7429
Polymers44,8803
Non-polymers8626
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-8.6 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.979, 81.801, 79.706
Angle α, β, γ (deg.)90.00, 90.77, 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: 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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 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 / Fragment: FRAGMENT RESIDUES 58-66 / 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
Source: (synth.) INFLUENZA A VIRUS

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Non-polymers , 3 types, 780 molecules

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


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


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 771 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsINITIALIZING METHIONINE (B0 AND D0) 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 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: VAPOUR DIFFUSION HANGING DROP AT 293K: 2 MICROLITER OF 5 MG/ML PROTEIN IN 0.1 M MES PH 6.0 WAS MIXED WITH 2 MICROLITER OF 0.1 M MES PH 6.5, 20-22% PEG 1500. SEEDING WAS USED TO GET BIGGER CRYSTALS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC QUANTUM 315r / 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
Reflection twinOperator: -h,-k,l / Fraction: 0.043
ReflectionResolution: 2→81.92 Å / Num. obs: 53033 / % possible obs: 97.2 % / Observed criterion σ(I): -3.7 / Redundancy: 2.3 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.9 / % possible all: 97.2

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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→19.925 Å / σ(F): 1.38 / Phase error: 24.29 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2249 2753 5.3 %
Rwork0.1589 --
obs0.1623 52222 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.018 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 32.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.2884 Å20 Å20.6302 Å2
2--2.7541 Å20 Å2
3----2.1396 Å2
Refinement stepCycle: LAST / Resolution: 2→19.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6332 0 78 771 7181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046770
X-RAY DIFFRACTIONf_angle_d1.2459186
X-RAY DIFFRACTIONf_dihedral_angle_d17.7812485
X-RAY DIFFRACTIONf_chiral_restr0.145924
X-RAY DIFFRACTIONf_plane_restr0.0031191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03450.26761400.21712483X-RAY DIFFRACTION98
2.0345-2.07140.24151240.2142533X-RAY DIFFRACTION98
2.0714-2.11120.24541330.20222471X-RAY DIFFRACTION98
2.1112-2.15430.28921540.2022508X-RAY DIFFRACTION98
2.1543-2.2010.24131370.19792467X-RAY DIFFRACTION98
2.201-2.25220.24451140.2012503X-RAY DIFFRACTION98
2.2522-2.30840.26021320.19142506X-RAY DIFFRACTION98
2.3084-2.37070.22741330.19172484X-RAY DIFFRACTION98
2.3707-2.44040.28321300.1932516X-RAY DIFFRACTION98
2.4404-2.5190.2621180.18682479X-RAY DIFFRACTION98
2.519-2.60890.28051460.18472488X-RAY DIFFRACTION98
2.6089-2.71310.24341310.18292502X-RAY DIFFRACTION98
2.7131-2.83620.28251230.18062487X-RAY DIFFRACTION98
2.8362-2.98530.23941300.17252471X-RAY DIFFRACTION98
2.9853-3.17160.23691590.1582448X-RAY DIFFRACTION98
3.1716-3.41540.23591200.1462468X-RAY DIFFRACTION98
3.4154-3.7570.20621380.13042424X-RAY DIFFRACTION98
3.757-4.29590.17371500.11042428X-RAY DIFFRACTION98
4.2959-5.39450.15321140.10742445X-RAY DIFFRACTION98
5.3945-19.92570.2121360.15882449X-RAY DIFFRACTION98
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)
11.13260.5334-0.0191.122-0.51632.2773-0.02030.0677-0.12160.05210.0376-0.3075-0.10480.0281-0.01960.0861-0.0013-0.00720.0387-0.02120.120127.0026-3.5404-3.3134
20.8669-0.01980.41940.54290.12791.04190.1882-0.0734-0.0804-0.1066-0.08730.2420.214-0.2808-0.06740.2026-0.0136-0.06330.1995-0.010.1792-4.1001-7.6257-19.8064
30.74560.0471-0.04520.3384-0.3451.37120.10650.05740.1256-0.02260.02160.0501-0.2816-0.1761-0.12740.21080.01770.0570.16130.02190.15656.271610.5079-12.5974
41.0540.00220.69190.5393-0.41151.90450.0460.03310.0159-0.01410.0399-0.1947-0.06370.1314-0.08950.1184-0.01340.01760.1184-0.02920.183457.63823.759521.2618
50.3641-0.2041-0.41530.77220.61551.72650.10890.02980.03870.0225-0.05080.0193-0.0459-0.2921-0.04120.1043-0.00460.01280.1604-0.01190.121626.44817.442636.9327
60.59420.17230.10311.109-0.20210.89250.0991-0.1447-0.10980.00450.0008-0.00780.043-0.0208-0.10170.1079-0.0082-0.02880.11750.01930.140236.552-10.600928.6928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:180)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 181:275)
3X-RAY DIFFRACTION3CHAIN B
4X-RAY DIFFRACTION4(CHAIN D AND RESID 0:179)
5X-RAY DIFFRACTION5(CHAIN D AND RESID 180:274)
6X-RAY DIFFRACTION6CHAIN E

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