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- PDB-3w0w: The complex between T36-5 TCR and HLA-A24 bound to HIV-1 Nef134-1... -

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Basic information

Entry
Database: PDB / ID: 3w0w
TitleThe complex between T36-5 TCR and HLA-A24 bound to HIV-1 Nef134-10(2F) peptide in space group P212121
Components
  • 10-mer peptide from Protein Nef
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-24 alpha chain
  • T36-5 TCR alpha chain
  • T36-5 TCR beta chain
KeywordsIMMUNE SYSTEM / HIV-1 / NEF / HLA-A24 / T CELL RECEPTOR / MHC CLASS I / TCR / MHC / IMMUNOGLOBURIN DOMAIN / IMMUNE RESPONSE
Function / homology
Function and homology information


symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation ...symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / host cell Golgi membrane / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / virion component / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / 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 / SH3 domain binding / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / virus-mediated perturbation of host defense response
Similarity search - Function
HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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 ...HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / Protein Nef
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.603 Å
AuthorsShimizu, A. / Fukai, S. / Yamagata, A. / Iwamoto, A.
CitationJournal: SCI REP / Year: 2013
Title: Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection
Authors: Shimizu, A. / Kawana-Tachikawa, A. / Yamagata, A. / Han, C. / Zhu, D. / Sato, Y. / Nakamura, H. / Koibuchi, T. / Carlson, J. / Martin, E. / Brumme, C.J. / Shi, Y. / Gao, G.F. / Brumme, Z.L. ...Authors: Shimizu, A. / Kawana-Tachikawa, A. / Yamagata, A. / Han, C. / Zhu, D. / Sato, Y. / Nakamura, H. / Koibuchi, T. / Carlson, J. / Martin, E. / Brumme, C.J. / Shi, Y. / Gao, G.F. / Brumme, Z.L. / Fukai, S. / Iwamoto, A.
History
DepositionNov 5, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: 10-mer peptide from Protein Nef
D: T36-5 TCR alpha chain
E: T36-5 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)96,9185
Polymers96,9185
Non-polymers00
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-55 kcal/mol
Surface area38220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.921, 86.441, 251.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 4 molecules ABDE

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


Mass: 33421.121 Da / Num. of mol.: 1 / Fragment: UNP residues 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: PET21D(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P05534, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#4: Protein T36-5 TCR alpha chain


Mass: 22764.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#5: Protein T36-5 TCR beta chain


Mass: 27577.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21

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Protein/peptide / Non-polymers , 2 types, 321 molecules C

#3: Protein/peptide 10-mer peptide from Protein Nef


Mass: 1274.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YYU3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.86 Å3/Da / Density % sol: 56.97 % / Mosaicity: 1.231 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 16% PEG 3350, 0.1 M diammonium tartrate, 0.2% n-dodecyl-N,N-dimethylamine-N-oxide (LDAO) 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.603→50 Å / Num. obs: 35008 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.115 / Χ2: 0.917 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.603-2.644.20.40217210.421198.9
2.64-2.694.40.38117020.42198.7
2.69-2.744.70.36716760.419199.1
2.74-2.84.70.33117380.427199.3
2.8-2.864.90.27417220.431199.3
2.86-2.934.90.2616790.455199.1
2.93-34.80.22717580.468199.5
3-3.084.70.19917020.488199.4
3.08-3.175.10.17417450.536199.5
3.17-3.285.50.15117000.519199.8
3.28-3.395.40.13917770.612199.7
3.39-3.535.50.1217080.662199.6
3.53-3.695.20.10417570.745199.8
3.69-3.885.60.09817630.832199.9
3.88-4.135.90.08717550.862199.9
4.13-4.455.80.0817551.031199.8
4.45-4.895.50.07817721.148199.8
4.89-5.660.07718051.007199.7
5.6-7.055.70.07918171.046199.7
7.05-505.80.08519564.294199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VXU

3vxu


Resolution: 2.603→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.2504 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.859 / SU B: 9.366 / SU ML: 0.203 / SU R Cruickshank DPI: 0.5777 / SU Rfree: 0.3055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.578 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1752 5 %RANDOM
Rwork0.186 ---
obs0.1892 34950 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.27 Å2 / Biso mean: 37.333 Å2 / Biso min: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0 Å20 Å2
2---0.38 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.603→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6699 0 0 320 7019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026882
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9369342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93824.028355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.033151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.691548
X-RAY DIFFRACTIONr_chiral_restr0.0870.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215402
LS refinement shellResolution: 2.603→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 112 -
Rwork0.239 2190 -
all-2302 -
obs--97.87 %

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