[English] 日本語
Yorodumi
- PDB-6wl2: preTCRbeta-pMHC complex crystal structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wl2
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: 3.3 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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)149,1799
Polymers149,1799
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)49,7263
Polymers49,7263
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)49,7263
Polymers49,7263
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)49,7263
Polymers49,7263
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.897, 108.897, 316.173
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

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


Mass: 21419.732 Da / Num. of mol.: 3 / Mutation: G56C, C121Q
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.85 %
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

-
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: 3.3→50 Å / Num. obs: 29673 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.059 / Rrim(I) all: 0.159 / Χ2: 0.663 / Net I/σ(I): 4 / Num. measured all: 211094
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.367.21.46414340.5940.5831.5790.6100
3.36-3.427.21.30314560.670.5181.4040.595100
3.42-3.487.10.95714380.7680.3851.0340.614100
3.48-3.556.50.82514300.7830.3460.8970.61799.9
3.55-3.636.80.71214910.840.290.7710.60999.9
3.63-3.727.60.57814140.910.2250.6210.62499.9
3.72-3.817.60.51814830.9360.20.5550.643100
3.81-3.917.50.40914600.9620.1590.4390.63100
3.91-4.037.50.32614590.9760.1270.350.629100
4.03-4.167.40.2614560.9790.1020.280.621100
4.16-4.317.30.19614680.9890.0770.2110.63399.9
4.31-4.487.20.14114690.9950.0560.1520.674100
4.48-4.686.50.11714940.9950.0490.1270.667100
4.68-4.937.10.10914770.9950.0430.1180.6799.9
4.93-5.247.50.10814920.9960.0420.1160.678100
5.24-5.647.40.10214870.9970.040.1090.6899.9
5.64-6.217.20.10114980.9940.040.1090.67999.7
6.21-7.16.40.08515290.9950.0360.0920.71199.5
7.1-8.947.20.05815510.9980.0230.0620.79699.9
8.94-506.20.04216870.9960.0180.0460.88799.4

-
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: 3.3→47.43 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 1445 4.89 %
Rwork0.228 28104 -
obs0.23 29549 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 247.05 Å2 / Biso mean: 112.1321 Å2 / Biso min: 57.58 Å2
Refinement stepCycle: final / Resolution: 3.3→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10279 0 0 0 10279
Num. residues----1265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210549
X-RAY DIFFRACTIONf_angle_d0.57114271
X-RAY DIFFRACTIONf_dihedral_angle_d25.7211421
X-RAY DIFFRACTIONf_chiral_restr0.041432
X-RAY DIFFRACTIONf_plane_restr0.0031879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.420.3831580.348527292887100
3.42-3.550.33041430.319527182861100
3.55-3.710.34581460.305627572903100
3.71-3.910.29271370.283627932930100
3.91-4.150.28171600.250727442904100
4.15-4.480.23361400.221827872927100
4.48-4.930.23971410.195328272968100
4.93-5.640.26291470.206828222969100
5.64-7.10.31231360.224328783014100
7.1-47.430.21681370.18563049318699

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more