[English] 日本語
Yorodumi
- PDB-8d5q: TCR TG6 in complex with Ld-HF10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8d5q
TitleTCR TG6 in complex with Ld-HF10
Components
  • Dense granule protein 6, HF10 peptide
  • H-2 class I histocompatibility antigen, L-D alpha chain
  • TCR-alpha
  • TCR-beta
KeywordsIMMUNE SYSTEM / MHCI / CD8 T cell
Function / homology
Function and homology information


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of tumor necrosis factor production / protein-folding chaperone binding / antibacterial humoral response / adaptive immune response / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / plasma membrane
Similarity search - Function
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 ...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, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Toxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsWang, Y. / Dai, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Front Immunol / Year: 2022
Title: Peptide Centric V beta Specific Germline Contacts Shape a Specialist T Cell Response.
Authors: Wang, Y. / Tsitsiklis, A. / Devoe, S. / Gao, W. / Chu, H.H. / Zhang, Y. / Li, W. / Wong, W.K. / Deane, C.M. / Neau, D. / Slansky, J.E. / Thomas, P.G. / Robey, E.A. / Dai, S.
History
DepositionJun 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TCR-alpha
B: TCR-beta
C: H-2 class I histocompatibility antigen, L-D alpha chain
E: Dense granule protein 6, HF10 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7297
Polymers73,3414
Non-polymers3873
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.963, 89.963, 105.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein TCR-alpha


Mass: 23161.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: Transgenic mouse line TG6 / Production host: Escherichia coli (E. coli)
#2: Protein TCR-beta


Mass: 27929.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: Transgenic mouse line TG6 / Production host: Escherichia coli (E. coli)
#3: Protein H-2 class I histocompatibility antigen, L-D alpha chain


Mass: 21101.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-L / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01897

-
Protein/peptide , 1 types, 1 molecules E

#4: Protein/peptide Dense granule protein 6, HF10 peptide


Mass: 1149.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Toxoplasma gondii (eukaryote)

-
Non-polymers , 3 types, 211 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 11 % w/v PEG 8000, 0.1 M MES 6.0, 0.24 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→90 Å / Num. obs: 29168 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rpim(I) all: 0.03 / Net I/σ(I): 26.6
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 2864 / Rpim(I) all: 0.29

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LD9, 3TO4

1ld9

3to4


Resolution: 2.501→45.022 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 15.549 / SU ML: 0.18 / Cross valid method: NONE / ESU R: 0.397 / ESU R Free: 0.248
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.222 1493 5.119 %
Rwork0.1688 27675 -
all0.172 --
obs-29168 99.839 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 65.211 Å2
Baniso -1Baniso -2Baniso -3
1--0.251 Å20 Å20 Å2
2---0.251 Å2-0 Å2
3---0.501 Å2
Refinement stepCycle: LAST / Resolution: 2.501→45.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5108 0 22 208 5338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135283
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174553
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.657181
X-RAY DIFFRACTIONr_angle_other_deg1.3721.57610582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5575633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11422.125320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36115829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.231540
X-RAY DIFFRACTIONr_chiral_restr0.0870.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026021
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021211
X-RAY DIFFRACTIONr_nbd_refined0.210.21009
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.24298
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22376
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.22540
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0630.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2620.215
X-RAY DIFFRACTIONr_nbd_other0.1920.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.26
X-RAY DIFFRACTIONr_mcbond_it4.1675.7652541
X-RAY DIFFRACTIONr_mcbond_other4.1665.7652540
X-RAY DIFFRACTIONr_mcangle_it6.1848.6323171
X-RAY DIFFRACTIONr_mcangle_other6.1838.6323172
X-RAY DIFFRACTIONr_scbond_it4.9966.2242742
X-RAY DIFFRACTIONr_scbond_other4.8546.2192740
X-RAY DIFFRACTIONr_scangle_it7.369.1314010
X-RAY DIFFRACTIONr_scangle_other7.3599.1344011
X-RAY DIFFRACTIONr_lrange_it10.02265.4515798
X-RAY DIFFRACTIONr_lrange_other10.02165.4685799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.5650.39970.32002X-RAY DIFFRACTION98.6372
2.565-2.6350.3341340.2431956X-RAY DIFFRACTION99.809
2.635-2.7120.271880.2071962X-RAY DIFFRACTION100
2.712-2.7950.2871090.1881836X-RAY DIFFRACTION100
2.795-2.8860.291030.1921827X-RAY DIFFRACTION100
2.886-2.9870.214990.1661762X-RAY DIFFRACTION100
2.987-3.0990.249770.1781720X-RAY DIFFRACTION100
3.099-3.2250.232900.1681627X-RAY DIFFRACTION100
3.225-3.3680.191600.1761585X-RAY DIFFRACTION100
3.368-3.5310.232900.1861515X-RAY DIFFRACTION100
3.531-3.7210.232870.1841411X-RAY DIFFRACTION99.8667
3.721-3.9450.244680.1731370X-RAY DIFFRACTION100
3.945-4.2150.2590.1451266X-RAY DIFFRACTION99.9246
4.215-4.550.156580.1321200X-RAY DIFFRACTION100
4.55-4.9790.175650.1181085X-RAY DIFFRACTION99.6534
4.979-5.5580.215560.149997X-RAY DIFFRACTION100
5.558-6.4020.261490.179873X-RAY DIFFRACTION100
6.402-7.8030.211400.168746X-RAY DIFFRACTION99.8729
7.803-10.8780.188390.14586X-RAY DIFFRACTION100
10.878-45.0220.234250.249349X-RAY DIFFRACTION99.4681
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0189-0.08450.75120.6865-0.6791.1210.1985-0.0539-0.2344-0.0315-0.1539-0.10660.15420.0805-0.04450.07110.0028-0.07810.0847-0.01110.150928.3932-103.34325.5415
21.7483-0.69380.6050.7174-0.34930.23970.0473-0.20150.01040.0157-0.03930.01630.0041-0.0192-0.00790.014-0.02920.00130.1876-0.06430.031936.1728-88.08615.2565
31.1624-0.45010.14530.79120.13770.35640.10440.04480.1106-0.0687-0.0136-0.0945-0.0533-0.0273-0.09080.0646-0.01710.06420.0252-0.00620.07238.2427-68.7207-17.4619
43.7884-0.4050.79960.19610.33251.32310.1907-0.15320.1586-0.0264-0.0231-0.0921-0.0083-0.1319-0.16750.0895-0.055-0.00050.05130.01010.105113.3186-71.9171-12.2034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA0 - 204
2X-RAY DIFFRACTION2ALLB0 - 243
3X-RAY DIFFRACTION3ALLC1 - 176
4X-RAY DIFFRACTION4ALLE1 - 10

+
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