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- PDB-3ffc: Crystal Structure of CF34 TCR in complex with HLA-B8/FLR -

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Basic information

Entry
Database: PDB / ID: 3ffc
TitleCrystal Structure of CF34 TCR in complex with HLA-B8/FLR
Components
  • Beta-2-microglobulin
  • CF34 alpha chain
  • CF34 beta chain
  • FLRGRAYGL peptide from an EBV protein
  • HLA class I histocompatibility antigen, B-8 alpha chain
KeywordsIMMUNE SYSTEM / TCR-peptide-MHC / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / alpha-beta T cell receptor complex / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / TAP binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / alpha-beta T cell receptor complex / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / TAP binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / 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 / detection of bacterium / : / : / secretory granule membrane / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / defense response / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / Interferon alpha/beta signaling / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / Downstream TCR signaling / T cell receptor signaling pathway / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome
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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like ...: / 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
: / T cell receptor beta constant 1 / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsGras, S. / Burrows, S.R. / Kjer-Nielsen, L. / Clements, C.S. / Liu, Y.C. / Sullivan, L.C. / Brooks, A.G. / Purcell, A.W. / McCluskey, J. / Rossjohn, J.
CitationJournal: Immunity / Year: 2009
Title: The shaping of T cell receptor recognition by self-tolerance.
Authors: Gras, S. / Burrows, S.R. / Kjer-Nielsen, L. / Clements, C.S. / Liu, Y.C. / Sullivan, L.C. / Bell, M.J. / Brooks, A.G. / Purcell, A.W. / McCluskey, J. / Rossjohn, J.
History
DepositionDec 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 9, 2013Group: Derived calculations
Revision 1.3Nov 13, 2019Group: Data collection / Database references / Source and taxonomy
Category: pdbx_entity_src_syn / reflns / struct_ref_seq_dif
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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-8 alpha chain
B: Beta-2-microglobulin
C: FLRGRAYGL peptide from an EBV protein
D: CF34 alpha chain
E: CF34 beta chain
F: HLA class I histocompatibility antigen, B-8 alpha chain
G: Beta-2-microglobulin
H: FLRGRAYGL peptide from an EBV protein
I: CF34 alpha chain
J: CF34 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,37741
Polymers190,63310
Non-polymers1,74431
Water543
1
A: HLA class I histocompatibility antigen, B-8 alpha chain
B: Beta-2-microglobulin
C: FLRGRAYGL peptide from an EBV protein
D: CF34 alpha chain
E: CF34 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,22922
Polymers95,3175
Non-polymers91317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, B-8 alpha chain
G: Beta-2-microglobulin
H: FLRGRAYGL peptide from an EBV protein
I: CF34 alpha chain
J: CF34 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,14819
Polymers95,3175
Non-polymers83114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.564, 171.807, 272.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11D-213-

NA

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12B
22G
13D
23I
14E
24J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1112AA1 - 401 - 40
2112FF1 - 401 - 40
1212AA45 - 18045 - 180
2212FF45 - 18045 - 180
1314AA181 - 277181 - 277
2314FF181 - 277181 - 277
1122BB1 - 991 - 99
2122GG1 - 991 - 99
1132DD3 - 1233 - 123
2132II3 - 1233 - 123
1232DD132 - 216132 - 216
2232II132 - 216132 - 216
1142EE2 - 1312 - 131
2142JJ2 - 1312 - 131
1242EE136 - 260136 - 260
2242JJ136 - 260136 - 260

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

#1: Protein HLA class I histocompatibility antigen, B-8 alpha chain / MHC class I antigen B*8


Mass: 32015.055 Da / Num. of mol.: 2
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: P30460, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


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: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein CF34 alpha chain


Mass: 22551.844 Da / Num. of mol.: 2
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 CF34 beta chain


Mass: 27816.137 Da / Num. of mol.: 2
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) / References: UniProt: P01850*PLUS

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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide FLRGRAYGL peptide from an EBV protein


