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- PDB-4p5k: Structural Basis of Chronic Beryllium Disease: Bridging the Gap B... -

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Basic information

Entry
Database: PDB / ID: 4p5k
TitleStructural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergy and Autoimmunity
Components
  • HLA class II histocompatibility antigen, DP alpha 1 chain
  • RAS peptide,HLA class II histocompatibility antigen, DP beta 1 chain
KeywordsIMMUNE SYSTEM / MHC / TCR / complex / HLA / Chronic Beryllium Disease / allergy / autoimmunity
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 Å
AuthorsClayton, 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. ...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.
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 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: RAS peptide,HLA class II histocompatibility antigen, DP beta 1 chain
D: HLA class II histocompatibility antigen, DP alpha 1 chain
E: RAS peptide,HLA class II histocompatibility antigen, DP beta 1 chain


Theoretical massNumber of molelcules
Total (without water)91,1814
Polymers91,1814
Non-polymers00
Water00
1
A: HLA class II histocompatibility antigen, DP alpha 1 chain
B: RAS peptide,HLA class II histocompatibility antigen, DP beta 1 chain


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers45,5912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-28 kcal/mol
Surface area18910 Å2
MethodPISA
2
D: HLA class II histocompatibility antigen, DP alpha 1 chain
E: RAS peptide,HLA class II histocompatibility antigen, DP beta 1 chain


Theoretical massNumber of molelcules
Total (without water)45,5912
Polymers45,5912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-29 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.779, 68.738, 71.133
Angle α, β, γ (deg.)90.000, 105.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

#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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20036
#2: Protein RAS peptide,HLA class II histocompatibility antigen, DP beta 1 chain


Mass: 24421.178 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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5EP54, UniProt: P04440*PLUS

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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: 49.36 %
Crystal growTemperature: 316 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.2 M ammonium formate and 25 % PEG 4000 in 0.1 M HEPES buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.99
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 26282 / % possible obs: 92.6 % / Redundancy: 3.1 % / Net I/σ(I): 18.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→44.62 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.875 / SU B: 33.305 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1243 5.1 %RANDOM
Rwork0.2213 23043 --
obs0.2245 24286 91.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 92.56 Å2 / Biso mean: 31.144 Å2 / Biso min: 7 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.04 Å2
2--0.09 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.59→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6222 0 1 0 6223
Biso mean--79.63 --
Num. residues----758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226400
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9288706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5995750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09724.444360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.84151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3781538
X-RAY DIFFRACTIONr_chiral_restr0.1130.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215080
X-RAY DIFFRACTIONr_mcbond_it0.6091.53784
X-RAY DIFFRACTIONr_mcangle_it1.18526146
X-RAY DIFFRACTIONr_scbond_it1.73232616
X-RAY DIFFRACTIONr_scangle_it2.8994.52560
LS refinement shellResolution: 2.591→2.658 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 39 -
Rwork0.311 724 -
all-763 -
obs--39.25 %
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)
11.991-1.0432-0.38881.7754-0.25810.90570.0285-0.01640.0348-0.061-0.18270.05540.0653-0.0390.15420.06560.01210.00090.1976-0.02050.087222.054-30.4426-18.1314
21.57080.2573-0.92783.41390.71391.50960.0621-0.4779-0.05030.2191-0.139-0.1742-0.0230.40110.07690.0439-0.0553-0.06340.25750.10050.109232.8812-28.1655-5.3167
31.84510.90590.09312.3842-0.24520.2289-0.0724-0.02940.01220.06540.07180.18960.0462-0.08980.00060.1006-0.01450.00210.16180.00580.091731.2423-2.1799-39.9001
41.039-0.5823-0.34343.52250.61041.319-0.14880.08220.0640.05490.1521-0.06650.16160.1901-0.00330.03610.0026-0.01690.11160.03050.043845.9597-2.2451-47.5694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 181
2X-RAY DIFFRACTION2B3 - 189
3X-RAY DIFFRACTION3D1 - 181
4X-RAY DIFFRACTION4E3 - 189

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