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- PDB-4p4k: Structural Basis of Chronic Beryllium Disease: Bridging the Gap B... -

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Basic information

Entry
Database: PDB / ID: 4p4k
TitleStructural Basis of Chronic Beryllium Disease: Bridging the Gap Between allergic hypersensitivity and auto immunity
Components
  • HLA class II histocompatibility antigen, DP alpha 1 chain
  • hTCRav22 alpha chain
  • hTCRav22 beta chain
  • mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain
KeywordsIMMUNE SYSTEM / Be bound complex / Chronic beryllium disease / TCR-MHC peptide-Be2+
Function / homology
Function and homology information


MHC class II receptor activity / alpha-beta T cell receptor complex / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / positive regulation of T cell proliferation / MHC class II antigen presentation ...MHC class II receptor activity / alpha-beta T cell receptor complex / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / 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 / response to bacterium / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class II protein complex / cellular response to type II interferon / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / positive regulation of type II interferon production / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / adaptive immune response / immune response / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / cell surface / membrane / plasma membrane
Similarity search - Function
T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / 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 ...T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / 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
BERYLLIUM / T cell receptor beta constant 2 / T cell receptor alpha chain constant / HLA class II histocompatibility antigen, DP beta 1 chain / HLA class II histocompatibility antigen, DP alpha 1 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 12, 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_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: hTCRav22 alpha chain
D: hTCRav22 beta chain
E: HLA class II histocompatibility antigen, DP alpha 1 chain
F: mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain
G: hTCRav22 alpha chain
H: hTCRav22 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,82117
Polymers191,6518
Non-polymers1,1709
Water5,945330
1
A: HLA class II histocompatibility antigen, DP alpha 1 chain
B: mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain
C: hTCRav22 alpha chain
D: hTCRav22 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5219
Polymers95,8254
Non-polymers6965
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12790 Å2
ΔGint-61 kcal/mol
Surface area36580 Å2
MethodPISA
2
E: HLA class II histocompatibility antigen, DP alpha 1 chain
F: mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain
G: hTCRav22 alpha chain
H: hTCRav22 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3008
Polymers95,8254
Non-polymers4744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12650 Å2
ΔGint-59 kcal/mol
Surface area36220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.400, 137.240, 213.130
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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Protein , 4 types, 8 molecules AEBFCGDH

#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 / Strain (production host): Bti Tn 5b1 4 / References: UniProt: P20036
#2: Protein mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain / HLA class II histocompatibility antigen / DP(W4) beta chain / MHC class II antigen DPB1


Mass: 24394.152 Da / Num. of mol.: 2 / Fragment: UNP residues 32-218
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: P04440
#3: Protein hTCRav22 alpha chain


Mass: 22995.461 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) / References: UniProt: P01848*PLUS
#4: Protein hTCRav22 beta chain


Mass: 27266.291 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) / References: UniProt: A0A5B9*PLUS

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Sugars , 1 types, 5 molecules

#5: 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.: 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, 334 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-0BE / BERYLLIUM / Beryllium


Mass: 9.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Be
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG8K, Na Cacodylate, glycerol / PH range: 5.5-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 58169 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 78.7 Å2 / Net I/σ(I): 15.67

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LQZ

3lqz


Resolution: 2.8→39.7 Å / Cor.coef. Fo:Fc: 0.9299 / Cor.coef. Fo:Fc free: 0.8869 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.959 / SU Rfree Blow DPI: 0.332 / SU Rfree Cruickshank DPI: 0.336
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 2949 5.07 %RANDOM
Rwork0.204 ---
obs0.2064 58168 99.97 %-
Displacement parametersBiso mean: 59.53 Å2
Baniso -1Baniso -2Baniso -3
1--5.9083 Å20 Å20 Å2
2--0.819 Å20 Å2
3---5.0893 Å2
Refine analyzeLuzzati coordinate error obs: 0.364 Å
Refinement stepCycle: 1 / Resolution: 2.8→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12873 0 74 330 13277
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113314HARMONIC1.5
X-RAY DIFFRACTIONt_angle_deg1.3918175HARMONIC1.5
X-RAY DIFFRACTIONt_dihedral_angle_d4349SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes354HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1954HARMONIC5
X-RAY DIFFRACTIONt_it13314HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1725SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance10HARMONIC1
X-RAY DIFFRACTIONt_utility_angle12HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14914SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3123 221 5.23 %
Rwork0.2461 4006 -
all0.2496 4227 -
obs--99.97 %

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