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- PDB-3kxf: Crystal Structure of SB27 TCR in complex with the 'restriction tr... -

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Basic information

Entry
Database: PDB / ID: 3kxf
TitleCrystal Structure of SB27 TCR in complex with the 'restriction triad' mutant HLA-B*3508-13mer
Components
  • (SB27 T cell receptor ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-35 alpha chain
  • peptide from Trans-activator protein BZLF1
KeywordsIMMUNE SYSTEM / MHC / HLA / TCR / Disulfide bond / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Immunoglobulin domain
Function / homology
Function and homology information


symbiont-mediated suppression of host tumor necrosis factor-mediated signaling pathway / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse ...symbiont-mediated suppression of host tumor necrosis factor-mediated signaling pathway / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / protection from natural killer cell mediated cytotoxicity / alpha-beta T cell activation / Generation of second messenger molecules / TAP binding / Co-inhibition by PD-1 / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / response to bacterium / beta-2-microglobulin binding / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / positive regulation of T cell mediated cytotoxicity / secretory granule membrane / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / defense response / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / T cell receptor signaling pathway / late endosome membrane / Downstream TCR signaling / protein-folding chaperone binding / ER-Phagosome pathway / early endosome membrane / sequence-specific DNA binding / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / protein dimerization activity / immune response / DNA-binding transcription factor activity / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / signaling receptor binding / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / host cell nucleus / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface
Similarity search - Function
Trans-activator protein BZLF1, human herpesvirus 4 / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / : / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like ...Trans-activator protein BZLF1, human herpesvirus 4 / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / : / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / T cell receptor beta constant 2 / T cell receptor alpha chain constant / HLA class I histocompatibility antigen, B alpha chain / Lytic switch protein BZLF1 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsArchbold, J.K. / Tynan, F.E. / Gras, S. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Hard wiring of T cell receptor specificity for the major histocompatibility complex is underpinned by TCR adaptability
Authors: Burrows, S.R. / Chen, Z. / Archbold, J.K. / Tynan, F.E. / Beddoe, T. / Kjer-Nielsen, L. / Miles, J.J. / Khanna, R. / Moss, D.J. / Liu, Y.C. / Gras, S. / Kostenko, L. / Brennan, R.M. / ...Authors: Burrows, S.R. / Chen, Z. / Archbold, J.K. / Tynan, F.E. / Beddoe, T. / Kjer-Nielsen, L. / Miles, J.J. / Khanna, R. / Moss, D.J. / Liu, Y.C. / Gras, S. / Kostenko, L. / Brennan, R.M. / Clements, C.S. / Brooks, A.G. / Purcell, A.W. / McCluskey, J. / Rossjohn, J.
History
DepositionDec 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-35 alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, B-35 alpha chain
D: SB27 T cell receptor alpha chain
E: SB27 T cell receptor beta chain
F: Beta-2-microglobulin
G: SB27 T cell receptor alpha chain
H: SB27 T cell receptor beta chain
K: HLA class I histocompatibility antigen, B-35 alpha chain
L: Beta-2-microglobulin
N: SB27 T cell receptor alpha chain
P: SB27 T cell receptor beta chain
Q: peptide from Trans-activator protein BZLF1
R: peptide from Trans-activator protein BZLF1
T: peptide from Trans-activator protein BZLF1
I: HLA class I histocompatibility antigen, B-35 alpha chain
J: Beta-2-microglobulin
M: SB27 T cell receptor alpha chain
O: SB27 T cell receptor beta chain
S: peptide from Trans-activator protein BZLF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,87244
Polymers381,82720
Non-polymers3,04624
Water73941
1
A: HLA class I histocompatibility antigen, B-35 alpha chain
B: Beta-2-microglobulin
D: SB27 T cell receptor alpha chain
E: SB27 T cell receptor beta chain
Q: peptide from Trans-activator protein BZLF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,34512
Polymers95,4575
Non-polymers8887
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HLA class I histocompatibility antigen, B-35 alpha chain
F: Beta-2-microglobulin
G: SB27 T cell receptor alpha chain
H: SB27 T cell receptor beta chain
R: peptide from Trans-activator protein BZLF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,34512
Polymers95,4575
Non-polymers8887
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: HLA class I histocompatibility antigen, B-35 alpha chain
L: Beta-2-microglobulin
N: SB27 T cell receptor alpha chain
P: SB27 T cell receptor beta chain
T: peptide from Trans-activator protein BZLF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,09110
Polymers95,4575
Non-polymers6355
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: HLA class I histocompatibility antigen, B-35 alpha chain
J: Beta-2-microglobulin
M: SB27 T cell receptor alpha chain
O: SB27 T cell receptor beta chain
S: peptide from Trans-activator protein BZLF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,09110
Polymers95,4575
Non-polymers6355
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.690, 207.077, 123.512
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11C
21K
12G
22N
13O
23E
14A
24I
15M
25D
16H
26P

