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- PDB-2bck: Crystal Structure of HLA-A*2402 Complexed with a telomerase peptide -

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Basic information

Entry
Database: PDB / ID: 2bck
TitleCrystal Structure of HLA-A*2402 Complexed with a telomerase peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-24 alpha chain
  • Telomerase reverse transcriptase
KeywordsIMMUNE SYSTEM / Immunoglobulin Domains / Beta barrels / MHC Fold
Function / homology
Function and homology information


positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / telomerase catalytic core complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase activity ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / telomerase catalytic core complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase activity / telomerase RNA reverse transcriptase activity / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / nuclear telomere cap complex / siRNA processing / telomerase RNA binding / telomerase holoenzyme complex / positive regulation of vascular associated smooth muscle cell migration / telomeric DNA binding / DNA biosynthetic process / RNA-templated transcription / positive regulation of stem cell proliferation / mitochondrial nucleoid / negative regulation of cellular senescence / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / Telomere Extension By Telomerase / TAP complex binding / positive regulation of Wnt signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class I / telomere maintenance via telomerase / Golgi medial cisterna / replicative senescence / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / positive regulation of G1/S transition of mitotic cell cycle / response to cadmium ion / endoplasmic reticulum exit site / beta-2-microglobulin binding / negative regulation of endothelial cell apoptotic process / TAP binding / protection from natural killer cell mediated cytotoxicity / positive regulation of vascular associated smooth muscle cell proliferation / 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 / telomere maintenance / mitochondrion organization / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / positive regulation of nitric-oxide synthase activity / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of glucose import / Formation of the beta-catenin:TCF transactivating complex / regulation of protein stability / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / transcription coactivator binding / HFE-transferrin receptor complex / PML body / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of miRNA transcription / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / RNA-directed DNA polymerase / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of angiogenesis / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II
Similarity search - Function
: / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / 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 ...: / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / 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 / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / 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 / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Telomerase reverse transcriptase / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRizkallah, P.J. / Jakobsen, B.K. / Cole, D.K. / Gao, G.F.
CitationJournal: Eur.J.Immunol. / Year: 2006
Title: Crystal structure of HLA-A*2402 complexed with a telomerase peptide.
Authors: Cole, D.K. / Rizkallah, P.J. / Gao, F. / Watson, N.I. / Boulter, J.M. / Bell, J.I. / Sami, M. / Gao, G.F. / Jakobsen, B.K.
History
DepositionOct 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-24 alpha chain
B: Beta-2-microglobulin
C: Telomerase reverse transcriptase
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: Telomerase reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,39218
Polymers93,2566
Non-polymers1,13712
Water2,306128
1
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: Telomerase reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,29210
Polymers46,6283
Non-polymers6657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-82 kcal/mol
Surface area20380 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: Telomerase reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1008
Polymers46,6283
Non-polymers4725
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-56 kcal/mol
Surface area20080 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12750 Å2
ΔGint-159 kcal/mol
Surface area38960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.505, 132.186, 91.197
Angle α, β, γ (deg.)90.00, 128.80, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22A
13E
23B
14F
24C

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLNGLNDD1 - 1801 - 180
21GLYGLYGLNGLNAA1 - 1801 - 180
12ARGARGASPASPDD181 - 284181 - 284
22ARGARGASPASPAA181 - 284181 - 284
13METMETMETMETEE0 - 991 - 100
23METMETMETMETBB0 - 991 - 100
14VALVALLEULEUFF1 - 91 - 9
24VALVALLEULEUCC1 - 91 - 9

NCS ensembles :
ID
1
2
3
4
DetailsOne biological unit is made up of 1 heavy chain, 1 light chain and 1 peptide. There are two copies in the asymmetric unit: Chains A,B and C make one biological unit; Chains D,E and F amke another biological unit

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA class I histocompatibility antigen, A-24 alpha chain / MHC class I antigen A*24 / Aw-24 / A-9 / HLA-A*2402 Heavy Chain / alpha chain


Mass: 33720.203 Da / Num. of mol.: 2 / Fragment: residues 1-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / References: UniProt: P05534, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / HLA-A*2402 Light Chain


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: residues 1-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Telomerase reverse transcriptase / / Telomerase catalytic subunit / HEST2 / Telomerase-associated protein 2 / TP2


Mass: 1028.248 Da / Num. of mol.: 2 / Fragment: residues 1-9 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in human.
References: UniProt: O14746, RNA-directed DNA polymerase

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Non-polymers , 3 types, 140 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 1.6M Ammonium Sulphate, 0.1M Sodium Chloride, 0.1M HEPES, 10% v/v Dioxane, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 2004
RadiationMonochromator: Si(111) sagittal bend / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.8→78.62 Å / Num. obs: 28450 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 79.3 Å2 / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 3.3
Reflection shellResolution: 2.8→2.95 Å / % possible obs: 99.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.917 / Mean I/σ(I) obs: 1.2 / Num. measured obs: 4174 / Num. unique all: 4174 / Rsym value: 0.917 / % possible all: 99.7

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Phasing

Phasing MRRfactor: 46 / R rigid body: 46.4 / Cor.coef. Fo:Fc: 53.9 / Cor.coef. Io to Ic: 26.1
Highest resolutionLowest resolution
Translation3 Å29.488 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AO7

1ao7


Resolution: 2.8→78.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.913 / SU B: 29.779 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.915 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, BUT NOT OUTPUT TO THE COORDINATE SET
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1438 5.1 %RANDOM
Rwork0.183 ---
all0.187 28388 --
obs0.187 28388 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.865 Å2
Baniso -1Baniso -2Baniso -3
1-7.81 Å20 Å25.7 Å2
2---4.21 Å20 Å2
3---3.55 Å2
Refinement stepCycle: LAST / Resolution: 2.8→78.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6422 0 64 128 6614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216652
X-RAY DIFFRACTIONr_bond_other_d0.0010.025690
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9419012
X-RAY DIFFRACTIONr_angle_other_deg0.687313240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9075784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.59123.333354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.361151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2161558
X-RAY DIFFRACTIONr_chiral_restr0.0770.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027446
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021448
X-RAY DIFFRACTIONr_nbd_refined0.2280.31532
X-RAY DIFFRACTIONr_nbd_other0.2130.36094
X-RAY DIFFRACTIONr_nbtor_refined0.190.53210
X-RAY DIFFRACTIONr_nbtor_other0.090.53623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.5365
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1220.510
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.325
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.380
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.512
X-RAY DIFFRACTIONr_mcbond_it3.7125051
X-RAY DIFFRACTIONr_mcbond_other0.89221612
X-RAY DIFFRACTIONr_mcangle_it4.78736320
X-RAY DIFFRACTIONr_scbond_it7.07743239
X-RAY DIFFRACTIONr_scangle_it9.97262692
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberRmsTypeWeight
1D27410.51MEDIUM POSITIONAL0.5
1D27411.95MEDIUM THERMAL2
2D15430.49MEDIUM POSITIONAL0.5
2D15432.03MEDIUM THERMAL2
3E15760.56MEDIUM POSITIONAL0.5
3E15761.97MEDIUM THERMAL2
4F1450.56MEDIUM POSITIONAL0.5
4F1451.84MEDIUM THERMAL2
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 103 -
Rwork0.367 1961 -
all-2064 -
obs--98.01 %

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