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- PDB-5u98: The crystal structure of a self-peptide complexed to Abacavir and... -

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Basic information

Entry
Database: PDB / ID: 5u98
TitleThe crystal structure of a self-peptide complexed to Abacavir and HLA-B*57:01
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-57 alpha chain
  • VAL-THR-THR-ASP-ILE-GLN-VAL-LYS-VAL
KeywordsIMMUNE SYSTEM / MHC / ANTIGEN PRESENTING CELL / T-CELL RECEPTOR / HUMAN LEUKOCYTE ANTIGEN / DRUG HYPERSENSITIVITY / ABACAVIR HYPERSENSITIVITY / REPERTOIRE-ALTERING SMALL MOLECULE / IMMUNE RESPONSE / IMMUNOGLOBULIN-LIKE BETA-SANDWICH
Function / homology
Function and homology information


negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / positive regulation of DNA-templated transcription, elongation / regulation of interleukin-6 production / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling ...negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / positive regulation of DNA-templated transcription, elongation / regulation of interleukin-6 production / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / TAP binding / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / protection from natural killer cell mediated cytotoxicity / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / 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 / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / detection of bacterium / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / : / : / secretory granule 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 / 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 / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / 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 / defense response / 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 / 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 / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response
Similarity search - Function
Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal ...Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain 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 / : / KOW (Kyprides, Ouzounis, Woese) motif. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / 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
Chem-1KX / Transcription elongation factor SPT5 / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOstrov, D.A. / Bracey, A.W. / Pompeu, Y.A. / Jakoncic, J. / Buus, S. / Buus, A.S. / Schutte, R.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1 AI103348 United States
CitationJournal: Int J Mol Sci / Year: 2017
Title: Structural Elements Recognized by Abacavir-Induced T Cells.
Authors: Yerly, D. / Pompeu, Y.A. / Schutte, R.J. / Eriksson, K.K. / Strhyn, A. / Bracey, A.W. / Buus, S. / Ostrov, D.A.
History
DepositionDec 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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, B-57 alpha chain
B: Beta-2-microglobulin
C: VAL-THR-THR-ASP-ILE-GLN-VAL-LYS-VAL
D: HLA class I histocompatibility antigen, B-57 alpha chain
E: Beta-2-microglobulin
F: VAL-THR-THR-ASP-ILE-GLN-VAL-LYS-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8108
Polymers89,2376
Non-polymers5732
Water15,133840
1
A: HLA class I histocompatibility antigen, B-57 alpha chain
B: Beta-2-microglobulin
C: VAL-THR-THR-ASP-ILE-GLN-VAL-LYS-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9054
Polymers44,6193
Non-polymers2861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-18 kcal/mol
Surface area18790 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, B-57 alpha chain
E: Beta-2-microglobulin
F: VAL-THR-THR-ASP-ILE-GLN-VAL-LYS-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9054
Polymers44,6193
Non-polymers2861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-17 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.134, 132.602, 87.964
Angle α, β, γ (deg.)90.00, 104.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, B-57 alpha chain / Bw-57 / MHC class I antigen B*57


Mass: 31867.363 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 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: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide VAL-THR-THR-ASP-ILE-GLN-VAL-LYS-VAL


Mass: 1003.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O00267*PLUS
#4: Chemical ChemComp-1KX / {(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]cyclopent-2-en-1-yl}methanol / Abacavir


Mass: 286.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N6O / Comment: medication, inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / Source method: isolated from a natural source / Formula: H2O
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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M NACACODYLATE, 0.1MNAACETATE, 25% PEG 8,000, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9436 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9436 Å / Relative weight: 1
ReflectionResolution: 2→28.323 Å / Num. obs: 69488 / % possible obs: 94.95 % / Redundancy: 4 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 30.398

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Coot0.7.2model building
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UPR

3upr


Resolution: 2→28.323 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 1844 2.89 %0.05
Rwork0.1727 ---
obs0.1739 63913 94.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6232 0 42 840 7114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076498
X-RAY DIFFRACTIONf_angle_d1.0528830
X-RAY DIFFRACTIONf_dihedral_angle_d14.9432414
X-RAY DIFFRACTIONf_chiral_restr0.044912
X-RAY DIFFRACTIONf_plane_restr0.0051156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.28361360.22794757X-RAY DIFFRACTION94
2.0541-2.11450.2551420.21324675X-RAY DIFFRACTION94
2.1145-2.18270.26991410.21084674X-RAY DIFFRACTION93
2.1827-2.26070.28281380.20484671X-RAY DIFFRACTION92
2.2607-2.35120.25381350.20094620X-RAY DIFFRACTION93
2.3512-2.45810.29181370.20624636X-RAY DIFFRACTION92
2.4581-2.58760.24271390.19464601X-RAY DIFFRACTION92
2.5876-2.74960.23111320.19464651X-RAY DIFFRACTION92
2.7496-2.96170.2481460.18564731X-RAY DIFFRACTION94
2.9617-3.25940.20861470.17154952X-RAY DIFFRACTION98
3.2594-3.73010.17681490.1555031X-RAY DIFFRACTION100
3.7301-4.69610.18261520.13325021X-RAY DIFFRACTION100
4.6961-28.32630.17451500.15185049X-RAY DIFFRACTION99

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