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- PDB-4p57: MHC TCR peptide complex -

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Basic information

Entry
Database: PDB / ID: 4p57
TitleMHC TCR peptide complex
Components
  • HLA class II histocompatibility antigen, DP alpha 1 chain
  • mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain
KeywordsIMMUNE SYSTEM / MHC TCR peptide Be2+ complex / Berylliosis
Function / homology
Function and homology information


MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / PD-1 signaling / positive regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane ...MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / PD-1 signaling / positive regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cellular response to type II interferon / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of type II interferon production / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / adaptive immune response / endosome membrane / immune response / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / cell surface / membrane / plasma membrane
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 / 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 ...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
HLA class II histocompatibility antigen, DP beta 1 chain / HLA class II histocompatibility antigen, DP alpha 1 chain / HLA class II histocompatibility antigen DP beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsClayton, G.M. / Crawford, F. / Kappler, J.W.
CitationJournal: Cell / Year: 2014
Title: Structural basis of chronic beryllium disease: linking allergic hypersensitivity and autoimmunity.
Authors: Clayton, G.M. / Wang, Y. / Crawford, F. / Novikov, A. / Wimberly, B.T. / Kieft, J.S. / Falta, M.T. / Bowerman, N.A. / Marrack, P. / Fontenot, A.P. / Dai, S. / Kappler, J.W.
History
DepositionMar 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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, DP alpha 1 chain
B: mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain
C: HLA class II histocompatibility antigen, DP alpha 1 chain
D: mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,40612
Polymers91,1284
Non-polymers1,2788
Water4,918273
1
A: HLA class II histocompatibility antigen, DP alpha 1 chain
B: mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3607
Polymers45,5642
Non-polymers7965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-26 kcal/mol
Surface area18310 Å2
MethodPISA
2
C: HLA class II histocompatibility antigen, DP alpha 1 chain
D: mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0465
Polymers45,5642
Non-polymers4823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-29 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.392, 102.392, 234.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein HLA class II histocompatibility antigen, DP alpha 1 chain / DP(W3) / DP(W4) / HLA-SB alpha chain / MHC class II DP3-alpha / MHC class II DPA1


Mass: 21169.566 Da / Num. of mol.: 2 / Fragment: UNP residues 32-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DPA1, HLA-DP1A, HLASB / Production host: unidentified baculovirus / References: UniProt: P20036
#2: Protein mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain / HLA class II histocompatibility antigen / DP(W2) beta chain / MHC class II antigen DPB1


Mass: 24394.219 Da / Num. of mol.: 2 / Fragment: UNP residues 32-218 / Mutation: E69K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DPB1, HLA-DP1B / Production host: unidentified baculovirus / References: UniProt: Q5EP54, UniProt: P04440*PLUS

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Sugars , 1 types, 5 molecules

#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / 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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Non-polymers , 3 types, 276 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ca acetate, tris, PEG300

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→90 Å / Num. obs: 37601 / % possible obs: 93.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 60.87 Å2 / Net I/σ(I): 10

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 2.6→77.1 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.429 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.266
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1891 5.03 %RANDOM
Rwork0.208 ---
obs0.21 37601 95.8 %-
Displacement parametersBiso mean: 44.56 Å2
Baniso -1Baniso -2Baniso -3
1-6.0235 Å20 Å20 Å2
2--6.0235 Å20 Å2
3----12.0471 Å2
Refine analyzeLuzzati coordinate error obs: 0.345 Å
Refinement stepCycle: 1 / Resolution: 2.6→77.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6022 0 78 274 6374
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016284HARMONIC1.5
X-RAY DIFFRACTIONt_angle_deg1.358578HARMONIC1.5
X-RAY DIFFRACTIONt_dihedral_angle_d2072SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes181HARMONIC2
X-RAY DIFFRACTIONt_gen_planes913HARMONIC5
X-RAY DIFFRACTIONt_it6284HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion21.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion806SEMIHARMONIC5
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_contact6689SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2993 152 5.34 %
Rwork0.2572 2692 -
all0.2596 2844 -
obs--95.82 %

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