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- PDB-2pxy: Crystal structures of immune receptor complexes -

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Basic information

Entry
Database: PDB / ID: 2pxy
TitleCrystal structures of immune receptor complexes
Components
  • (H-2 class II histocompatibility antigen, A-U ...) x 2
  • (T cell receptor ...) x 2
  • Myelin basic protein (MBP)-peptide
KeywordsIMMUNE SYSTEM / complex
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / T cell receptor complex / antigen processing and presentation / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation ...antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / T cell receptor complex / antigen processing and presentation / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / MHC class II protein complex binding / late endosome membrane / adaptive immune response / early endosome / lysosome / lysosomal membrane / external side of plasma membrane / cell surface / Golgi apparatus / 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 ...: / : / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
Beta-chain / H-2 class II histocompatibility antigen, A-U beta chain / H-2 class II histocompatibility antigen, A-U alpha chain / TRAV6D-7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsFeng, D. / Bond, C.J. / Ely, L.K. / Garcia, K.C.
CitationJournal: Nat.Immunol. / Year: 2007
Title: Structural evidence for a germline-encoded T cell receptor-major histocompatibility complex interaction 'codon'.
Authors: Feng, D. / Bond, C.J. / Ely, L.K. / Maynard, J. / Garcia, K.C.
History
DepositionMay 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: T cell receptor alpha chain
B: T cell receptor beta chain
C: H-2 class II histocompatibility antigen, A-U alpha chain
D: H-2 class II histocompatibility antigen, A-U beta chain
P: Myelin basic protein (MBP)-peptide


Theoretical massNumber of molelcules
Total (without water)69,3885
Polymers69,3885
Non-polymers00
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.603, 97.603, 175.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11C-211-

HOH

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Components

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T cell receptor ... , 2 types, 2 molecules AB

#1: Protein T cell receptor alpha chain


Mass: 12537.667 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PAK400 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5R1F5
#2: Protein T cell receptor beta chain


Mass: 12079.190 Da / Num. of mol.: 1 / Mutation: G17E,H47Y,I75T,L78S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PAK400 / Production host: Escherichia coli (E. coli) / References: UniProt: A2NTY6

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H-2 class II histocompatibility antigen, A-U ... , 2 types, 2 molecules CD

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


Mass: 20771.111 Da / Num. of mol.: 1 / Fragment: extracellular alpha-1, extracellular alpha-2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14438
#4: Protein H-2 class II histocompatibility antigen, A-U beta chain


Mass: 22566.240 Da / Num. of mol.: 1 / Fragment: extracellular beta-1, extracellular beta-2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P06344

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Protein/peptide / Non-polymers , 2 types, 330 molecules P

#5: Protein/peptide Myelin basic protein (MBP)-peptide


Mass: 1433.511 Da / Num. of mol.: 1 / Mutation: K4Y / Source method: obtained synthetically
Details: Synthetic construct. The sequence can be naturally found in Mus musculus (Mouse)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.01 Å3/Da / Density % sol: 59.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Potassium sodium tartrate tetrahydrate, 0.1M succinic acid (pH7.0), 16% polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9785
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→47 Å / Num. all: 42263 / Num. obs: 42263 / Redundancy: 4.3 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 23.4
Reflection shellResolution: 2.2→2.29 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→47 Å / σ(F): -1
RfactorNum. reflection% reflection
Rfree0.253 --
Rwork0.218 --
all-42263 -
obs-42263 100 %
Displacement parametersBiso mean: 37.2 Å2
Refinement stepCycle: LAST / Resolution: 2.23→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4883 0 0 329 5212

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