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- PDB-6wl3: preTCRbeta-pMHC complex crystal structure -

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Basic information

Entry
Database: PDB / ID: 6wl3
TitlepreTCRbeta-pMHC complex crystal structure
Components
  • ARG-GLY-TYR-LEU-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: 3.45 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 23, 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-LEU-TYR-GLN-GLY-LEU
C: N15 preTCR beta
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: ARG-GLY-TYR-LEU-TYR-GLN-GLY-LEU
F: N15 preTCR beta
G: H-2 class I histocompatibility antigen, K-B alpha chain
H: ARG-GLY-TYR-LEU-TYR-GLN-GLY-LEU
I: N15 preTCR beta


Theoretical massNumber of molelcules
Total (without water)149,2219
Polymers149,2219
Non-polymers00
Water00
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: ARG-GLY-TYR-LEU-TYR-GLN-GLY-LEU
C: N15 preTCR beta


Theoretical massNumber of molelcules
Total (without water)49,7403
Polymers49,7403
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-LEU-TYR-GLN-GLY-LEU
F: N15 preTCR beta


Theoretical massNumber of molelcules
Total (without water)49,7403
Polymers49,7403
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-LEU-TYR-GLN-GLY-LEU
I: N15 preTCR beta


Theoretical massNumber of molelcules
Total (without water)49,7403
Polymers49,7403
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.430, 109.430, 316.464
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: 21419.732 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-LEU-TYR-GLN-GLY-LEU


Mass: 970.105 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: 3.17 Å3/Da / Density % sol: 61.25 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.100 M Bicine pH 9.0, 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: 3.45→50 Å / Num. obs: 25989 / % possible obs: 98.6 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.07 / Rrim(I) all: 0.228 / Χ2: 0.63 / Net I/σ(I): 3 / Num. measured all: 262230
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.45-3.529.61.14314190.6870.3831.2080.59199.6
3.52-3.599.41.17313370.7240.3931.240.61195.3
3.59-3.6710.51.01914390.8370.321.070.60599
3.67-3.7510.70.81614220.890.2530.8560.61599.5
3.75-3.8510.60.77314160.8940.2420.8110.60299.6
3.85-3.9510.50.62814260.920.1970.6590.61699.4
3.95-4.0710.60.51714430.9570.1620.5430.61199.7
4.07-4.210.40.39514330.9690.1250.4150.60399.8
4.2-4.3510.20.28214430.9840.090.2970.61499.5
4.35-4.52100.22914420.9880.0740.2410.63799.7
4.52-4.739.30.1813610.9880.0610.1910.63694.2
4.73-4.9710.40.17914570.9920.0560.1880.62999.5
4.97-5.2910.50.16914400.9940.0530.1770.6399.7
5.29-5.6910.40.17114830.9920.0540.180.63599.5
5.69-6.2710.20.16514640.9920.0530.1740.62299.3
6.27-7.179.30.13414330.9910.0450.1410.67195.7
7.17-9.0210.10.07615360.9980.0240.080.69199.4
9.02-508.90.045159510.0160.0480.73296.2

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Processing

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

1pku

1nfd


Resolution: 3.45→48.94 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.56
RfactorNum. reflection% reflection
Rfree0.2559 1307 5.05 %
Rwork0.2196 --
obs0.2214 25874 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 228.28 Å2 / Biso mean: 96.8528 Å2 / Biso min: 36.33 Å2
Refinement stepCycle: final / Resolution: 3.45→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10292 0 0 0 10292
Num. residues----1267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210562
X-RAY DIFFRACTIONf_angle_d0.56514288
X-RAY DIFFRACTIONf_dihedral_angle_d24.7931423
X-RAY DIFFRACTIONf_chiral_restr0.041434
X-RAY DIFFRACTIONf_plane_restr0.0031881
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.45-3.590.37251520.31362596274897
3.59-3.750.32211640.27962690285499
3.75-3.950.30841220.257627192841100
3.95-4.190.26951730.233126932866100
4.19-4.520.24611430.199627362879100
4.52-4.970.23781430.18162670281397
4.97-5.690.21911320.19792780291299
5.69-7.170.23741410.22282752289398
7.17-48.940.22831370.2042931306897

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