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- PDB-4g9f: Crystal Structure of C12C TCR-HLAB2705-KK10-L6M -

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Basic information

Entry
Database: PDB / ID: 4g9f
TitleCrystal Structure of C12C TCR-HLAB2705-KK10-L6M
Components
  • Beta-2-microglobulin
  • Gag protein
  • HLA class I histocompatibility antigen, B-27 alpha chain
  • alpha chain C12C TCR
  • beta chain C12C TCR
KeywordsIMMUNE SYSTEM / TCR / T cell / HLA B*2705 / KK10 / KK10-L6M / 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 / 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 / viral process / detection of bacterium ...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 / 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 / viral process / detection of bacterium / negative regulation of receptor binding / secretory granule membrane / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / peptide antigen assembly with MHC class II protein complex / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / exoribonuclease H activity / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / defense response / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / host multivesicular body / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / DNA integration / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / Interferon alpha/beta signaling / viral penetration into host nucleus / Modulation by Mtb of host immune system / specific granule lumen / RNA stem-loop binding / phagocytic vesicle membrane / recycling endosome membrane / RNA-directed DNA polymerase activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / RNA-DNA hybrid ribonuclease activity / MHC class II protein complex binding / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / late endosome membrane / sensory perception of smell / viral capsid / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / host cell / protein-folding chaperone binding / negative regulation of neuron projection development / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination / protein homotetramerization / adaptive immune response / amyloid fibril formation / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / DNA-directed DNA polymerase activity / learning or memory / immune response / Amyloid fiber formation / symbiont-mediated suppression of host gene expression / endoplasmic reticulum lumen / viral translational frameshifting / Golgi membrane
Similarity search - Function
: / 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, 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 / : / Reverse transcriptase thumb / MHC class I-like antigen recognition-like / Reverse transcriptase thumb domain / MHC class I-like antigen recognition-like superfamily / 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 / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase 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
HLA class I histocompatibility antigen, B alpha chain / Gag-Pol polyprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Gag protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 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 1.3Apr 22, 2020Group: Database references / Structure summary / Category: entity / struct / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct.pdbx_descriptor / _struct_ref_seq_dif.details
Revision 1.4Nov 27, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-27 alpha chain
B: Beta-2-microglobulin
C: Gag protein
D: alpha chain C12C TCR
E: beta chain C12C TCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2678
Polymers95,9795
Non-polymers2883
Water8,755486
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.406, 71.312, 109.566
Angle α, β, γ (deg.)90.00, 98.80, 90.00
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 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: 27822.943 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 , 1 types, 1 molecules C

#3: Protein/peptide Gag protein


Mass: 1261.602 Da / Num. of mol.: 1 / Fragment: UNP residues 22-31 / Source method: obtained synthetically / Details: from manufacturer / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YNZ1, UniProt: P03366*PLUS

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Non-polymers , 2 types, 489 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% PEG 8000 and 0.1M MES, pH 7, 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: Jul 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 68882 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.87 Å2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
Blu-Iceicedata collection
SCALAdata scaling
BUSTER2.10.0refinement
RefinementResolution: 1.9→59.56 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.8999 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 3485 5.06 %RANDOM
Rwork0.187 ---
obs0.1896 68863 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.78 Å2
Baniso -1Baniso -2Baniso -3
1--2.6347 Å20 Å24.8715 Å2
2---0.1505 Å20 Å2
3---2.7852 Å2
Refine analyzeLuzzati coordinate error obs: 0.221 Å
Refinement stepCycle: LAST / Resolution: 1.9→59.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 0 15 486 7257
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017080HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.079638HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2441SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes209HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1030HARMONIC5
X-RAY DIFFRACTIONt_it7080HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2459 262 5.18 %
Rwork0.217 4796 -
all0.2185 5058 -
obs--99.75 %

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