[English] 日本語
Yorodumi
- PDB-6myd: Structure of zebrafish TRAF6 in complex with STING CTT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6myd
TitleStructure of zebrafish TRAF6 in complex with STING CTT
Components
  • STING CTT, Transmembrane protein 173
  • TNF receptor-associated factor 6
KeywordsIMMUNE SYSTEM / Innate Immunity / STING / NF-kappaB / TRAF6 / TMEM173
Function / homology
Function and homology information


cytoplasmic pattern recognition receptor signaling pathway => GO:0002753 / STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / : / Regulation of innate immune responses to cytosolic DNA / p75NTR recruits signalling complexes / Interleukin-1 signaling / NOD1/2 Signaling Pathway / Ovarian tumor domain proteases / Ub-specific processing proteases ...cytoplasmic pattern recognition receptor signaling pathway => GO:0002753 / STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / : / Regulation of innate immune responses to cytosolic DNA / p75NTR recruits signalling complexes / Interleukin-1 signaling / NOD1/2 Signaling Pathway / Ovarian tumor domain proteases / Ub-specific processing proteases / Neutrophil degranulation / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / reticulophagy / non-canonical NF-kappaB signal transduction / autophagosome membrane / protein K63-linked ubiquitination / positive regulation of macroautophagy / autophagosome assembly / autophagosome / positive regulation of type I interferon production / lipopolysaccharide-mediated signaling pathway / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / lipid droplet / regulation of autophagy / response to bacterium / RING-type E3 ubiquitin transferase / response to virus / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / cell cortex / cytoplasmic vesicle / regulation of apoptotic process / defense response to virus / membrane => GO:0016020 / innate immune response / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / endoplasmic reticulum / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Stimulator of interferon genes protein, C-terminal / TNF receptor-associated factor 6 / TNF receptor-associated factor 6, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A ...Stimulator of interferon genes protein, C-terminal / TNF receptor-associated factor 6 / TNF receptor-associated factor 6, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
Stimulator of interferon genes protein / TNF receptor-associated factor 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
Authorsde Oliveira Mann, C.C. / Orzalli, M.H. / King, D.S. / Kagan, J.C. / Lee, A.S.Y. / Kranzusch, P.J.
CitationJournal: Cell Rep / Year: 2019
Title: Modular Architecture of the STING C-Terminal Tail Allows Interferon and NF-kappa B Signaling Adaptation.
Authors: de Oliveira Mann, C.C. / Orzalli, M.H. / King, D.S. / Kagan, J.C. / Lee, A.S.Y. / Kranzusch, P.J.
History
DepositionNov 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TNF receptor-associated factor 6
B: STING CTT, Transmembrane protein 173
C: TNF receptor-associated factor 6
D: STING CTT, Transmembrane protein 173
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8369
Polymers38,3564
Non-polymers4805
Water8,539474
1
A: TNF receptor-associated factor 6
B: STING CTT, Transmembrane protein 173
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2743
Polymers19,1782
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-28 kcal/mol
Surface area8690 Å2
MethodPISA
2
C: TNF receptor-associated factor 6
D: STING CTT, Transmembrane protein 173
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5626
Polymers19,1782
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-17 kcal/mol
Surface area8440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.621, 84.377, 53.720
Angle α, β, γ (deg.)90.00, 115.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein TNF receptor-associated factor 6 / E3 ubiquitin-protein ligase TRAF6 / RING-type E3 ubiquitin transferase TRAF6


Mass: 18224.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: traf6, si:dkey-56p7.3, zgc:63704 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6IWL4, RING-type E3 ubiquitin transferase
#2: Protein/peptide STING CTT, Transmembrane protein 173


Mass: 952.958 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Danio rerio (zebrafish) / References: UniProt: E7F4N7
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 1.5 M LiSO4

