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- PDB-6wl4: preTCRbeta-pMHC complex crystal structure -

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Basic information

Entry
Database: PDB / ID: 6wl4
TitlepreTCRbeta-pMHC complex crystal structure
Components
  • ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • N15 preTCR beta
KeywordsIMMUNE SYSTEM / preTCR / H-2Kb / T cell development / beta selection
Function / homology
Function and homology information


RNA replication / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / viral transcription ...RNA replication / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / viral transcription / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / MHC class I protein complex / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / negative regulation of neuron projection development / viral nucleocapsid / host cell cytoplasm / defense response to bacterium / ribonucleoprotein complex / external side of plasma membrane / RNA binding
Similarity search - Function
Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : ...Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
H-2 class I histocompatibility antigen, K-B alpha chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Vesicular stomatitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsLi, X. / Mallis, R.J. / Mizsei, R. / Tan, K. / Reinherz, E.L. / Wang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01AI136301 United States
CitationJournal: Science / Year: 2021
Title: Pre-T cell receptors topologically sample self-ligands during thymocyte beta-selection.
Authors: Li, X. / Mizsei, R. / Tan, K. / Mallis, R.J. / Duke-Cohan, J.S. / Akitsu, A. / Tetteh, P.W. / Dubey, A. / Hwang, W. / Wagner, G. / Lang, M.J. / Arthanari, H. / Wang, J.H. / Reinherz, E.L.
History
DepositionApr 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU
C: N15 preTCR beta
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU
F: N15 preTCR beta
G: H-2 class I histocompatibility antigen, K-B alpha chain
H: ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU
I: N15 preTCR beta


Theoretical massNumber of molelcules
Total (without water)148,8799
Polymers148,8799
Non-polymers00
Water00
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU
C: N15 preTCR beta


Theoretical massNumber of molelcules
Total (without water)49,6263
Polymers49,6263
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU
F: N15 preTCR beta


Theoretical massNumber of molelcules
Total (without water)49,6263
Polymers49,6263
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: H-2 class I histocompatibility antigen, K-B alpha chain
H: ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU
I: N15 preTCR beta


Theoretical massNumber of molelcules
Total (without water)49,6263
Polymers49,6263
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.546, 110.546, 316.917
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2K(B)


Mass: 21319.590 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01901
#2: Protein/peptide ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU


Mass: 956.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Vesicular stomatitis virus / References: UniProt: P03521*PLUS
#3: Protein N15 preTCR beta


Mass: 27350.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria)
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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.100 M Bicine pH 9.5, 15% (w/v)PEG 20000 / PH range: 6.5-9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 23600 / % possible obs: 99.1 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.099 / Rrim(I) all: 0.298 / Χ2: 0.779 / Net I/σ(I): 2.3 / Num. measured all: 204887
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.6-3.718.61.41619200.5840.5081.5060.67899.5
3.71-3.8391.37919400.6670.481.4610.65299.6
3.83-3.9690.99619210.790.3471.0550.66699.8
3.96-4.128.80.76819420.8650.270.8150.67899.8
4.12-4.318.50.51319250.910.1840.5460.72199.2
4.31-4.548.90.37919110.9650.1320.4010.79298.2
4.54-4.8290.31619640.9650.1090.3350.82299.6
4.82-5.198.90.29119580.9670.1020.3090.85599.8
5.19-5.718.40.27519590.9730.0990.2930.84698.9
5.71-6.548.80.24620110.9770.0860.2610.78499.2
6.54-8.238.50.15720120.9890.0560.1680.8598.9
8.23-507.90.07421370.9970.0270.0791.01397

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
PDB_EXTRACT3.25data extraction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PKU, 1NFD

1pku

1nfd


Resolution: 3.6→49.44 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 1128 4.8 %
Rwork0.2263 22389 -
obs0.2284 23517 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 225.98 Å2 / Biso mean: 107.4094 Å2 / Biso min: 47.35 Å2
Refinement stepCycle: final / Resolution: 3.6→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10281 0 0 0 10281
Num. residues----1269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210551
X-RAY DIFFRACTIONf_angle_d0.5414276
X-RAY DIFFRACTIONf_dihedral_angle_d25.731422
X-RAY DIFFRACTIONf_chiral_restr0.041432
X-RAY DIFFRACTIONf_plane_restr0.0031882
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6-3.760.36761420.33127392881100
3.76-3.960.28911420.282227562898100
3.96-4.210.27811280.249327762904100
4.21-4.530.28331380.21042730286898
4.53-4.990.23371500.192227902940100
4.99-5.710.23961520.21272787293999
5.71-7.190.31261270.23822863299099
7.19-49.440.24751490.19992948309797

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