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYPROPRO4CC1 - 2761 - 276
211GLYGLYPROPRO4KI1 - 2761 - 276
112VALVALSERSER4GG3 - 2043 - 204
212VALVALSERSER4NK3 - 2043 - 204
113GLYGLYPHEPHE4OS3 - 901 - 88
213GLYGLYPHEPHE4EE3 - 901 - 88
123CYSCYSGLYGLY2OS91 - 10589 - 103
223CYSCYSGLYGLY2EE91 - 10589 - 103
133PHEPHEGLYGLY4OS120 - 240118 - 238
233PHEPHEGLYGLY4EE120 - 240118 - 238
114GLYGLYPROPRO4AA1 - 2761 - 276
214GLYGLYPROPRO4IP1 - 2761 - 276
115VALVALSERSER4MR3 - 2043 - 204
215VALVALSERSER4DD3 - 2043 - 204
116GLYGLYGLYGLY4HH3 - 2401 - 238
216GLYGLYGLYGLY4PL3 - 2401 - 238

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 2 types, 8 molecules ACKIBFLJ

#1: Protein
HLA class I histocompatibility antigen, B-35 alpha chain / MHC class I antigen B*35


Mass: 31840.152 Da / Num. of mol.: 4 / Fragment: residues in UNP 25-300 / Mutation: Q65A, T69A, Q155A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein
Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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SB27 T cell receptor ... , 2 types, 8 molecules DGNMEHPO

#3: Protein
SB27 T cell receptor alpha chain


Mass: 23251.533 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848*PLUS
#4: Protein
SB27 T cell receptor beta chain


Mass: 27190.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A5B9*PLUS

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Protein/peptide , 1 types, 4 molecules QRTS

#5: Protein/peptide
peptide from Trans-activator protein BZLF1 / EB1 / Protein zebra


Mass: 1426.612 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: synthetic peptide of naturally occurring viral peptide
References: UniProt: P03206

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Non-polymers , 2 types, 65 molecules

#6: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE 156TH IN CHAIN A,C,K,I IS VARIANT, B*3508. THE SEQUENCE DATABASE REFERENCE FOR CHAIN D,G,N,M ...THE 156TH IN CHAIN A,C,K,I IS VARIANT, B*3508. THE SEQUENCE DATABASE REFERENCE FOR CHAIN D,G,N,M AND CHAIN E,H,P,O DO NOT CURRENTLY EXIST.

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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: 2.64 Å3/Da / Density % sol: 53.33 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.7
Details: 0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2
DetectorDate: Mar 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→80 Å / Num. obs: 71533 / Redundancy: 5.1 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 3.1→3.2 Å / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→80 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.785 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 52.171 / SU ML: 0.463 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.582 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The file contains friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 3612 5.1 %RANDOM
Rwork0.213 ---
obs0.217 67602 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 154.8 Å2 / Biso mean: 24.944 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0.14 Å2
2--2.24 Å20 Å2
3----2.62 Å2
Refinement stepCycle: LAST / Resolution: 3.1→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26910 0 24 41 26975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02227677
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.93537658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75853318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53923.8961458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.133154405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.15615209
X-RAY DIFFRACTIONr_chiral_restr0.0710.23939
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0221825
X-RAY DIFFRACTIONr_nbd_refined0.1940.211342
X-RAY DIFFRACTIONr_nbtor_refined0.3020.218093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2938
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.214
X-RAY DIFFRACTIONr_mcbond_it0.619316757
X-RAY DIFFRACTIONr_mcangle_it1.198526986
X-RAY DIFFRACTIONr_scbond_it1.62712230
X-RAY DIFFRACTIONr_scangle_it2.7141010669
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C2246MEDIUM POSITIONAL0.580.5
1C2246MEDIUM THERMAL0.252
2G1616MEDIUM POSITIONAL0.620.5
2G1616MEDIUM THERMAL0.262
3O60TIGHT POSITIONAL0.030.05
3O1723MEDIUM POSITIONAL0.450.5
3O60TIGHT THERMAL0.040.5
3O1723MEDIUM THERMAL0.292
4A2238MEDIUM POSITIONAL0.510.5
4A2238MEDIUM THERMAL0.242
5M1619MEDIUM POSITIONAL0.650.5
5M1619MEDIUM THERMAL0.232
6H1885MEDIUM POSITIONAL0.50.5
6H1885MEDIUM THERMAL0.32
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 283 -
Rwork0.273 4966 -
all-5249 -
obs--99.83 %

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