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- PDB-2x4o: Crystal structure of MHC CLass I HLA-A2.1 bound to HIV-1 envelope... -

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Basic information

Entry
Database: PDB / ID: 2x4o
TitleCrystal structure of MHC CLass I HLA-A2.1 bound to HIV-1 envelope peptide env120-128
Components
  • BETA-2-MICROGLOBULIN
  • ENVELOPE GLYCOPROTEIN GP160
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
KeywordsIMMUNE SYSTEM / GLYCOPROTEIN / TRANSMEMBRANE / PHOSPHOPROTEIN / IMMUNE RESPONSE / SECRETED / GLYCATION / AMYLOIDOSIS / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / AMYLOID / MEMBRANE / PHOTOCLEAVABLE PEPTIDE / PYRROLIDONE CARBOXYLIC ACID / ENVELOPE PROTEIN / DISEASE MUTATION
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 / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Dectin-2 family / 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 / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Dectin-2 family / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / positive regulation of ferrous iron binding / positive regulation of transferrin 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 / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / antibacterial humoral response / MHC class II protein complex binding / E3 ubiquitin ligases ubiquitinate target proteins / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / clathrin-dependent endocytosis of virus by host cell / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / viral protein processing / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / innate immune response / signaling receptor binding
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / Envelope glycoprotein gp160 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN IMMUNODEFICIENCY VIRUS 1
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.
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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: ENVELOPE GLYCOPROTEIN GP160
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
E: BETA-2-MICROGLOBULIN
F: ENVELOPE GLYCOPROTEIN GP160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,77716
Polymers89,4446
Non-polymers1,33410
Water7,512417
1
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
E: BETA-2-MICROGLOBULIN
F: ENVELOPE GLYCOPROTEIN GP160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,76811
Polymers44,7223
Non-polymers1,0468
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-16.2 kcal/mol
Surface area18510 Å2
MethodPISA
2
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: ENVELOPE GLYCOPROTEIN GP160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0095
Polymers44,7223
Non-polymers2872
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-17.1 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.988, 81.904, 79.748
Angle α, β, γ (deg.)90.00, 90.87, 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 ENVELOPE GLYCOPROTEIN GP160 / ENV POLYPROTEIN


Mass: 988.264 Da / Num. of mol.: 2 / Fragment: ENVELOPE PROTEIN, RESIDUES 120-128 / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS 1 / References: UniProt: P04583

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Non-polymers , 3 types, 427 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.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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 Å3/Da / Density % sol: 41.3 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97932
DetectorType: ADSC CCD / 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: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.3→81.92 Å / Num. obs: 35564 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 3.6 % / Biso Wilson estimate: 31.89 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.24 / % possible all: 99.9

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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→48.58 Å / SU ML: 0.34 / σ(F): 1.37 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 1996 5.6 %
Rwork0.1747 --
obs0.1784 35523 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.489 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 36.55 Å2
Baniso -1Baniso -2Baniso -3
1--1.2924 Å20 Å20.0073 Å2
2--4.2771 Å20 Å2
3----2.9847 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6304 0 84 417 6805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086684
X-RAY DIFFRACTIONf_angle_d1.4269061
X-RAY DIFFRACTIONf_dihedral_angle_d19.3322449
X-RAY DIFFRACTIONf_chiral_restr0.153918
X-RAY DIFFRACTIONf_plane_restr0.0041178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.35760.27371440.19122399X-RAY DIFFRACTION100
2.3576-2.42130.25221390.18862383X-RAY DIFFRACTION100
2.4213-2.49260.27221390.18212413X-RAY DIFFRACTION100
2.4926-2.5730.27271490.1942367X-RAY DIFFRACTION100
2.573-2.6650.29751480.19782369X-RAY DIFFRACTION100
2.665-2.77170.31961270.19872365X-RAY DIFFRACTION100
2.7717-2.89780.28161460.20452389X-RAY DIFFRACTION100
2.8978-3.05060.26551400.19512422X-RAY DIFFRACTION100
3.0506-3.24170.28571400.18452391X-RAY DIFFRACTION100
3.2417-3.49190.22961410.17562391X-RAY DIFFRACTION100
3.4919-3.84320.21721530.16122384X-RAY DIFFRACTION100
3.8432-4.3990.19581390.14242416X-RAY DIFFRACTION100
4.399-5.5410.18121450.12812402X-RAY DIFFRACTION100
5.541-48.59040.1941460.16882436X-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)
11.98890.27170.93321.44260.2672.73110.0724-0.05830.04890.00410.03820.3426-0.1256-0.22180.00010.09440.03560.04190.10530.02760.16173.67243.099318.7464
21.82660.5350.02191.5739-0.79632.08120.18910.09280.1203-0.1566-0.0481-0.1188-0.19810.40680.03880.053-0.00850.02490.12910.00850.07434.90556.85392.7111
31.1864-0.1456-0.44082.04890.29271.34670.09310.2282-0.1887-0.0663-0.0106-0.02010.03890.090400.10570.0084-0.03090.066-0.02020.067225.1599-11.355211.1326
41.98790.4964-0.27791.8629-0.2143.12970.00920.1459-0.1597-0.02840.0078-0.4835-0.00860.0292-0.00010.05640.0006-0.02520.0207-0.02110.156926.580436.645136.5352
51.6828-0.57680.48892.42-0.60881.98860.30080.1684-0.288-0.46-0.02220.70810.4566-0.44030.19530.1091-0.0315-0.08730.1899-0.01230.0545-4.838832.27720.0331
61.34550.22690.38251.574-0.2732.14820.09210.15320.2868-0.03850.02930.1161-0.331-0.298500.17820.06220.08530.13060.03960.11115.68150.696627.2836
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 DIFFRACTION3(CHAIN B AND RESID 0:99)
4X-RAY DIFFRACTION4(CHAIN D AND RESID 1:180)
5X-RAY DIFFRACTION5(CHAIN D AND RESID 181:275)
6X-RAY DIFFRACTION6(CHAIN E AND RESID 0:99)

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