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- PDB-1eez: Crystal Structure Determination of HLA-A2.1 Complexed to GP2 Pept... -

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Basic information

Entry
Database: PDB / ID: 1eez
TitleCrystal Structure Determination of HLA-A2.1 Complexed to GP2 Peptide Variant(I2L/V5L)
Components
  • BETA-2-MICROGLOBULIN (LIGHT CHAIN)
  • GP2 PEPTIDE
  • HLA-A2.1 MHC CLASS I (HEAVY CHAIN)
KeywordsIMMUNE SYSTEM / major histocompatibility complex / peptide binding
Function / homology
Function and homology information


: / : / regulation of membrane depolarization / retina homeostasis / 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 ...: / : / regulation of membrane depolarization / retina homeostasis / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / cellular response to lipopolysaccharide / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / 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
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
Beta-2-microglobulin / 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)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsSharma, A.K. / Kuhns, J.J. / Collins, E.J.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Class I major histocompatibility complex anchor substitutions alter the conformation of T cell receptor contacts.
Authors: Sharma, A.K. / Kuhns, J.J. / Yan, S. / Friedline, R.H. / Long, B. / Tisch, R. / Collins, E.J.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Poor Binding of HER-2/neu Epitope (GP2) to HLA-A2.1 is Due to a Lack of Interactions with the Center of the Peptide
Authors: Kuhns, J.J. / Batalia, M.A. / Yan, S. / Collins, E.J.
History
DepositionFeb 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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-A2.1 MHC CLASS I (HEAVY CHAIN)
B: BETA-2-MICROGLOBULIN (LIGHT CHAIN)
C: GP2 PEPTIDE
D: HLA-A2.1 MHC CLASS I (HEAVY CHAIN)
E: BETA-2-MICROGLOBULIN (LIGHT CHAIN)
F: GP2 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)89,2636
Polymers89,2636
Non-polymers00
Water63135
1
A: HLA-A2.1 MHC CLASS I (HEAVY CHAIN)
B: BETA-2-MICROGLOBULIN (LIGHT CHAIN)
C: GP2 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,6323
Polymers44,6323
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-25 kcal/mol
Surface area18790 Å2
MethodPISA
2
D: HLA-A2.1 MHC CLASS I (HEAVY CHAIN)
E: BETA-2-MICROGLOBULIN (LIGHT CHAIN)
F: GP2 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,6323
Polymers44,6323
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-24 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.210, 62.320, 74.660
Angle α, β, γ (deg.)82.15, 76.38, 78.33
Int Tables number1
Space group name H-MP1
DetailsHLA_A2.1 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). Heavy chain is made of three sununits alpha1, alpha2 and alpha3. Peptide binds to the groove formed by the alpha1 and alpha2 domains

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Components

#1: Protein HLA-A2.1 MHC CLASS I (HEAVY CHAIN)


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-275 OF EXTRACELLULAR PORTION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN (LIGHT CHAIN)


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01884, UniProt: P61769*PLUS
#3: Protein/peptide GP2 PEPTIDE


Mass: 898.142 Da / Num. of mol.: 2 / Mutation: I2L,V5L / Source method: obtained synthetically
Details: The peptide was synthesized at the peptide synthesis facility of University of North Carolina at Chapel Hill.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHLA_A2.1 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). ...HLA_A2.1 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). Heavy chain is made of three subunits alpha1, alpha2 and alpha3. Peptide binds to the groove formed by the alpha1 and alpha2 domains.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG8000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114-20 %PEG80001reservoir
225 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 114345 / Num. obs: 33403 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 4.73
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2 % / Rmerge(I) obs: 0.293 / Num. unique all: 5095 / % possible all: 84.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 114345
Reflection shell
*PLUS
% possible obs: 84.8 % / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementResolution: 2.3→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 974700.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood function
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1670 5 %RANDOM
Rwork0.263 ---
all0.263 33403 --
obs0.263 33403 87.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.79 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.29 Å2-0.11 Å20.63 Å2
2---3.8 Å20.68 Å2
3----2.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6294 0 0 35 6329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 259 4.8 %
Rwork0.31 5095 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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