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- PDB-7jl4: Crystal structure of TRIM65 PSpry domain -

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Basic information

Entry
Database: PDB / ID: 7jl4
TitleCrystal structure of TRIM65 PSpry domain
ComponentsTripartite motif-containing protein 65
KeywordsIMMUNE SYSTEM / RIG-I-like helicase / Ubiquitin E3 ligase
Function / homology
Function and homology information


positive regulation of protein oligomerization / type I interferon-mediated signaling pathway / protein K63-linked ubiquitination / antiviral innate immune response / positive regulation of interferon-alpha production / protein K48-linked ubiquitination / positive regulation of autophagy / positive regulation of interferon-beta production / RING-type E3 ubiquitin transferase / negative regulation of inflammatory response ...positive regulation of protein oligomerization / type I interferon-mediated signaling pathway / protein K63-linked ubiquitination / antiviral innate immune response / positive regulation of interferon-alpha production / protein K48-linked ubiquitination / positive regulation of autophagy / positive regulation of interferon-beta production / RING-type E3 ubiquitin transferase / negative regulation of inflammatory response / ubiquitin protein ligase activity / positive regulation of protein phosphorylation / zinc ion binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
: / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SPRY domain / B30.2/SPRY domain ...: / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsKato, K. / Ahmad, S. / Hur, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Mol Cell / Year: 2021
Title: Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases.
Authors: Kazuki Kato / Sadeem Ahmad / Zixiang Zhu / Janet M Young / Xin Mu / Sehoon Park / Harmit S Malik / Sun Hur /
Abstract: RNA helicases and E3 ubiquitin ligases mediate many critical functions in cells, but their actions have largely been studied in distinct biological contexts. Here, we uncover evolutionarily conserved ...RNA helicases and E3 ubiquitin ligases mediate many critical functions in cells, but their actions have largely been studied in distinct biological contexts. Here, we uncover evolutionarily conserved rules of engagement between RNA helicases and tripartite motif (TRIM) E3 ligases that lead to their functional coordination in vertebrate innate immunity. Using cryoelectron microscopy and biochemistry, we show that RIG-I-like receptors (RLRs), viral RNA receptors with helicase domains, interact with their cognate TRIM/TRIM-like E3 ligases through similar epitopes in the helicase domains. Their interactions are avidity driven, restricting the actions of TRIM/TRIM-like proteins and consequent immune activation to RLR multimers. Mass spectrometry and phylogeny-guided biochemical analyses further reveal that similar rules of engagement may apply to diverse RNA helicases and TRIM/TRIM-like proteins. Our analyses suggest not only conserved substrates for TRIM proteins but also, unexpectedly, deep evolutionary connections between TRIM proteins and RNA helicases, linking ubiquitin and RNA biology throughout animal evolution.
History
DepositionJul 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tripartite motif-containing protein 65
C: Tripartite motif-containing protein 65
B: Tripartite motif-containing protein 65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2987
Polymers64,9303
Non-polymers3684
Water7,620423
1
A: Tripartite motif-containing protein 65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9204
Polymers21,6431
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tripartite motif-containing protein 65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7352
Polymers21,6431
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Tripartite motif-containing protein 65


Theoretical massNumber of molelcules
Total (without water)21,6431
Polymers21,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.269, 76.269, 82.720
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein Tripartite motif-containing protein 65 / TRIM65


Mass: 21643.365 Da / Num. of mol.: 3 / Fragment: TRIM65 PSpry domain (UNP residues 312-502)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM65 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PJ69
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Bicine, pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 14, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.92→38.13 Å / Num. obs: 41070 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 27.09 Å2 / CC1/2: 0.996 / Net I/σ(I): 13.34
Reflection shellResolution: 1.92→1.99 Å / Num. unique obs: 4050 / CC1/2: 0.952

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Processing

Software
NameVersionClassification
XDSdata processing
PHENIX1.18.2-3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6FLN

