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- PDB-2x4q: Crystal structure of MHC CLass I HLA-A2.1 bound to a photocleavab... -

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Basic information

Entry
Database: PDB / ID: 2x4q
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 / PHOTOCLEAVABLE PEPTIDE
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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / antibacterial humoral response / positive regulation of cellular senescence / 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 / Golgi membrane / signaling receptor binding / 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: 1.9 Å
AuthorsCelie, P.H.N. / Toebes, M. / Rodenko, B. / Ovaa, H. / Perrakis, A. / Schumacher, T.N.M.
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 2.0Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_proc ...entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
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)90,72310
Polymers90,0456
Non-polymers6784
Water5,621312
1
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)45,4135
Polymers45,0233
Non-polymers3902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-12.1 kcal/mol
Surface area18650 Å2
MethodPISA
2
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)45,3105
Polymers45,0233
Non-polymers2872
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-19.1 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.030, 86.486, 80.466
Angle α, β, γ (deg.)90.00, 90.21, 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 HLA-A2.1-RESTRICTED INFLUENZA A MATRIX EPITOPE


Mass: 1195.225 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, 316 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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 SME

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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: 2.38 Å3/Da / Density % sol: 44.9 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M MES PH 6.5, 20% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9779
DetectorType: ADSC CCD / Detector: CCD / 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: 0.337
ReflectionResolution: 1.9→50 Å / Num. obs: 64908 / % possible obs: 97.2 % / Observed criterion σ(I): -3.7 / Redundancy: 3.4 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.1 / % possible all: 95.2

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Processing

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

1eey


Resolution: 1.9→32.434 Å / σ(F): 1.38 / Phase error: 38.52 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2059 3415 5.3 %
Rwork0.1673 --
obs0.1693 64885 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.283 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 41.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.0298 Å2-0 Å20.515 Å2
2---0.8337 Å2-0 Å2
3----1.3371 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 42 312 6684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066605
X-RAY DIFFRACTIONf_angle_d1.3378933
X-RAY DIFFRACTIONf_dihedral_angle_d18.5082364
X-RAY DIFFRACTIONf_chiral_restr0.136899
X-RAY DIFFRACTIONf_plane_restr0.0041157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93280.26111510.24042978X-RAY DIFFRACTION98
1.9328-1.96790.26261740.23572974X-RAY DIFFRACTION98
1.9679-2.00570.2631470.23123033X-RAY DIFFRACTION98
2.0057-2.04670.25881700.22433003X-RAY DIFFRACTION98
2.0467-2.09120.25271600.2163029X-RAY DIFFRACTION98
2.0912-2.13980.24741510.21553064X-RAY DIFFRACTION98
2.1398-2.19330.21321780.21543045X-RAY DIFFRACTION98
2.1933-2.25260.25941630.20453071X-RAY DIFFRACTION98
2.2526-2.31890.23351790.20623085X-RAY DIFFRACTION98
2.3189-2.39370.24411500.2043079X-RAY DIFFRACTION98
2.3937-2.47920.24631600.20043098X-RAY DIFFRACTION98
2.4792-2.57840.27261510.19593054X-RAY DIFFRACTION98
2.5784-2.69570.24961780.18873089X-RAY DIFFRACTION98
2.6957-2.83780.24531550.18713117X-RAY DIFFRACTION98
2.8378-3.01550.26171590.18583113X-RAY DIFFRACTION98
3.0155-3.24810.21441820.16873112X-RAY DIFFRACTION98
3.2481-3.57460.18441710.16153125X-RAY DIFFRACTION98
3.5746-4.0910.15981930.13283137X-RAY DIFFRACTION98
4.091-5.15090.13421590.10963161X-RAY DIFFRACTION98
5.1509-32.43910.20171690.14683218X-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)
12.49410.0146-0.01321.0291-0.61641.2116-0.0124-0.1562-0.16950.08750.0002-0.2676-0.10590.12510.02280.1722-0.0294-0.01590.1704-0.06290.194725.5706-2.713135.1883
20.68170.1833-0.18530.8410.00450.82270.14980.1625-0.1399-0.0166-0.01660.41160.0656-0.0587-0.04590.1792-0.0251-0.05390.249-0.08680.3135-5.9971-6.950419.2538
31.06850.17120.08111.1982-0.50280.91220.02910.22430.22990.0168-0.00720.1413-0.0931-0.0938-0.02390.1556-0.01960.03990.1711-0.04090.17244.642111.322826.4965
41.4345-0.43020.36650.54810.33052.13320.0005-0.2538-0.09210.08920.04790.27960.0015-0.1212-0.08020.20610.02030.02490.18560.06080.20465.2894-38.599819.7621
51.6506-0.0571-0.16911.1902-1.07790.57060.1020.0950.1183-0.0569-0.1613-0.0641-0.23560.15770.06860.1656-0.004-0.00150.1920.02820.091136.4277-34.65874.0039
61.6812-0.28280.3351.1107-0.09190.82060.10460.0381-0.6523-0.14140.02780.12460.06490.0215-0.13190.14670.0105-0.04540.07020.03420.246526.0418-52.942911.7041
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 C AND RESID :180)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 181:275)
6X-RAY DIFFRACTION6CHAIN D

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