[English] 日本語
Yorodumi
- PDB-5mep: Human Leukocyte Antigen A02 presenting ILGKFLHWL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mep
TitleHuman Leukocyte Antigen A02 presenting ILGKFLHWL
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • ILE-LEU-GLY-LYS-PHE-LEU-HIS-TRP-LEU
KeywordsIMMUNE SYSTEM / HLA A02 / HLAA / MHC / Immuno / Telomerase
Function / homology
Function and homology information


positive regulation of hair cycle / template-free RNA nucleotidyltransferase activity / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / RNA-templated DNA biosynthetic process ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase activity / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / telomerase activity / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / siRNA processing / nuclear telomere cap complex / telomere maintenance via recombination / positive regulation of vascular associated smooth muscle cell migration / telomerase holoenzyme complex / telomerase RNA binding / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / DNA biosynthetic process / RNA-templated transcription / positive regulation of stem cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / telomeric repeat DNA binding / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / negative regulation of cellular senescence / beta-2-microglobulin binding / mitochondrial nucleoid / endoplasmic reticulum exit site / replicative senescence / TAP binding / Telomere Extension By Telomerase / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / detection of bacterium / response to cadmium ion / 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 / negative regulation of endothelial cell apoptotic process / positive regulation of G1/S transition of mitotic cell cycle / telomere maintenance via telomerase / positive regulation of Wnt signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / T cell receptor binding / telomere maintenance / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / positive regulation of D-glucose import across plasma membrane / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / mitochondrion organization / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / response to molecule of bacterial origin / regulation of protein stability / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / Formation of the beta-catenin:TCF transactivating complex / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / PML body / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / RNA-directed DNA polymerase / multicellular organismal-level iron ion homeostasis / positive regulation of miRNA transcription / positive regulation of T cell mediated cytotoxicity / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / RNA-directed DNA polymerase activity / phagocytic vesicle membrane / positive regulation of type II interferon production / transcription coactivator binding / recycling endosome membrane
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 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 / Immunoglobulin-like fold / Immunoglobulins / DNA/RNA polymerase superfamily / 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 / molecular replacement / Resolution: 2.71 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Lloyd, A. / Crowther, M. / Sewell, A.K.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural Mechanism Underpinning Cross-reactivity of a CD8+ T-cell Clone That Recognizes a Peptide Derived from Human Telomerase Reverse Transcriptase.
Authors: Cole, D.K. / van den Berg, H.A. / Lloyd, A. / Crowther, M.D. / Beck, K. / Ekeruche-Makinde, J. / Miles, J.J. / Bulek, A.M. / Dolton, G. / Schauenburg, A.J. / Wall, A. / Fuller, A. / Clement, ...Authors: Cole, D.K. / van den Berg, H.A. / Lloyd, A. / Crowther, M.D. / Beck, K. / Ekeruche-Makinde, J. / Miles, J.J. / Bulek, A.M. / Dolton, G. / Schauenburg, A.J. / Wall, A. / Fuller, A. / Clement, M. / Laugel, B. / Rizkallah, P.J. / Wooldridge, L. / Sewell, A.K.
History
DepositionNov 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: 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 / struct_ncs_dom_lim
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: ILE-LEU-GLY-LYS-PHE-LEU-HIS-TRP-LEU
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: ILE-LEU-GLY-LYS-PHE-LEU-HIS-TRP-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,69718
Polymers89,9186
Non-polymers77912
Water1,47782
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: ILE-LEU-GLY-LYS-PHE-LEU-HIS-TRP-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,42810
Polymers44,9593
Non-polymers4687
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-25 kcal/mol
Surface area19070 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: ILE-LEU-GLY-LYS-PHE-LEU-HIS-TRP-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2698
Polymers44,9593
Non-polymers3105
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-6 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.410, 169.550, 47.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21D
12B
22E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPRODD1 - 2761 - 276
12METMETMETMETBB0 - 991 - 100
22METMETMETMETEE0 - 991 - 100

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ADBE

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31951.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / 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) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

-
Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide ILE-LEU-GLY-LYS-PHE-LEU-HIS-TRP-LEU


Mass: 1128.408 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) / References: UniProt: O14746*PLUS

-
Non-polymers , 3 types, 94 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium sulphate, 0.1M MES pH7, 15% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.71→42.39 Å / Num. obs: 26894 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.045 / Net I/σ(I): 14.1 / Num. measured all: 195005
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.71-2.787.10.9052.30.7141100
12.12-42.396.20.05332.30.998198.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.56 Å42.39 Å
Translation7.56 Å42.39 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4W

4i4w


Resolution: 2.71→42.39 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 26.531 / SU ML: 0.252 / SU R Cruickshank DPI: 0.2939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.333
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1333 5 %RANDOM
Rwork0.182 ---
obs0.1849 25511 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 124.96 Å2 / Biso mean: 52.235 Å2 / Biso min: 28.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å20 Å2
2---0.42 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 2.71→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 49 82 6475
Biso mean--66.57 41.83 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196571
X-RAY DIFFRACTIONr_bond_other_d0.0040.025937
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9238892
X-RAY DIFFRACTIONr_angle_other_deg1.145313641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0245764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39323.086350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.863151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5381556
X-RAY DIFFRACTIONr_chiral_restr0.0980.2899
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027426
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021662
X-RAY DIFFRACTIONr_mcbond_it1.9653.123074
X-RAY DIFFRACTIONr_mcbond_other1.9643.123073
X-RAY DIFFRACTIONr_mcangle_it3.1794.6743832
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A144710.14
12D144710.14
21B55550.12
22E55550.12
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 93 -
Rwork0.32 1869 -
all-1962 -
obs--99.95 %
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)
12.61770.22540.95483.1421-1.56363.9792-0.04770.04610.15170.0185-0.096-0.0943-0.1650.04550.14370.0082-0.0059-0.00490.06750.00420.078-22.352923.9324-13.002
26.9208-1.8596-0.97173.89190.65491.9996-0.0829-0.1542-0.52820.2482-0.04190.75740.0207-0.31910.12480.13640.0257-0.01540.12430.05020.2615-54.658534.6248-24.8589
33.05820.73741.86092.82440.71785.4596-0.0283-0.0497-0.0335-0.12910.06580.20860.0494-0.3496-0.03760.0369-0.0064-0.00570.02920.01790.0793-44.019514.4445-26.8826
43.8359-0.455-0.21042.3422-0.76071.13040.03990.1478-0.171-0.1433-0.0086-0.09450.15430.0266-0.03140.1550.02030.00290.0563-0.01850.0231-50.386953.25471.7442
52.75342.81010.936.3530.35091.64960.0515-0.3096-0.28940.4287-0.0453-0.55290.05530.0627-0.00630.1850.09430.0190.1684-0.00210.1005-20.345273.97041.4982
67.16881.6706-1.26493.7656-1.54443.3139-0.1230.60350.0628-0.5910.2313-0.0057-0.005-0.0215-0.10830.3074-0.0706-0.01690.1090.00420.0154-37.096971.4029-14.2263
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 180
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more