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- PDB-5jzi: Crystal structure of 1406 TCR bound to HLA-A2 with HCV 1406-1415 ... -

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Basic information

Entry
Database: PDB / ID: 5jzi
TitleCrystal structure of 1406 TCR bound to HLA-A2 with HCV 1406-1415 antigen peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HCV1406 TCR alpha chain
  • HCV1406 TCR beta chain
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • KLV peptide
KeywordsProtein binding/Immune System / HCV1406 TCR / HLA-A2 / HCV NS3:1406-1415 peptide / decapeptide / Protein binding / Immune System complex / Protein binding-Immune System complex
Function / homology
Function and homology information


positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / negative regulation of protein secretion / 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 / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / detection of bacterium / endoplasmic reticulum-Golgi intermediate compartment membrane / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / SH3 domain binding / kinase binding / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / nucleoside-triphosphate phosphatase / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / protein complex oligomerization / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / monoatomic ion channel activity / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway
Similarity search - Function
Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b ...Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / DEAD box, Flavivirus / Flavivirus DEAD domain / 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 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 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 / Genome polyprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, Y. / Piepenbrink, K.H. / Baker, B.M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: How an alloreactive T-cell receptor achieves peptide and MHC specificity.
Authors: Wang, Y. / Singh, N.K. / Spear, T.T. / Hellman, L.M. / Piepenbrink, K.H. / McMahan, R.H. / Rosen, H.R. / Vander Kooi, C.W. / Nishimura, M.I. / Baker, B.M.
History
DepositionMay 16, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionMay 31, 2017ID: 4ZEZ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 31, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Jun 24, 2020Group: Advisory / Category: pdbx_database_PDB_obs_spr / Item: _pdbx_database_PDB_obs_spr.replace_pdb_id
Revision 1.4Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-2 alpha chain
B: Beta-2-microglobulin
C: KLV peptide
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: KLV peptide
D: HCV1406 TCR alpha chain
E: HCV1406 TCR beta chain
I: HCV1406 TCR alpha chain
J: HCV1406 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)193,36510
Polymers193,36510
Non-polymers00
Water1,74797
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: KLV peptide
D: HCV1406 TCR alpha chain
E: HCV1406 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)96,6835
Polymers96,6835
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: KLV peptide
I: HCV1406 TCR alpha chain
J: HCV1406 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)96,6835
Polymers96,6835
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.760, 128.760, 223.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

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


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / 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 / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: P61769
#4: Protein HCV1406 TCR alpha chain


Mass: 23914.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#5: Protein HCV1406 TCR beta chain


Mass: 28036.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Protein/peptide / Non-polymers , 2 types, 99 molecules CH

#3: Protein/peptide KLV peptide


Mass: 998.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: P27958*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 13% PEG 3350, 0.1M Sodium Cacodylate, 0.2m Ammonium Sulfate, 3% w/v 1,5-Diaminopentane dihydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→48.72 Å / Num. obs: 78081 / % possible obs: 86 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 1.13

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
PHENIXdev_1958phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MRM

