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- PDB-4g8g: Crystal Structure of C12C TCR-HA B2705-KK10 -

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Basic information

Entry
Database: PDB / ID: 4g8g
TitleCrystal Structure of C12C TCR-HA B2705-KK10
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-27 alpha chain
  • P24
  • alpha chain C12C TCR
  • beta chain C12C TCR
KeywordsIMMUNE SYSTEM / TCR / T cell / HLA B*2705 / KK10 / HIV / immune escape
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / viral process / : / : ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / viral process / : / : / 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 / secretory granule membrane / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / 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 / retroviral ribonuclease H / exoribonuclease H / 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 / exoribonuclease H activity / 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 / defense response / MHC class I protein complex / host multivesicular body / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / DNA integration / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / recycling endosome membrane / specific granule lumen / establishment of integrated proviral latency / 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 / RNA-directed DNA polymerase activity / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / viral capsid / Interferon alpha/beta signaling / RNA-DNA hybrid ribonuclease activity / sensory perception of smell / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / protein-folding chaperone binding / early endosome membrane / symbiont-mediated suppression of host gene expression / protein refolding / viral nucleocapsid / protein homotetramerization / DNA recombination / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / learning or memory / DNA-directed DNA polymerase activity / symbiont entry into host cell / immune response
Similarity search - Function
gag protein p24 N-terminal 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin ...gag protein p24 N-terminal 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / MHC classes I/II-like antigen recognition protein / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Gag-Pol polyprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / p24
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsGras, S. / Wilmann, P.G. / Rossjohn, J.
CitationJournal: Immunity / Year: 2013
Title: A Molecular Basis for the Control of Preimmune Escape Variants by HIV-Specific CD8(+) T Cells.
Authors: Ladell, K. / Hashimoto, M. / Iglesias, M.C. / Wilmann, P.G. / McLaren, J.E. / Gras, S. / Chikata, T. / Kuse, N. / Fastenackels, S. / Gostick, E. / Bridgeman, J.S. / Venturi, V. / Arkoub, Z.A. ...Authors: Ladell, K. / Hashimoto, M. / Iglesias, M.C. / Wilmann, P.G. / McLaren, J.E. / Gras, S. / Chikata, T. / Kuse, N. / Fastenackels, S. / Gostick, E. / Bridgeman, J.S. / Venturi, V. / Arkoub, Z.A. / Agut, H. / van Bockel, D.J. / Almeida, J.R. / Douek, D.C. / Meyer, L. / Venet, A. / Takiguchi, M. / Rossjohn, J. / Price, D.A. / Appay, V.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 1.4Apr 25, 2018Group: Data collection / Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.5Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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, B-27 alpha chain
B: Beta-2-microglobulin
C: P24
D: alpha chain C12C TCR
E: beta chain C12C TCR


Theoretical massNumber of molelcules
Total (without water)95,7755
Polymers95,7755
Non-polymers00
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.682, 70.320, 107.767
Angle α, β, γ (deg.)90.000, 98.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen, B-27 alpha chain / MHC class I antigen B*27


Mass: 31928.160 Da / Num. of mol.: 1 / 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) / Strain (production host): BL21(DE3) / References: UniProt: P03989, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1 / 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) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein alpha chain C12C TCR


Mass: 23086.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#5: Protein beta chain C12C TCR


Mass: 27637.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Protein/peptide / Non-polymers , 2 types, 338 molecules C

#3: Protein/peptide P24


Mass: 1243.564 Da / Num. of mol.: 1 / Fragment: UNP residues 99-108 / Source method: obtained synthetically / Details: from manufacturer / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YXW1, UniProt: P03366*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% PEG 8000 and 0.1M MES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 32993 / % possible obs: 100 % / Redundancy: 7.4 %

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
Blu-Iceicedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KGC,1OGT

1kgc

1ogt


Resolution: 2.4→46.729 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8089 / SU ML: 0.87 / σ(F): 1.38 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 1674 5.08 %
Rwork0.1779 --
obs0.182 32976 99.98 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.775 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 89.64 Å2 / Biso mean: 22.3514 Å2 / Biso min: 3.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.2452 Å20 Å2-2.2831 Å2
2--0.5722 Å20 Å2
3----2.8174 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6742 0 0 337 7079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086978
X-RAY DIFFRACTIONf_angle_d1.1289469
X-RAY DIFFRACTIONf_chiral_restr0.071988
X-RAY DIFFRACTIONf_plane_restr0.0051256
X-RAY DIFFRACTIONf_dihedral_angle_d15.9572570
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.47070.34571230.23526142737
2.4707-2.55040.30721300.21425792709
2.5504-2.64160.33361230.200125992722
2.6416-2.74730.28941410.208225932734
2.7473-2.87230.28791480.198825892737
2.8723-3.02370.29411480.191726022750
3.0237-3.21310.29611410.191925832724
3.2131-3.46120.2541210.187726282749
3.4612-3.80930.26991520.165626072759
3.8093-4.36020.1831330.136426252758
4.3602-5.4920.18841520.131126042756
5.492-46.73760.23721620.183526792841

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