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- PDB-2x4s: Crystal structure of MHC CLass I HLA-A2.1 bound to a peptide repr... -

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Basic information

Entry
Database: PDB / ID: 2x4s
TitleCrystal structure of MHC CLass I HLA-A2.1 bound to a peptide representing the epitope of the H5N1 (Avian Flu) Nucleoprotein
Components
  • BETA-2-MICROGLOBULIN
  • H5N1 INFLUENZA A NUCLEOPROTEIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
KeywordsIMMUNE SYSTEM / PHOTOCLEAVABLE PEPTIDE / 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 / helical viral capsid / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...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 / helical viral capsid / 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 / viral penetration into host nucleus / 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 / host cell / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / 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 / ribonucleoprotein complex / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / symbiont entry into host cell / endoplasmic reticulum membrane / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 / : ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 / Nucleoprotein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
INFLUENZA VIRUS TYPE A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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

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Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
B: BETA-2-MICROGLOBULIN
C: H5N1 INFLUENZA A NUCLEOPROTEIN
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
E: BETA-2-MICROGLOBULIN
F: H5N1 INFLUENZA A NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1239
Polymers89,6416
Non-polymers4833
Water2,522140
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
B: BETA-2-MICROGLOBULIN
C: H5N1 INFLUENZA A NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1085
Polymers44,8203
Non-polymers2872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-18.4 kcal/mol
Surface area18610 Å2
MethodPISA
2
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2.1
E: BETA-2-MICROGLOBULIN
F: H5N1 INFLUENZA A NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0164
Polymers44,8203
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-13.3 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.377, 84.112, 80.035
Angle α, β, γ (deg.)90.00, 90.97, 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 / 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: 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 H5N1 INFLUENZA A NUCLEOPROTEIN


Mass: 993.090 Da / Num. of mol.: 2 / Fragment: EPITOPE 373-381 / Source method: obtained synthetically / Source: (synth.) INFLUENZA VIRUS TYPE A / References: UniProt: Q33CG5*PLUS

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Non-polymers , 3 types, 143 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / 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.: 140 / 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

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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: 2.3 Å3/Da / Density % sol: 47.5 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9792
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2008 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.048
ReflectionResolution: 2.55→50 Å / Num. obs: 27072 / % possible obs: 99.7 % / Observed criterion σ(I): -3.7 / Redundancy: 3 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.8
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8

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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: 2.55→19.926 Å / σ(F): 1.38 / Phase error: 27.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2475 1369 5.1 %
Rwork0.1782 --
obs0.1818 26956 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.651 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso mean: 69.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.5397 Å20 Å23.4215 Å2
2---1.6357 Å20 Å2
3---0.4371 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6304 0 30 140 6474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066505
X-RAY DIFFRACTIONf_angle_d1.1218809
X-RAY DIFFRACTIONf_dihedral_angle_d17.8052346
X-RAY DIFFRACTIONf_chiral_restr0.11898
X-RAY DIFFRACTIONf_plane_restr0.0041148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.61890.35631180.27961946X-RAY DIFFRACTION98
2.6189-2.69580.3057840.26071988X-RAY DIFFRACTION98
2.6958-2.78260.29841030.24641933X-RAY DIFFRACTION98
2.7826-2.88170.2976840.23241993X-RAY DIFFRACTION98
2.8817-2.99670.30421080.23051960X-RAY DIFFRACTION98
2.9967-3.13260.3097970.2031965X-RAY DIFFRACTION98
3.1326-3.29710.2805990.19831964X-RAY DIFFRACTION98
3.2971-3.50260.31130.17811949X-RAY DIFFRACTION98
3.5026-3.77140.231160.17591942X-RAY DIFFRACTION98
3.7714-4.14780.2266980.15771992X-RAY DIFFRACTION98
4.1478-4.74090.19961080.13451971X-RAY DIFFRACTION98
4.7409-5.94660.25521150.15991975X-RAY DIFFRACTION98
5.9466-19.92640.20721060.16892029X-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)
11.5742-0.27320.35811.0394-0.11532.34060.109-0.3404-0.12430.1110.09110.3401-0.1531-0.1739-0.20930.33080.0110.0390.37820.12960.41484.0673.011218.9339
22.16470.05360.03991.5371-0.65970.76720.1778-0.160.09030-0.0499-0.19370.04310.1014-0.06460.2726-0.02590.00280.31790.03950.288935.62976.73093.1961
31.9317-0.7945-1.46441.4349-0.30871.10970.0978-0.3248-0.9945-0.1286-0.10510.05870.20630.06550.00910.3478-0.0055-0.06810.33180.13110.627325.2454-11.480811.3657
41.5659-0.62710.581.46230.42281.95280.1345-0.41910.14250.3130.1011-0.39870.21110.3315-0.20920.3945-0.0112-0.1260.485-0.08840.414725.833537.99736.0708
51.1062-0.7106-0.53071.78640.50731.17590.28620.0799-0.2742-0.0804-0.27320.38830.0748-0.2683-0.00930.33560.0372-0.05360.4148-0.01370.4111-5.625332.803720.465
61.94470.2871-0.08240.47260.35191.22870.1389-0.07430.49750.0856-0.02470.0348-0.3590.0209-0.11650.4350.01670.08540.31590.00860.40914.873551.63626.8179
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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