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- PDB-8erx: Structure of chimeric HLA-A*11:01-A*02:01 bound to HIV-1 RT peptide -

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Basic information

Entry
Database: PDB / ID: 8erx
TitleStructure of chimeric HLA-A*11:01-A*02:01 bound to HIV-1 RT peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HIV-1 RT
  • HLA-A*02:01
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex (MHC)
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / 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
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsFlorio, T.J. / Ani, O. / Young, M.C. / Mallik, L. / Sgourakis, N.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI143997 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM125034 United States
Citation
Journal: Front Immunol / Year: 2023
Title: Decoupling peptide binding from T cell receptor recognition with engineered chimeric MHC-I molecules.
Authors: Papadaki, G.F. / Ani, O. / Florio, T.J. / Young, M.C. / Danon, J.N. / Sun, Y. / Dersh, D. / Sgourakis, N.G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-A*02:01
B: Beta-2-microglobulin
C: HIV-1 RT


Theoretical massNumber of molelcules
Total (without water)44,5083
Polymers44,5083
Non-polymers00
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-17 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.355, 79.324, 57.645
Angle α, β, γ (deg.)90.000, 116.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA-A*02:01


Mass: 31746.994 Da / Num. of mol.: 1
Mutation: G62Q, K66N, H70Q, H74D, V95I, R97I, H114R, Y116D, V152E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide HIV-1 RT


Mass: 1013.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.02 Sodium/Potassium phosphate, 0.1 M BIS-TRIS propane pH 8.5, 18-22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 30209 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.075 / Rrim(I) all: 0.141 / Χ2: 2.473 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.50.41615080.8590.2590.4921.35699.7
2.03-2.073.60.36515210.8550.2250.431.44199.9
2.07-2.113.70.36615050.8810.2220.4291.46799.9
2.11-2.153.70.30915020.9180.1870.3621.63299.9
2.15-2.23.70.28715080.9230.1740.3361.74899.9
2.2-2.253.70.26714990.920.1620.3131.9599.7
2.25-2.313.70.24915150.9430.1510.2921.84799.7
2.31-2.373.70.24314830.9390.1490.285299.8
2.37-2.443.70.21215220.9490.130.2492.17399.9
2.44-2.523.70.215070.960.1230.2352.24499.7
2.52-2.613.70.1815180.9580.110.2112.42899.8
2.61-2.713.60.16315080.9650.1020.1932.51799.9
2.71-2.833.60.14515000.9720.090.1712.82299.5
2.83-2.983.60.12714990.9760.080.153.04599.6
2.98-3.173.50.11515440.9780.0730.1363.4799.8
3.17-3.413.40.09414790.9850.0610.1123.46398.8
3.41-3.753.40.08515230.9860.0560.1023.82498.8
3.75-4.283.40.07515010.9870.0490.0894.00398.9
4.28-5.353.40.06715180.9920.0430.083.71898.9
5.35-153.60.05915490.9940.0370.072.899.2

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HHN, 1S9W, 4QRT, 5VGE, 1Q94, 2BNR, 6RPB

5hhn

1s9w

4qrt

5vge

1q94

2bnr

6rpb


Resolution: 2.07→14.93 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1397 5.05 %
Rwork0.1922 26244 -
obs0.1941 27641 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.87 Å2 / Biso mean: 24.2865 Å2 / Biso min: 10.14 Å2
Refinement stepCycle: final / Resolution: 2.07→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 0 359 3494
Biso mean---31.58 -
Num. residues----382
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.140.26591530.219225992752100
2.14-2.230.25571450.206826252770100
2.23-2.330.27981390.209826062745100
2.33-2.450.2651280.205226322760100
2.45-2.610.22871290.208926172746100
2.61-2.810.2571470.211626222769100
2.81-3.090.2231420.206826232765100
3.09-3.530.23881430.18662622276599
3.53-4.420.19741300.16762641277199
4.43-14.930.20391410.17472657279899

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