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- PDB-6ptb: Crystal Structure of ILNAMIAKI peptide bound to HLA-A2 -

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Basic information

Entry
Database: PDB / ID: 6ptb
TitleCrystal Structure of ILNAMIAKI peptide bound to HLA-A2
Components
  • Beta-2-microglobulin
  • HAUS augmin-like complex subunit 3
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / MHC class I / HLA A2 / immune system complex / neoantigen
Function / homology
Function and homology information


HAUS complex / regulation of microtubule nucleation / microtubule organizing center organization / mitotic spindle microtubule / centrosome cycle / 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 ...HAUS complex / regulation of microtubule nucleation / microtubule organizing center organization / mitotic spindle microtubule / centrosome cycle / 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 / microtubule organizing center / 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 / intercellular bridge / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / AURKA Activation by TPX2 / 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 / mitotic spindle / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / Regulation of PLK1 Activity at G2/M Transition / 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 / microtubule cytoskeleton / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory
Similarity search - Function
HAUS augmin-like complex subunit 3 / HAUS augmin-like complex subunit 3, N-terminal / HAUS augmin-like complex subunit 3 / 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 ...HAUS augmin-like complex subunit 3 / HAUS augmin-like complex subunit 3, N-terminal / HAUS augmin-like complex subunit 3 / 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 / HAUS augmin-like complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKeller, G.L.J. / Arbuiso, A. / Baker, B.M.
CitationJournal: Front Immunol / Year: 2019
Title: Structure Based Prediction of Neoantigen Immunogenicity.
Authors: Riley, T.P. / Keller, G.L.J. / Smith, A.R. / Davancaze, L.M. / Arbuiso, A.G. / Devlin, J.R. / Baker, B.M.
History
DepositionJul 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 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

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: HAUS augmin-like complex subunit 3
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: HAUS augmin-like complex subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6268
Polymers89,4426
Non-polymers1842
Water9,674537
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: HAUS augmin-like complex subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9055
Polymers44,7213
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-23 kcal/mol
Surface area18720 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: HAUS augmin-like complex subunit 3


Theoretical massNumber of molelcules
Total (without water)44,7213
Polymers44,7213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-23 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.676, 63.671, 75.175
Angle α, β, γ (deg.)81.472, 75.849, 77.225
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#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: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P61769
#3: Protein/peptide HAUS augmin-like complex subunit 3


Mass: 987.280 Da / Num. of mol.: 2 / Fragment: UNP residues 154-162 / Mutation: T160A / Source method: obtained synthetically
Details: Processed peptide fragment from full-length protein containing SNP, derived from 2098 MEL cell line
Source: (synth.) Homo sapiens (human) / References: UniProt: Q68CZ6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 15% v/v PEG3350, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→72.53 Å / Num. obs: 47203 / % possible obs: 98.12 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.01 Å2 / CC1/2: 0.944 / Rpim(I) all: 0.1295 / Net I/σ(I): 4.6
Reflection shellResolution: 2.15→2.19 Å / Num. unique obs: 2366 / CC1/2: 0.744 / Rpim(I) all: 0.4366 / % possible all: 96.57

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
DIALSdata reduction
DIALSdata scaling
PHENIX1.15.2-3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3PWL

3pwl


Resolution: 2.15→30.89 Å / SU ML: 0.2809 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.895
RfactorNum. reflection% reflection
Rfree0.2324 4711 10.01 %
Rwork0.1933 --
obs0.1973 47073 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.1 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6304 0 12 537 6853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00466488
X-RAY DIFFRACTIONf_angle_d0.68138794
X-RAY DIFFRACTIONf_chiral_restr0.0451898
X-RAY DIFFRACTIONf_plane_restr0.00371146
X-RAY DIFFRACTIONf_dihedral_angle_d15.6332394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.170.29441580.25761403X-RAY DIFFRACTION96.3
2.17-2.20.29451530.25921379X-RAY DIFFRACTION94.98
2.2-2.230.31271520.27051373X-RAY DIFFRACTION97.44
2.23-2.250.31671570.27371420X-RAY DIFFRACTION96.75
2.25-2.280.27981550.251381X-RAY DIFFRACTION96.12
2.28-2.320.29341560.23591398X-RAY DIFFRACTION97.74
2.32-2.350.24011580.22411414X-RAY DIFFRACTION96.74
2.35-2.380.2761530.20891394X-RAY DIFFRACTION97.42
2.38-2.420.28281580.21731434X-RAY DIFFRACTION97.85
2.42-2.460.25911520.20521347X-RAY DIFFRACTION96.21
2.46-2.50.26611590.2071438X-RAY DIFFRACTION98.22
2.5-2.550.251570.20411405X-RAY DIFFRACTION96.9
2.55-2.60.23611550.21141407X-RAY DIFFRACTION98.55
2.6-2.650.27211570.22311400X-RAY DIFFRACTION96.59
2.65-2.710.2711560.21571399X-RAY DIFFRACTION98.42
2.71-2.770.27771600.22311447X-RAY DIFFRACTION97.51
2.77-2.840.27181560.20521402X-RAY DIFFRACTION98.67
2.84-2.920.26221570.20261413X-RAY DIFFRACTION98.06
2.92-30.23911620.20741447X-RAY DIFFRACTION98.47
3-3.10.26661540.20361389X-RAY DIFFRACTION98.59
3.1-3.210.22771570.20051415X-RAY DIFFRACTION98.37
3.21-3.340.23141600.19761437X-RAY DIFFRACTION98.46
3.34-3.490.21851550.19751398X-RAY DIFFRACTION98.67
3.49-3.670.22681600.1811444X-RAY DIFFRACTION98.89
3.67-3.90.21551600.16981436X-RAY DIFFRACTION99.07
3.9-4.210.1711600.16321438X-RAY DIFFRACTION98.89
4.21-4.630.18161560.14161408X-RAY DIFFRACTION99.05
4.63-5.290.16831600.14561437X-RAY DIFFRACTION99.25
5.29-6.660.23021590.16271433X-RAY DIFFRACTION99.69
6.66-30.890.17771590.16871426X-RAY DIFFRACTION98.88

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