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.399→48.52 Å / Num. obs: 73125 / % possible obs: 99 % / Redundancy: 3.5 % / CC1/2: 0.989 / Rpim(I) all: 0.07 / Net I/σ(I): 4.8
Reflection shellResolution: 1.399→1.42 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 3560 / CC1/2: 0.495 / Rpim(I) all: 0.584 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LB5
Resolution: 1.399→48.52 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.76
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 2002 2.74 %10
Rwork0.1807 ---
obs0.1812 73076 98.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.399→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 25 474 3134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052729
X-RAY DIFFRACTIONf_angle_d0.8593711
X-RAY DIFFRACTIONf_dihedral_angle_d25.2061009
X-RAY DIFFRACTIONf_chiral_restr0.084394
X-RAY DIFFRACTIONf_plane_restr0.006484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3993-1.43430.26971310.27294866X-RAY DIFFRACTION95
1.4343-1.47310.2761480.25185081X-RAY DIFFRACTION99
1.4731-1.51640.27341440.23465058X-RAY DIFFRACTION99
1.5164-1.56540.26061410.22245040X-RAY DIFFRACTION99
1.5654-1.62130.22321420.20565111X-RAY DIFFRACTION99
1.6213-1.68620.24111470.19625078X-RAY DIFFRACTION99
1.6862-1.7630.20451410.1875058X-RAY DIFFRACTION99
1.763-1.85590.22791430.17985127X-RAY DIFFRACTION99
1.8559-1.97220.19831390.17425068X-RAY DIFFRACTION99
1.9722-2.12450.19081430.16865072X-RAY DIFFRACTION98
2.1245-2.33830.18051460.17135128X-RAY DIFFRACTION99
2.3383-2.67660.20741430.17585084X-RAY DIFFRACTION99
2.6766-3.37210.21021450.17515149X-RAY DIFFRACTION100
3.3721-48.54910.15811490.16585154X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.64310.8670.43813.48211.65794.0107-0.067-0.24870.13290.35730.14960.30820.0786-0.2079-0.05650.17540.01260.03790.13130.04140.1305-6.00436.41342.8005
21.7866-0.4772-3.10041.6531-0.52226.8545-0.02410.506-0.2967-0.1518-0.08360.17050.2178-0.57060.20410.1149-0.02110.0110.1834-0.05390.12182.2902-4.0689-20.6281
31.163-0.5894-0.64941.91650.79230.8493-0.04240.0678-0.01070.06780.03090.03470.05920.04980.00890.0806-0.00880.00610.0739-0.00870.07173.46595.9377-12.3314
44.2667-6.15360.28318.9067-0.53850.25540.040.11990.3663-0.0601-0.0615-0.45610.01270.1187-0.03770.1287-0.00380.01220.1666-0.03630.133411.28319.31-16.45
52.6628-1.6887-1.13982.72840.7241.18410.0135-0.0735-0.02050.0158-0.0025-0.16170.06090.07890.00430.0982-0.0059-0.00750.0969-0.00040.07759.2423.2065-10.1811
65.813.10511.26747.54231.04554.3354-0.30560.16450.2917-0.25130.18910.5537-0.5158-0.31590.14580.17180.03950.02530.1410.01840.1498-11.336515.5397-5.9317
76.2925-2.2948-3.37293.42141.48175.29310.18650.23550.048-0.3962-0.0101-0.1252-0.23960.1762-0.18850.131-0.03180.00660.1653-0.02270.1157-1.14117.2614-18.9217
84.9662-0.81750.34088.2235-1.21783.4586-0.0013-0.4215-0.24540.27320.26290.17250.11850.0747-0.29610.1846-0.00730.0140.2078-0.01430.208711.95655.6809-6.1421
93.96760.6293.06672.57880.47996.1191-0.0876-0.38790.29140.042-0.07570.015-0.3331-0.18160.22190.11450.0080.02180.1267-0.03920.1305-2.79-3.045320.5888