3mrm


Resolution: 2.5→37.17 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.232 1384 1.86 %
Rwork0.1955 --
obs0.2012 74522 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13228 0 0 97 13325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513589
X-RAY DIFFRACTIONf_angle_d0.76818383
X-RAY DIFFRACTIONf_dihedral_angle_d11.264956
X-RAY DIFFRACTIONf_chiral_restr0.0281926
X-RAY DIFFRACTIONf_plane_restr0.0042390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.59030.28351360.29197198X-RAY DIFFRACTION97
2.5903-2.69390.31741360.29347156X-RAY DIFFRACTION97
2.6939-2.81630.29851380.28757254X-RAY DIFFRACTION98
2.8163-2.96460.29241400.26927199X-RAY DIFFRACTION98
2.9646-3.150.25321360.25137242X-RAY DIFFRACTION98
3.15-3.39270.26251370.23377304X-RAY DIFFRACTION98
3.3927-3.73320.22441390.21227268X-RAY DIFFRACTION98
3.7332-4.27130.2341390.17927335X-RAY DIFFRACTION98
4.2713-5.37320.21161390.14257415X-RAY DIFFRACTION98
5.3732-25.63850.19881440.16537646X-RAY DIFFRACTION98
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)
13.161-0.59120.43992.6652-0.29233.2765-0.1274-0.34340.17570.18640.0422-0.0096-0.3915-0.04540.0570.3030.05930.00820.3017-0.10170.2842-88.107977.90425.72
22.8948-1.79180.08361.597-0.01042.27530.02940.0447-0.16460.6510.42261.4025-0.3187-0.1543-0.37141.07710.07160.31510.8704-0.12991.5874-96.6406106.161243.4898
33.01560.4750.62522.2321-0.04683.5675-0.3103-0.11730.9658-0.3264-0.1506-0.0262-0.64930.33250.5060.76730.0842-0.04380.5006-0.04590.8904-81.5301103.525728.6518
40.6619-0.26240.14892.3383-2.18313.5331-0.01250.03460.181-0.25720.0768-0.34110.72850.06690.11860.26240.10130.07740.58360.0010.3848-87.868970.212422.6497
52.4990.20690.51221.66140.16252.4615-0.20480.62310.302-0.10720.108-0.0681-0.29490.46950.07230.3294-0.1577-0.00860.65340.19170.4666-41.197175.675710.6636
60.8351-0.39760.60030.66090.44521.5468-0.05760.39970.77010.23540.8846-0.21130.0998-0.1085-0.85760.9719-0.05780.04920.83950.25521.4212-31.9756100.1845-12.8804
72.2927-0.4271.62130.8490.83832.8373-0.40730.16340.9337-0.1657-0.1818-0.0916-0.7251-0.23220.56960.7808-0.0531-0.01650.63170.19811.171-46.7697100.95144.5188
82.3353-1.5583-0.18562.95230.07891.1122-0.13820.7605-0.8776-0.1429-0.3497-0.35010.25930.22980.5290.49-0.1380.1910.60590.07730.6054-41.749868.909514.683
92.0335-0.37150.82684.70110.39743.968-0.0144-0.2828-0.34240.3892-0.06690.17460.7418-0.08290.09540.3803-0.04060.05320.3160.04730.2971-81.476547.077122.9143
101.21060.86430.59581.8554-0.20372.27140.12730.1939-0.1360.43630.0841-0.490.81570.1675-0.24931.15150.2548-0.07680.5002-0.06620.5168-66.71619.5157.0306
114.9846-1.7334-1.29352.20010.68813.94710.10780.3978-0.1583-0.1396-0.13180.25890.0386-0.22410.02450.2803-0.0016-0.04940.2666-0.00860.2047-75.931158.98335.4376
122.34360.87630.02655.5157-1.051.2639-0.00720.0079-0.07470.04120.1506-0.07050.25510.067-0.12030.65420.06950.0130.4474-0.05120.2276-70.637130.9943-5.917
131.0342-0.2866-0.01824.0266-0.44732.62540.0210.2534-0.1415-0.2791-0.1039-0.02830.30540.19560.10370.29380.01920.01480.4042-0.05310.3485-48.61546.274417.635
145.1532-0.43971.07273.69010.25234.35730.23310.0798-0.1574-0.0194-0.10490.41180.41170.0713-0.12350.5971-0.03610.04880.3170.00620.3305-62.965421.409336.5252
154.33881.139-1.94532.83310.30243.5827-0.03950.012-0.27140.11710.0726-0.33820.15830.258-0.02790.2706-0.0237-0.07460.32250.01540.2475-54.158660.746333.345
162.8222-1.6265-0.12356.3226-0.67791.37690.0867-0.0793-0.062-0.1735-0.04330.19370.11520.0733-0.05580.4219-0.06320.06170.3907-0.01650.1652-59.782134.706148.2353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 272 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 99 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 10 )
5X-RAY DIFFRACTION5chain 'F' and (resid 1 through 180)
6X-RAY DIFFRACTION6chain 'F' and (resid 181 through 274 )
7X-RAY DIFFRACTION7chain 'G' and (resid 0 through 99 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 10 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 117 )
10X-RAY DIFFRACTION10chain 'D' and (resid 118 through 208 )
11X-RAY DIFFRACTION11chain 'E' and (resid 1 through 111 )
12X-RAY DIFFRACTION12chain 'E' and (resid 112 through 240 )
13X-RAY DIFFRACTION13chain 'I' and (resid 1 through 117)
14X-RAY DIFFRACTION14chain 'I' and (resid 118 through 208 )
15X-RAY DIFFRACTION15chain 'J' and (resid 1 through 111 )
16X-RAY DIFFRACTION16chain 'J' and (resid 112 through 240 )

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