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- PDB-2p24: I-Au/MBP125-135 -

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Basic information

Entry
Database: PDB / ID: 2p24
TitleI-Au/MBP125-135
Components
  • H-2 class II histocompatibility antigen, A-U alpha chain
  • H-2 class II histocompatibility antigen, A-U beta chain
KeywordsIMMUNE SYSTEM / MHC / I-Au / immunoglobulin fold / MBP
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / 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 / positive regulation of immune response ...antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / 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 / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / early endosome / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / Golgi apparatus / cell surface / 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
H-2 class II histocompatibility antigen, A-U beta chain / H-2 class II histocompatibility antigen, A-U alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMcBeth, C. / Strong, R.K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: A new twist in TCR diversity revealed by a forbidden alphabeta TCR.
Authors: McBeth, C. / Seamons, A. / Pizarro, J.C. / Fleishman, S.J. / Baker, D. / Kortemme, T. / Goverman, J.M. / Strong, R.K.
History
DepositionMar 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 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_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999sequence Chain B contains MHC beta chain with peptide. The peptide is cloned in-frame with the beta ...sequence Chain B contains MHC beta chain with peptide. The peptide is cloned in-frame with the beta chain, and is attached from the c-terminus of the peptide to the n-terminus of the beta chain.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class II histocompatibility antigen, A-U alpha chain
B: H-2 class II histocompatibility antigen, A-U beta chain


Theoretical massNumber of molelcules
Total (without water)56,0982
Polymers56,0982
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-28 kcal/mol
Surface area17250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.656, 103.656, 97.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

21B-385-

HOH

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Components

#1: Protein H-2 class II histocompatibility antigen, A-U alpha chain


Mass: 26426.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P14438
#2: Protein H-2 class II histocompatibility antigen, A-U beta chain


Mass: 29671.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: I-Au / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P06344
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M NaOAc, 25% (w/v) PEG 1000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 28, 2006
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→46.4 Å / Num. obs: 29462 / % possible obs: 99.9 % / Redundancy: 13.8 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 18.7
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 5.99 / Num. unique all: 2879

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K2D

1k2d


Resolution: 2.15→46.37 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.988 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25996 1456 4.9 %RANDOM
Rwork0.20878 ---
obs0.21138 27960 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.293 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati sigma a0.133 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.15→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 0 206 3203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223083
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.9354208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6585372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00223.742155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54315456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0621519
X-RAY DIFFRACTIONr_chiral_restr0.1350.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022423
X-RAY DIFFRACTIONr_nbd_refined0.2070.21253
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22018
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.26
X-RAY DIFFRACTIONr_mcbond_it1.7661.51930
X-RAY DIFFRACTIONr_mcangle_it2.22223030
X-RAY DIFFRACTIONr_scbond_it3.32131358
X-RAY DIFFRACTIONr_scangle_it4.7764.51178
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 93 -
Rwork0.218 2036 -
obs--99.25 %

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