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- PDB-3c60: Crystal structure of mouse MHC class II I-Ab/3K peptide complexed... -

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Basic information

Entry
Database: PDB / ID: 3c60
TitleCrystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR YAe62
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 YAe62 alpha chain
  • TCR YAe62 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 / molecular replacement / Resolution: 3.05 Å
AuthorsDai, S.
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 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 5, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Oct 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 1.5Nov 20, 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 YAe62 alpha chain
B: TCR YAe62 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 YAe62 alpha chain
F: TCR YAe62 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)188,2358
Polymers188,2358
Non-polymers00
Water00
1
A: TCR YAe62 alpha chain
B: TCR YAe62 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)


Theoretical massNumber of molelcules
Total (without water)94,1174
Polymers94,1174
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: TCR YAe62 alpha chain
F: TCR YAe62 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)94,1174
Polymers94,1174
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.058, 126.168, 277.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TCR YAe62 alpha chain


Mass: 22109.203 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 YAe62 TCRs fused to human Ca and Cb
Plasmid: PET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: PDB-3C6O
#2: Protein TCR YAe62 beta chain


Mass: 26471.277 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 YAe62 TCRs fused to human Ca and Cb
Plasmid: PET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: PDB-3C6O
#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 ealpha3K 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, PDB-3C6O
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: 3.07 Å3/Da / Density % sol: 59.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 15% PEG 4000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 43981 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 85.8 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.918 / Net I/σ(I): 13
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4349 / Χ2: 1.831 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→40.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2141643.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.309 2087 5 %RANDOM
Rwork0.267 ---
obs-41880 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.29 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso mean: 81.2 Å2
Baniso -1Baniso -2Baniso -3
1--14.12 Å20 Å20 Å2
2--11.39 Å20 Å2
3---2.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 3.05→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13102 0 0 0 13102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.05→3.24 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.457 321 4.6 %
Rwork0.409 6612 -
all-6933 -
obs-6612 93.4 %
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

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