106.9176-3.3859-5.58223.25043.21724.6741-0.09940.1619-0.1582-0.0917-0.06080.41680.2021-0.66360.18920.1416-0.0183-0.02340.20580.02320.1405-9.4742-8.4115-2.1659
111.70480.26781.31110.60810.4672.7842-0.0885-0.17220.1935-0.0538-0.0670.0608-0.1378-0.19980.19160.10890.00470.00580.079-0.01610.10611.01340.09513.0067
121.24571.12551.82632.28852.55243.6841-0.0363-0.07250.0593-0.1103-0.0176-0.051-0.1106-0.00660.01930.1091-0.01120.00860.0816-0.00610.08894.9066-4.99288.5552
135.02563.35933.51092.86792.26482.47130.06-0.0913-0.15210.09410.0374-0.17080.08960.0028-0.12470.0920.01780.0060.1179-0.02790.08079.0382-5.911821.611
143.71182.8421.82336.1333-2.26188.7813-0.1194-0.3705-0.31170.0418-0.0561.09150.4371-0.73750.08160.1444-0.02920.06130.1615-0.02540.2776-11.1695-17.524217.091
153.44614.97120.6927.62610.31911.50650.00380.0059-0.42880.06770.0702-0.56030.06360.2046-0.10.13640.02520.00180.1675-0.03090.176711.4986-10.278916.6164
162.99683.00111.78835.38292.03442.2586-0.0828-0.04890.2106-0.1082-0.0228-0.0049-0.17460.13130.11320.12770.01480.01040.1247-0.00760.12288.958-3.877210.5039
176.7601-3.5661-1.95562.01960.55374.4617-0.1862-0.0287-0.23660.01480.18640.28490.3819-0.35480.08080.1455-0.0351-0.00120.12050.00930.1394-11.2723-16.13236.4843
187.28751.74081.27970.61150.4140.43220.0944-0.5924-0.07990.1191-0.0554-0.06230.1045-0.0788-0.16120.13320.01570.00250.1515-0.02020.11221.071-8.73220.7325
194.226-1.33691.13725.111-0.61743.9894-0.03890.35320.3877-0.22580.18720.1994-0.29250.1476-0.16990.2314-0.00160.01430.21040.01990.215811.9303-6.19496.4524
202.7344-0.2628-1.03583.62260.59455.0960.02190.4119-0.2315-0.18990.0017-0.2150.3981-0.05320.32430.10510.0196-0.00810.1458-0.04260.1231-4.41312.0671-17.1051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 384 through 400 )
2X-RAY DIFFRACTION2chain 'C' and (resid 401 through 411 )
3X-RAY DIFFRACTION3chain 'C' and (resid 412 through 466 )
4X-RAY DIFFRACTION4chain 'C' and (resid 467 through 480 )
5X-RAY DIFFRACTION5chain 'C' and (resid 481 through 499 )
6X-RAY DIFFRACTION6chain 'C' and (resid 500 through 513 )
7X-RAY DIFFRACTION7chain 'C' and (resid 514 through 522 )
8X-RAY DIFFRACTION8chain 'D' and (resid 377 through 384 )
9X-RAY DIFFRACTION9chain 'A' and (resid 369 through 383 )
10X-RAY DIFFRACTION10chain 'A' and (resid 384 through 392 )
11X-RAY DIFFRACTION11chain 'A' and (resid 393 through 412 )
12X-RAY DIFFRACTION12chain 'A' and (resid 413 through 445 )
13X-RAY DIFFRACTION13chain 'A' and (resid 446 through 458 )
14X-RAY DIFFRACTION14chain 'A' and (resid 459 through 466 )
15X-RAY DIFFRACTION15chain 'A' and (resid 467 through 480 )
16X-RAY DIFFRACTION16chain 'A' and (resid 481 through 499 )
17X-RAY DIFFRACTION17chain 'A' and (resid 500 through 513 )
18X-RAY DIFFRACTION18chain 'A' and (resid 514 through 523 )
19X-RAY DIFFRACTION19chain 'B' and (resid 377 through 384 )
20X-RAY DIFFRACTION20chain 'C' and (resid 372 through 383 )

+
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://pdbjlvh1.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