[English] 日本語
Yorodumi
- PDB-6dfv: Mouse diabetogenic TCR 8F10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dfv
TitleMouse diabetogenic TCR 8F10
Components
  • TCR alpha chain
  • TCR beta chain
KeywordsIMMUNE SYSTEM / T cell receptor / Type 1 Diabetes / Autoimmunity
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.71 Å
AuthorsWang, Y. / Dai, S.
CitationJournal: Sci Immunol / Year: 2019
Title: How C-terminal additions to insulin B-chain fragments create superagonists for T cells in mouse and human type 1 diabetes.
Authors: Wang, Y. / Sosinowski, T. / Novikov, A. / Crawford, F. / White, J. / Jin, N. / Liu, Z. / Zou, J. / Neau, D. / Davidson, H.W. / Nakayama, M. / Kwok, W.W. / Gapin, L. / Marrack, P. / Kappler, J.W. / Dai, S.
History
DepositionMay 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TCR alpha chain
B: TCR beta chain
C: TCR alpha chain
D: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6966
Polymers100,5724
Non-polymers1242
Water5,747319
1
A: TCR alpha chain
B: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3483
Polymers50,2862
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-16 kcal/mol
Surface area20340 Å2
MethodPISA
2
C: TCR alpha chain
D: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3483
Polymers50,2862
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-22 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.016, 69.691, 69.699
Angle α, β, γ (deg.)111.66, 111.03, 94.86
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNALAALAAA3 - 1923 - 192
21GLNGLNALAALACC3 - 1923 - 192
12ALAALAASPASPBB2 - 2412 - 241
22ALAALAASPASPDD2 - 2412 - 241

NCS ensembles :
ID
1
2

-
Components

#1: Protein TCR alpha chain


Mass: 23405.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli / Strain (production host): BL21-Gold(DE3)pLysS AG
#2: Protein TCR beta chain


Mass: 26880.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 14% PEG 3350, 100mM sodium acetate at pH6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 91564 / % possible obs: 91.5 % / Redundancy: 4.1 % / Net I/σ(I): 11.62
Reflection shellResolution: 1.71→1.8 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.71→48.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.789 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23113 4820 5 %RANDOM
Rwork0.17081 ---
obs0.17389 91564 90.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.346 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20.32 Å2-0.41 Å2
2---0.53 Å2-0.47 Å2
3---1.13 Å2
Refinement stepCycle: 1 / Resolution: 1.71→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6770 0 8 319 7097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0156990
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175975
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.7479497
X-RAY DIFFRACTIONr_angle_other_deg0.6081.71114058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8615878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21520.36278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66115990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3751541
X-RAY DIFFRACTIONr_chiral_restr0.0860.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021321
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3562.4143495
X-RAY DIFFRACTIONr_mcbond_other4.3583496
X-RAY DIFFRACTIONr_mcangle_it5.1963.6084362
X-RAY DIFFRACTIONr_mcangle_other5.19713.3574363
X-RAY DIFFRACTIONr_scbond_it5.2792.683495
X-RAY DIFFRACTIONr_scbond_other5.2792.683495
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0953.9065130
X-RAY DIFFRACTIONr_long_range_B_refined6.3587129
X-RAY DIFFRACTIONr_long_range_B_other6.3587130
X-RAY DIFFRACTIONr_rigid_bond_restr5.69836984
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded19.45656813
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A50440.13
12C50440.13
21B72940.11
22D72940.11
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 333 -
Rwork0.345 6505 -
obs--87.48 %
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)
11.21130.7601-0.53712.5005-1.68213.9076-0.15350.1291-0.0854-0.2560.08610.1050.6417-0.04050.06740.1631-0.00320.04780.0159-0.00250.0387-47.117413.4893-33.0016
20.9111-0.32971.02540.9807-1.35723.37540.0292-0.06040.0189-0.21070.12270.15950.5475-0.4778-0.15180.1284-0.1053-0.02720.09610.01070.0376-64.217616.4262-26.3488
32.55580.8934-1.55791.3408-0.94713.2480.1155-0.2450.15540.1357-0.1458-0.1255-0.10630.48390.03030.0369-0.0257-0.01830.0760.00710.0456-41.030121.55249.5427
40.8243-0.2778-0.99521.06280.60712.48540.0817-0.1040.1457-0.0313-0.04630.1231-0.35640.1294-0.03540.0725-0.023-0.01240.0408-0.00540.0952-49.218937.28222.4255
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 193
2X-RAY DIFFRACTION2B2 - 241
3X-RAY DIFFRACTION3C3 - 206
4X-RAY DIFFRACTION4D2 - 241

+
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