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- PDB-4e41: Structural basis for the recognition of mutant self by a tumor-sp... -

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Basic information

Entry
Database: PDB / ID: 4.0E+41
TitleStructural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor G4
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • (T cell receptor G4 ...) x 2
  • Triosephosphate isomerase
KeywordsIMMUNE SYSTEM / Ig domain / adaptive immunity / T cell receptor / MHC
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / positive regulation of kinase activity / inflammatory response to antigenic stimulus / canonical glycolysis / Glycolysis / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / gluconeogenesis / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / glycolytic process / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / cell surface / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 / Aldolase-type TIM barrel / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain / Triosephosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDeng, L. / Langley, R.J. / Wang, Q. / Topalian, S.L. / Mariuzza, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor G4
Authors: Deng, L. / Langley, R.J. / Wang, Q. / Topalian, S.L. / Mariuzza, R.A.
History
DepositionMar 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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 II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: Triosephosphate isomerase
D: T cell receptor G4 alpha chain
E: T cell receptor G4 beta chain
F: HLA class II histocompatibility antigen, DR alpha chain
G: HLA class II histocompatibility antigen, DRB1-1 beta chain
H: Triosephosphate isomerase
I: T cell receptor G4 alpha chain
J: T cell receptor G4 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,13312
Polymers189,08710
Non-polymers462
Water3,099172
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: Triosephosphate isomerase
D: T cell receptor G4 alpha chain
E: T cell receptor G4 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5897
Polymers94,5435
Non-polymers462
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class II histocompatibility antigen, DR alpha chain
G: HLA class II histocompatibility antigen, DRB1-1 beta chain
H: Triosephosphate isomerase
I: T cell receptor G4 alpha chain
J: T cell receptor G4 beta chain


Theoretical massNumber of molelcules
Total (without water)94,5435
Polymers94,5435
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.133, 175.611, 88.646
Angle α, β, γ (deg.)90.00, 110.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

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HLA class II histocompatibility antigen, ... , 2 types, 4 molecules AFBG

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21155.904 Da / Num. of mol.: 2 / Fragment: unp residues 26-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR-1 / DR1


Mass: 22080.664 Da / Num. of mol.: 2 / Fragment: unp residues 30-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04229, UniProt: P01911*PLUS

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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide Triosephosphate isomerase / / TIM / Triose-phosphate isomerase


Mass: 1481.713 Da / Num. of mol.: 2 / Fragment: unp residues 60-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPI1, TPI / Production host: Escherichia coli (E. coli) / References: UniProt: P60174, triose-phosphate isomerase

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T cell receptor G4 ... , 2 types, 4 molecules DIEJ

#4: Protein T cell receptor G4 alpha chain


Mass: 22670.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein T cell receptor G4 beta chain


Mass: 27154.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 174 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 20% (wt/vol) polyethylene glycol 1000, 0.2 M calcium acetate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 53716 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.6 / % possible all: 83.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IAM

2iam


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.888 / SU B: 11.852 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26374 2704 5 %RANDOM
Rwork0.19743 ---
obs0.20076 51068 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.044 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å2-1.31 Å2
2---0.69 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12805 0 2 172 12979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213156
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.93717911
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.92251569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80423.988682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04152078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9721595
X-RAY DIFFRACTIONr_chiral_restr0.0940.21928
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210281
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.25407
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.28679
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2541
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6411.57931
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.227212872
X-RAY DIFFRACTIONr_scbond_it1.49135479
X-RAY DIFFRACTIONr_scangle_it2.5374.55039
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 163 -
Rwork0.273 3097 -
obs--80.75 %

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