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- PDB-6myd: Structure of zebrafish TRAF6 in complex with STING CTT -

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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


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 ...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 / regulation of type I interferon production / cyclic-di-GMP binding / tumor necrosis factor receptor binding / proton channel activity / cGAS/STING signaling pathway / non-canonical NF-kappaB signal transduction / regulation of canonical NF-kappaB signal transduction / reticulophagy / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of macroautophagy / autophagosome membrane / autophagosome assembly / protein K63-linked ubiquitination / positive regulation of type I interferon production / signaling adaptor activity / positive regulation of defense response to virus by host / lipid droplet / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / autophagosome / lipopolysaccharide-mediated signaling pathway / response to bacterium / positive regulation of non-canonical NF-kappaB signal transduction / RING-type E3 ubiquitin transferase / response to virus / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / cell cortex / cytoplasmic vesicle / regulation of apoptotic process / defense response to virus / regulation of autophagy / Golgi membrane / innate immune response / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
TNF receptor-associated factor 6 / TNF receptor-associated factor 6, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A ...TNF receptor-associated factor 6 / TNF receptor-associated factor 6, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / 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 / STING ligand-binding domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 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

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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

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LB5

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

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)
11.64310.8670.43813.48211.65794.0107-0.067-0.24870.13290.35730.14960.30820.0786-0.2079-0.05650.17540.01260.03790.13130.04140.1305-6.00436.41342.8005
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 )

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