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- PDB-4z7u: S13 complex -

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Basic information

Entry
Database: PDB / ID: 4z7u
TitleS13 complex
Components
  • (MHC class II HLA-DQ- ...) x 2
  • (T-CELL RECEPTOR, S13 ...) x 2
  • deamidated DQ8-glia-alpha1 peptide
KeywordsIMMUNE SYSTEM / IMMUNE RECEPTOR-LIGAND COMPLEX
Function / homology
Function and homology information


nutrient reservoir activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane
Similarity search - Function
Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain 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 ...Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain 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 / 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 / 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
MHC class II HLA-DQ-beta-1 / Alpha/beta-gliadin MM1 / MHC class II HLA-DQ-alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPetersen, J. / Rossjohn, J. / Reid, H.H. / Koning, F.
CitationJournal: J Immunol. / Year: 2015
Title: Determinants of Gliadin-Specific T Cell Selection in Celiac Disease.
Authors: Petersen, J. / van Bergen, J. / Loh, K.L. / Kooy-Winkelaar, Y. / Beringer, D.X. / Thompson, A. / Bakker, S.F. / Mulder, C.J. / Ladell, K. / McLaren, J.E. / Price, D.A. / Rossjohn, J. / Reid, H.H. / Koning, F.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / entity / entity_src_gen / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class II HLA-DQ-alpha chain
B: MHC class II HLA-DQ-beta-1
C: MHC class II HLA-DQ-alpha chain
D: MHC class II HLA-DQ-beta-1
E: T-CELL RECEPTOR, S13 ALPHA CHAIN
F: T-CELL RECEPTOR, S13 BETA CHAIN
G: T-CELL RECEPTOR, S13 ALPHA CHAIN
H: T-CELL RECEPTOR, S13 BETA CHAIN
I: deamidated DQ8-glia-alpha1 peptide
J: deamidated DQ8-glia-alpha1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,81714
Polymers196,94110
Non-polymers1,8764
Water4,738263
1
A: MHC class II HLA-DQ-alpha chain
B: MHC class II HLA-DQ-beta-1
G: T-CELL RECEPTOR, S13 ALPHA CHAIN
H: T-CELL RECEPTOR, S13 BETA CHAIN
J: deamidated DQ8-glia-alpha1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4097
Polymers98,4715
Non-polymers9382
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MHC class II HLA-DQ-alpha chain
D: MHC class II HLA-DQ-beta-1
E: T-CELL RECEPTOR, S13 ALPHA CHAIN
F: T-CELL RECEPTOR, S13 BETA CHAIN
I: deamidated DQ8-glia-alpha1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4097
Polymers98,4715
Non-polymers9382
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.454, 123.813, 223.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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MHC class II HLA-DQ- ... , 2 types, 4 molecules ACBD

#1: Protein MHC class II HLA-DQ-alpha chain


Mass: 21882.221 Da / Num. of mol.: 2 / Fragment: UNP residues 1-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q30069
#2: Protein MHC class II HLA-DQ-beta-1


Mass: 24484.211 Da / Num. of mol.: 2 / Fragment: UNP residues 1-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O19707

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T-CELL RECEPTOR, S13 ... , 2 types, 4 molecules EGFH

#3: Protein T-CELL RECEPTOR, S13 ALPHA CHAIN /


Mass: 22750.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#4: Protein T-CELL RECEPTOR, S13 BETA CHAIN /


Mass: 27550.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21

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Protein/peptide / Non-polymers , 2 types, 265 molecules IJ

#5: Protein/peptide deamidated DQ8-glia-alpha1 peptide


Mass: 1803.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P18573*PLUS
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 4 molecules

#6: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 140 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 7.5, 15% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→39.53 Å / Num. obs: 60719 / % possible obs: 94.41 % / Redundancy: 4.1 % / Biso Wilson estimate: 66.7 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.5
Reflection shellResolution: 2.7→2.797 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.3 / % possible all: 87.19

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GG8

4gg8


Resolution: 2.7→39.53 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9196 / SU R Cruickshank DPI: 0.609 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.601 / SU Rfree Blow DPI: 0.276 / SU Rfree Cruickshank DPI: 0.281
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 3020 4.97 %RANDOM
Rwork0.1778 ---
obs0.1799 60705 94.43 %-
Displacement parametersBiso mean: 67.59 Å2
Baniso -1Baniso -2Baniso -3
1--5.1563 Å20 Å20 Å2
2---5.8522 Å20 Å2
3---11.0085 Å2
Refine analyzeLuzzati coordinate error obs: 0.382 Å
Refinement stepCycle: 1 / Resolution: 2.7→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12689 0 124 263 13076
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113171HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1518011HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5861SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes330HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1916HARMONIC5
X-RAY DIFFRACTIONt_it13171HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion3.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1767SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14083SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2982 196 4.79 %
Rwork0.2142 3892 -
all0.2182 4088 -
obs--94.43 %
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)
12.2307-0.4234-0.11881.8728-0.78622.0913-0.01770.47730.4259-0.52530.06150.30430.0714-0.8084-0.0438-0.2058-0.0343-0.13490.2456-0.0165-0.246786.15745.1441120.922
21.9299-0.7110.45292.4819-0.45352.0222-0.0941-0.15460.12480.00210.12120.53540.1208-1.2342-0.0271-0.5026-0.0393-0.00160.4791-0.0955-0.296277.224244.4851134.828
32.4253-1.19050.68910.9986-1.02742.02450.2250.7280.1472-0.3547-0.1660.12560.2065-0.2052-0.059-0.12270.0665-0.0970.2306-0.0424-0.267244.708232.48329.2854
42.7424-1.22960.56622.495-0.9923.18620.08950.1294-0.0948-0.02690.27560.35970.0058-1.044-0.3651-0.37720.0133-0.01520.20920.0115-0.343635.426331.924823.0802
53.4321-0.9971.09471.1943-0.3591.2123-0.0548-0.0937-0.233-0.035-0.0234-0.25110.1356-0.0130.0783-0.0290.01130.0545-0.07240.0024-0.098881.109314.386152.3965
63.7815-1.78342.51591.6798-1.24851.82150.35651.0049-0.3251-0.3815-0.4604-0.32530.42880.57820.1039-0.08580.21870.12120.0680.0183-0.191488.91638.331135.7182
73.1633-0.23940.74290.74030.03781.3932-0.1499-0.2479-0.27380.05250.01-0.3210.028-0.07660.1399-0.0803-0.01240.0591-0.03720.0103-0.0836123.06629.3543164.408
82.7628-0.64741.70350.9941-0.28011.8930.03140.2074-0.3515-0.1791-0.0393-0.44230.23270.07290.0079-0.10140.00080.133-0.16420.00880.0304131.21123.4227147.599
95.688-7.0253-4.31201.93493.27520.0650.34720.0473-0.15980.0482-0.04660.21280.0054-0.11320.11330.0495-0.07670.076-0.1365-0.243954.186219.624.9951
103.7014-2.5464-1.8380-0.87465.7589-0.04490.01920.2843-0.18680.0771-0.04680.3558-0.3031-0.0323-0.0495-0.0936-0.02330.1601-0.1175-0.222496.342434.3483137.481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }

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