Mass: 1054.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 34 molecules

#6: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsIN CHAINS D, E, I, J, RESIDUE NUMBERS ARE SIMPLY SKIPPED

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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: 3.43 Å3/Da / Density % sol: 64.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 11% PEG 20000, 0.2M LiSO4, 0.1M Tris, 6mM CdCl, 4% ethylene glycol, 4% dioxane, pH 8.4, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→72.739 Å / Num. obs: 72044 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.0335 / Rsym value: 0.335 / Net I/σ(I): 1.889
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.857.50.677950104111.314100
2.85-3.027.50.87376598620.913100
3.02-3.237.51.26964892990.599100
3.23-3.497.51.76485186720.405100
3.49-3.827.42.15925479640.32100
3.82-4.277.42.45359572840.254100
4.27-4.937.22.84635164020.216100
4.93-6.047.22.83927954620.213100
6.04-8.546.932990743070.197100
8.54-72.7463.21427623810.16997.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MI5

1mi5


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.872 / SU B: 24.534 / SU ML: 0.27 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.878 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26779 3232 5 %RANDOM
Rwork0.22073 ---
obs0.2231 61005 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.008 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å20 Å20 Å2
2---4.2 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13425 0 31 3 13459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02213857
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.93518840
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75551671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33623.978724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.451152234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.14415103
X-RAY DIFFRACTIONr_chiral_restr0.0910.21959
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210927
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.26100
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.29216
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2502
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.290.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0280.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5841.58370
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.082213532
X-RAY DIFFRACTIONr_scbond_it0.95435757
X-RAY DIFFRACTIONr_scangle_it1.6414.55308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A696tight positional0.030.05
2B392tight positional0.060.05
3D768tight positional0.030.05
4E968tight positional0.030.05
1A1506medium positional0.460.5
2B426medium positional0.490.5
3D725medium positional0.480.5
4E954medium positional0.40.5
1A696tight thermal0.060.5
2B392tight thermal0.060.5
3D768tight thermal0.320.5
4E968tight thermal0.060.5
1A1506medium thermal0.372
2B426medium thermal0.392
3D725medium thermal0.382
4E954medium thermal0.352
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 224 -
Rwork0.366 4304 -
obs--100 %
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)
10.00150.0099-0.01590.2898-0.1740.1874-0.00920.00970.0171-0.0035-0.0253-0.08590.0282-0.00750.03460.0041-0.01060.00110.0040.01440.0335-33.32762.4527-67.8006
20.11360.03350.01362.30090.85610.3910.0266-0.02350.01990.0211-0.09520.0656-0.0237-0.04810.0687000000-38.22272.4807-67.7496
30.0033-0.03190.02840.81950.30510.9180.00840.03340.00690.01140.0323-0.0603-0.0807-0.0267-0.040800.000100-0.0003-0.0001-38.62821.3006-67.9779
40.01490.01570.04640.5004-0.52331.10150.02990.00370.00840.0254-0.0525-0.2338-0.03150.12910.0226000000-11.4362.3013-68.6181
50.01450.0080.00232.0457-2.16992.46570.086-0.0009-0.05880.112-0.1364-0.3382-0.12390.25980.05030000001.33222.04-69.4192
60.04590.0512-0.04620.6379-0.40950.3387-0.0046-0.0014-0.00220.02-0.0233-0.1102-0.01830.01140.02790.0001-0.00320.0029-0.0040.0104-0.0049-21.96782.442-68.3553
70.01990.0137-0.03231.0486-0.60090.3771-0.0398-0.0045-0.0098-0.0046-0.0344-0.27760.00420.00050.0742-0.00010.0061-0.0043-0.00020.00010-13.2532.2232-68.9211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1F1 - 180
3X-RAY DIFFRACTION2A181 - 277
4X-RAY DIFFRACTION2F181 - 276
5X-RAY DIFFRACTION3B1 - 99
6X-RAY DIFFRACTION3H1 - 9
7X-RAY DIFFRACTION4D3 - 111
8X-RAY DIFFRACTION4I3 - 111
9X-RAY DIFFRACTION5D120 - 204
10X-RAY DIFFRACTION5I120 - 204
11X-RAY DIFFRACTION6E2 - 120
12X-RAY DIFFRACTION6J2 - 120
13X-RAY DIFFRACTION7E121 - 248
14X-RAY DIFFRACTION7J121 - 248

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