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- PDB-2x4p: Crystal structure of MHC CLass I HLA-A2.1 bound to a photocleavab... -

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Basic information

Entry
Database: PDB / ID: 2x4p
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 / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / MATRIX (M1)
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 / 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 / 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 receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / 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 / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / 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
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: 2.3 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)91,38617
Polymers89,8586
Non-polymers1,52911
Water7,819434
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)45,5037
Polymers44,9293
Non-polymers5754
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-10.1 kcal/mol
Surface area18370 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)45,88310
Polymers44,9293
Non-polymers9547
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-9.1 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.201, 86.496, 80.783
Angle α, β, γ (deg.)90.00, 90.04, 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
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, 445 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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 ...INITIALIZING METHIONINE (B0 AND D0) ADDED TO SEQUENCE ORIGINAL SEQUENCE IS GILGFVFTL. G AT P1 IS REPLACED BY MSE

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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: 45.3 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES PH 6.5, 20% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9786
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2007 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.329
ReflectionResolution: 2.3→50 Å / Num. obs: 37987 / % possible obs: 99.6 % / Observed criterion σ(I): -3.7 / Redundancy: 3.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.7 / % possible all: 99.4

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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: 2.3→19.822 Å / σ(F): 1.45 / Phase error: 38.98 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2222 1930 5.1 %
Rwork0.158 --
obs0.1614 37907 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.797 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 44.86 Å2
Baniso -1Baniso -2Baniso -3
1--7.886 Å20 Å218.2459 Å2
2--7.3122 Å2-0 Å2
3----6.8285 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 96 434 6860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056676
X-RAY DIFFRACTIONf_angle_d1.369043
X-RAY DIFFRACTIONf_dihedral_angle_d17.6082419
X-RAY DIFFRACTIONf_chiral_restr0.16909
X-RAY DIFFRACTIONf_plane_restr0.0041168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.34180.277880.22061898X-RAY DIFFRACTION98
2.3418-2.38680.28961040.2221894X-RAY DIFFRACTION98
2.3868-2.43540.33831030.21441835X-RAY DIFFRACTION98
2.4354-2.48830.2991950.21031925X-RAY DIFFRACTION98
2.4883-2.54610.2756940.211877X-RAY DIFFRACTION98
2.5461-2.60960.3106990.21211895X-RAY DIFFRACTION98
2.6096-2.680.26451050.19761862X-RAY DIFFRACTION98
2.68-2.75870.235950.19831876X-RAY DIFFRACTION98
2.7587-2.84750.25851000.19651908X-RAY DIFFRACTION98
2.8475-2.94890.2627870.17971903X-RAY DIFFRACTION98
2.9489-3.06660.24431100.17451869X-RAY DIFFRACTION98
3.0666-3.20560.20761090.1641892X-RAY DIFFRACTION98
3.2056-3.37380.25781110.16031868X-RAY DIFFRACTION98
3.3738-3.5840.2029960.14841929X-RAY DIFFRACTION98
3.584-3.85890.17161110.13491864X-RAY DIFFRACTION98
3.8589-4.24380.18691090.12241920X-RAY DIFFRACTION98
4.2438-4.850.18351120.10991894X-RAY DIFFRACTION98
4.85-6.08110.2363870.12681932X-RAY DIFFRACTION98
6.0811-19.82280.18451060.15521945X-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)
10.20.05310.1173-0.07730.04950.1812-0.0298-0.0151-0.05290.0497-0.0099-0.0954-0.08730.0050.04550.2289-0.0211-0.1540.0087-0.03360.2437-5.3725-3.6582-4.9386
20.10210.2090.13050.29660.22210.1643-0.0202-0.01210.0349-0.0682-0.06150.1713-0.0742-0.03870.12440.1451-0.0255-0.15060.0924-0.13460.2311-36.7603-7.9462-20.8649
30.07390.04460.05020.02070.03290.0592-0.05610.01510.0449-0.0140.01980.0064-0.0495-0.00230.0710.1758-0.0348-0.09960.0662-0.05390.1681-26.369110.3926-13.7547
40.85750.89920.75910.94170.79770.6611-0.00020.1771-0.17950.08380.1964-0.35390.02060.1455-0.16240.1377-0.0205-0.09120.0359-0.13350.22125.70523.759220.6896
50.03460.04790.05230.05110.10530.1126-0.0122-0.03020.0351-0.0879-0.03610.0965-0.0554-0.02130.05790.2095-0.0116-0.13280.0374-0.06440.1433-5.34927.602236.3886
60.56160.36150.28290.18410.20960.15640.2920.0506-0.44040.202-0.0334-0.20330.18060.0152-0.24660.2670.0012-0.2453-0.0284-0.08050.37624.4807-10.661628.5719
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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