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- PDB-4gg8: Immune Receptor -

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Basic information

Entry
Database: PDB / ID: 4gg8
TitleImmune Receptor
Components
  • T-CELL RECEPTOR, SP3.4 ALPHA CHAIN
  • T-CELL RECEPTOR, SP3.4 BETA CHAIN
KeywordsIMMUNE SYSTEM / IMMUNE RECEPTOR
Function / homology
Function and homology information


alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response ...alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / immune response / membrane / plasma membrane
Similarity search - Function
: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Mainly Beta
Similarity search - Domain/homology
sucrose / T-cell receptor, sp3.4 alpha chain / T cell receptor beta constant 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBroughton, S.E. / Theodossis, A. / Petersen, J. / Reid, H.H. / Rossjohn, J.
CitationJournal: Immunity / Year: 2012
Title: Biased T cell receptor usage directed against human leukocyte antigen DQ8-restricted gliadin peptides is associated with celiac disease.
Authors: Broughton, S.E. / Petersen, J. / Theodossis, A. / Scally, S.W. / Loh, K.L. / Thompson, A. / van Bergen, J. / Kooy-Winkelaar, Y. / Henderson, K.N. / Beddoe, T. / Tye-Din, J.A. / Mannering, S. ...Authors: Broughton, S.E. / Petersen, J. / Theodossis, A. / Scally, S.W. / Loh, K.L. / Thompson, A. / van Bergen, J. / Kooy-Winkelaar, Y. / Henderson, K.N. / Beddoe, T. / Tye-Din, J.A. / Mannering, S.I. / Purcell, A.W. / McCluskey, J. / Anderson, R.P. / Koning, F. / Reid, H.H. / Rossjohn, J.
History
DepositionAug 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 20, 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
E: T-CELL RECEPTOR, SP3.4 ALPHA CHAIN
F: T-CELL RECEPTOR, SP3.4 BETA CHAIN
B: T-CELL RECEPTOR, SP3.4 BETA CHAIN
A: T-CELL RECEPTOR, SP3.4 ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8806
Polymers101,1964
Non-polymers6852
Water00
1
E: T-CELL RECEPTOR, SP3.4 ALPHA CHAIN
F: T-CELL RECEPTOR, SP3.4 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9403
Polymers50,5982
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-24 kcal/mol
Surface area19990 Å2
MethodPISA
2
B: T-CELL RECEPTOR, SP3.4 BETA CHAIN
A: T-CELL RECEPTOR, SP3.4 ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9403
Polymers50,5982
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-23 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.562, 124.562, 61.098
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21A
12F
22B
13E
23A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112E3 - 202
2112A3 - 202
1122F1 - 244
2122B1 - 244
1134E - C301
2134A - D301

NCS ensembles :
ID
1
2
3

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Components

#1: Protein T-CELL RECEPTOR, SP3.4 ALPHA CHAIN


Mass: 23039.484 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS / Mutation: T160C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K7N5N2*PLUS
#2: Protein T-CELL RECEPTOR, SP3.4 BETA CHAIN


Mass: 27558.459 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS / Mutation: S172C, C190A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850*PLUS
#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
Has protein modificationY
Sequence detailsTHE SEQUENCES OF THESE PROTEINS WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCES OF THESE PROTEINS WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. ACCORDING TO AUTHOR, RESIDUE 176 (T176C) IN ENTITY 1 AND RESIDUES 184 (S184C) AND 202 (C202A) IN ENTITY 2 ARE ENGINEERED MUTATIONS.

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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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.8M SODIUM FORMATE, 0.1M TRIS PH 7.5, 5% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956591 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956591 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 15462 / % possible obs: 87.2 % / Redundancy: 2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.2 / % possible all: 89.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GG6

4gg6


Resolution: 3.2→30.99 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.815 / SU B: 79.502 / SU ML: 0.564 / Cross valid method: THROUGHOUT / ESU R Free: 0.732 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1507 10.1 %RANDOM
Rwork0.261 ---
obs0.265 13354 84.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å2-0.89 Å2-0 Å2
2---1.78 Å20 Å2
3---2.67 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6107 0 46 0 6153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0216315
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.9388663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47524.091264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.62915782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9091527
X-RAY DIFFRACTIONr_chiral_restr0.0690.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214911
X-RAY DIFFRACTIONr_mcbond_it0.1521.54168
X-RAY DIFFRACTIONr_mcangle_it0.31126557
X-RAY DIFFRACTIONr_scbond_it0.51332147
X-RAY DIFFRACTIONr_scangle_it0.8954.52106
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1E696tight positional0.010.05
2F976tight positional0.010.05
1E546medium positional0.010.5
2F810medium positional0.020.5
3E23medium positional0.120.5
1E696tight thermal0.020.5
2F976tight thermal0.020.5
1E546medium thermal0.022
2F810medium thermal0.022
3E23medium thermal0.192
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 144 -
Rwork0.275 1019 -
obs--89.26 %
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)
13.95160.87621.92557.3375-2.69158.665-0.14990.097-0.19780.24410.2685-0.3963-0.3006-0.1115-0.11850.02960.00370.02220.0913-0.00290.09423.90614.549-8.069
22.08692.98731.37345.08841.19635.13630.30770.155-0.55160.968-0.2474-1.39770.02741.0474-0.06030.5055-0.1238-0.4430.7340.10580.862235.506-12.37.872
33.9501-4.48660.391510.3749-1.92563.17610.5140.4047-0.0691-0.5257-0.4173-0.26640.248-0.0323-0.09670.1912-0.08770.02660.2163-0.07450.064818.6980.282-26.606
42.2876-0.693-0.93783.58832.78629.83640.1530.17960.12020.413-0.0277-0.52190.41490.4749-0.12520.1385-0.0048-0.03470.0793-0.03760.302823.749-19.731-3.764
56.2414-0.9543-0.40364.26183.18727.87960.1286-0.0645-0.36190.0247-0.1089-0.120.0083-0.034-0.01980.0221-0.02490.01180.04660.0130.10437.69722.5633.76
68.0937-0.65943.23860.111-0.54443.3260.22350.8904-1.558-0.0398-0.02370.12520.6617-0.2036-0.19990.7015-0.159-0.00170.5169-0.35640.764455.114-0.909-12.251
74.074-3.9532-0.036410.22430.97153.2439-0.1953-0.0438-0.19660.75830.20460.01240.10130.225-0.00940.0789-0.0442-0.01940.22580.05030.040252.60220.07222.41
82.1501-0.97292.19023.2291-2.64859.90190.30470.2856-0.38810.1426-0.1960.27150.67230.1468-0.10880.11530.0282-0.03430.1327-0.06750.298867.3895.52-0.405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E3 - 113
2X-RAY DIFFRACTION1E301
3X-RAY DIFFRACTION2E114 - 202
4X-RAY DIFFRACTION3F1 - 117
5X-RAY DIFFRACTION4F118 - 244
6X-RAY DIFFRACTION5A3 - 113
7X-RAY DIFFRACTION5A301
8X-RAY DIFFRACTION6A114 - 202
9X-RAY DIFFRACTION7B1 - 117
10X-RAY DIFFRACTION8B118 - 244

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