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- PDB-3c5z: Crystal structure of mouse MHC class II I-Ab/3K peptide complexed... -

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Basic information

Entry
Database: PDB / ID: 3c5z
TitleCrystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR B3K506
Components
  • 3K peptide, Linker, and H-2 class II histocompatibility antigen (A beta chain)
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • TCR B3K506 Alpha Chain
  • TCR B3K506 Beta Chain
KeywordsSUGAR BINDING PROTEIN/IMMUNE SYSTEM / TCR-pMHC complex / Glycoprotein / Immune response / Membrane / MHC II / Transmembrane / SUGAR BINDING PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / antigen processing and presentation / response to type II interferon / toxic substance binding ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / antigen processing and presentation / response to type II interferon / toxic substance binding / multivesicular body / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / cellular response to type II interferon / adaptive immune response / early endosome / lysosome / immune response / external side of plasma membrane / ubiquitin protein ligase binding / Golgi apparatus / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsDai, S. / Kappler, J.
CitationJournal: Immunity / Year: 2008
Title: Crossreactive T Cells spotlight the germline rules for alphabeta T cell-receptor interactions with MHC molecules.
Authors: Dai, S. / Huseby, E.S. / Rubtsova, K. / Scott-Browne, J. / Crawford, F. / Macdonald, W.A. / Marrack, P. / Kappler, J.W.
History
DepositionFeb 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TCR B3K506 Alpha Chain
B: TCR B3K506 Beta Chain
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: 3K peptide, Linker, and H-2 class II histocompatibility antigen (A beta chain)
E: TCR B3K506 Alpha Chain
F: TCR B3K506 Beta Chain
G: H-2 class II histocompatibility antigen, A-B alpha chain
H: 3K peptide, Linker, and H-2 class II histocompatibility antigen (A beta chain)


Theoretical massNumber of molelcules
Total (without water)189,9198
Polymers189,9198
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.300, 117.800, 136.200
Angle α, β, γ (deg.)90.000, 99.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TCR B3K506 Alpha Chain


Mass: 22465.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: The mouse Va and Vb of B3K506 TCRs fused to human Ca and Cb
Plasmid: PET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#2: Protein TCR B3K506 Beta Chain


Mass: 26956.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: The mouse Va and Vb of B3K506 TCRs fused to human Ca and Cb
Plasmid: PET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#3: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 20597.957 Da / Num. of mol.: 2 / Fragment: UNP residues 27-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P14434
#4: Protein 3K peptide, Linker, and H-2 class II histocompatibility antigen (A beta chain)


Mass: 24938.830 Da / Num. of mol.: 2
Fragment: Fusion protein of ealpha 3K peptide residues 1-13, linker 14-28 and MHC class II Ab UNP residues 30-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1, H2-iabeta / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P14483
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsBASED ON RELATED ENTRY 1LNU,TWO SEPARATE SEQUENCES, AN EALPHA3KPEPTIDE(1-13) AND LINKER(14-28), ...BASED ON RELATED ENTRY 1LNU,TWO SEPARATE SEQUENCES, AN EALPHA3KPEPTIDE(1-13) AND LINKER(14-28), WHICH START FROM RESIDUE 1 TO RESIDUE 28 WERE ADDED TO THE N-TERMINUS OF THE BETACHAIN OF THE CLASS II MHC IAB OF CHAINS D AND H

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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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% PEG 4000 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97243 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2006 / Details: Mirrors
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 57142 / % possible obs: 86.1 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3558 / % possible all: 54

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→40 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2155857.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2882 4.3 %RANDOM
Rwork0.246 ---
obs-56990 86 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.549 Å2 / ksol: 0.291 e/Å3
Displacement parametersBiso mean: 66.7 Å2
Baniso -1Baniso -2Baniso -3
1-25.667 Å20 Å2-8.698 Å2
2---31.622 Å20 Å2
3---5.955 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 2.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13222 0 0 66 13288
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011.5
X-RAY DIFFRACTIONc_angle_deg1.92
X-RAY DIFFRACTIONc_dihedral_angle_d27.32
X-RAY DIFFRACTIONc_improper_angle_d1.072.5
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.434 325 5.2 %
Rwork0.425 5867 -
all-6192 -
obs-5867 56.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water_rep.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3ion.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4fs2.par&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5fs4.par&_1_TOPOLOGY_INFILE_5
X-RAY DIFFRACTION6CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION7CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION8CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION9CNS_TOPPAR:ion.param

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