6fln


Resolution: 1.92→38.13 Å / SU ML: 0.1891 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.3609
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 1967 4.79 %
Rwork0.1675 39091 -
obs0.1695 41058 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.54 Å2
Refinement stepCycle: LAST / Resolution: 1.92→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 24 423 4771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864570
X-RAY DIFFRACTIONf_angle_d1.61236252
X-RAY DIFFRACTIONf_chiral_restr0.076657
X-RAY DIFFRACTIONf_plane_restr0.0102820
X-RAY DIFFRACTIONf_dihedral_angle_d19.0998631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.28631400.20182780X-RAY DIFFRACTION99.76
1.97-2.020.2561130.19042847X-RAY DIFFRACTION99.76
2.02-2.080.23361840.17782736X-RAY DIFFRACTION99.93
2.08-2.150.21591690.17612731X-RAY DIFFRACTION99.76
2.15-2.220.25931060.18462846X-RAY DIFFRACTION99.9
2.23-2.310.231500.17882797X-RAY DIFFRACTION99.93
2.31-2.420.23281400.17412743X-RAY DIFFRACTION99.9
2.42-2.550.25071080.21322872X-RAY DIFFRACTION100
2.55-2.710.23021580.20232755X-RAY DIFFRACTION100
2.71-2.910.22691400.18782790X-RAY DIFFRACTION100
2.92-3.210.2181310.16812826X-RAY DIFFRACTION100
3.21-3.670.20291540.15292771X-RAY DIFFRACTION100
3.67-4.630.16581540.13282773X-RAY DIFFRACTION100
4.63-38.130.18891200.16242824X-RAY DIFFRACTION99.93
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)
16.70162243531.356557323611.542145665015.597646141814.155977850076.16746056805-0.237385641650.3670423531460.384981496767-0.1389200712910.176041730146-0.494323343335-0.1012347221430.1942022530990.0001294861416090.236840824996-0.00636521969722-0.006835109309170.2287501238090.05122950552920.30022008705219.449512657912.5623668311-7.86954370909
28.54593237596-2.54582800314-6.341001898034.357728571490.573603230367.679144988150.206081576860.3828326865380.3280433593010.1641191535160.1198776035520.0636903717389-0.359314905968-0.65061135848-0.3342941404470.2256964144440.0176060485142-0.02222036821950.1944656680040.01274696787420.176936477553-2.6315880311414.2382528144-3.77922299431
34.95866679763-2.82938492897-2.319263571647.000051817584.973646472654.031801314720.2398327455750.07047726874820.5155312828070.3855758860510.151129099970.116625158808-1.26274460046-0.296691115299-0.4549261617040.5049656406650.1006310814860.01756666742910.2231940336170.004269502810420.322723747462-3.1802512198822.49941575330.313336169155
43.553027593070.001683567986370.3225597733786.561762697261.388497388754.25939065747-0.0785259421209-0.2768717652540.07646928102190.138734932834-0.08059420745890.993994632204-0.944688277801-1.364148480290.120572366420.324776761060.1407052274720.002865464946690.478765837231-0.01508629557150.369362021327-10.729641556912.99290230574.63065620224
51.56498736652-0.708967021054-1.005607919321.38651674743-0.1197917314593.582891352040.02811872333670.01926024876650.08767019455350.1763674008590.0497002699165-0.0214520485031-0.2404053844350.100001387382-0.07988927613440.17140867453-0.0140006067548-0.02104253244380.123387319743-0.003432608161420.1932264304645.15936640858.98470526492-1.67564457008
67.06651945899-6.32779900085-5.630717013976.641922846866.624498236438.00131876377-0.336010748928-0.606254249967-0.3190547380671.1178350307-0.1637967400490.9610231369790.585333816044-0.7245663972120.3242149752180.339284417648-0.09560776424180.0854387455320.577901393584-0.05081502297460.396498782746-10.1582468513.774526118236.3451779999
75.687045894240.568814229034-0.679355654466.86457682433-0.3564045298685.20079596881-0.0376955151543-0.2869701275160.1989862458990.2951357826590.111926362952-0.0052813058426-0.271358775689-0.105290800933-0.07270031744420.183468334347-0.01076645695850.002688433805550.1695124269790.0001669089147350.1307136192192.168143829634.5386497949811.0362710556
81.488892639540.148191794186-0.7906139157630.64069124785-1.339008490043.34085201022-0.0285773361073-0.1030586756730.02779368437910.112228598018-0.0953193955216-0.147496898127-0.3013149952980.2535238409150.1255374039220.18430678141-0.0455045356926-0.02421766991110.156216874865-0.01435325869110.2297457689610.60685358333.510284078763.81285625897
94.178360363051.33203505366-1.782773369893.86136071052-1.616408654016.20914680958-0.118688403853-0.3476971887680.326737445868-0.120425789967-0.197960375079-0.334967657857-0.2781579914650.6182749368980.2257710746020.134770716103-0.0160863061847-0.05974422763240.197103792885-0.01906381234870.32086810455515.85754416444.755546329273.45225450532
103.001716828110.269695562546-0.1736165208812.515870311830.3836088352444.117059835420.00372903227789-0.07416894949190.1973402440860.3949854639940.11835561240.0408643300044-0.16137044471-0.102029106444-0.1430973647470.2411150436790.0134553283615-0.03105968641520.1050648349910.002639980832730.1437903419961.619302126659.560363674430.611953065349
115.270461372293.774282638242.10917649495.147243760262.790482464475.20807842672-0.05129289212570.572631881970.03903285289550.075147905611-0.1084611290630.05269585212670.276549832166-0.1222108111420.1952966486260.224288490735-0.02911008882960.006896280093550.40726137169-0.02017644116610.23339334213416.530871718342.141602181628.9475432089
122.946332594081.16664748916-1.8238982532.92822439893-0.8118974020233.121549841470.1041251467870.407821201035-0.127479130370.218241272412-0.0543697062642-0.05463274920140.1456114406-0.371132547094-0.05554397928550.246183682044-0.0546463437381-0.0609917899510.345079892384-0.02111137157310.1957467689315.5858598351337.64997501433.6202148229
134.24654687828-1.41551308791-0.9748938840662.82035322489-0.2957420272472.98455948616-0.1182036159410.3369231357520.03142108068750.0855476387351-0.105199672166-0.00193505982439-0.474292749591-0.1447940668830.1858502305120.326627750362-0.0569741773847-0.02602891336080.326463137217-0.04596503750970.19988731461430.554501765836.04821701668.96820128392
143.18881094333-0.07388896350381.659871801822.713086554820.6241675185265.686274357320.02275363590790.2928764899410.291774575856-0.171062816319-0.189150527231-0.084108504562-0.5835091864430.3690869023560.09037128054930.190623024972-0.02204410880060.0075248739230.2630424514550.04507165396290.21008507466636.534519588431.1822882014-0.685263537732
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 313 through 329 )AA313 - 3291 - 17
22chain 'A' and (resid 330 through 343 )AA330 - 34318 - 31
33chain 'A' and (resid 344 through 360 )AA344 - 36032 - 50
44chain 'A' and (resid 361 through 374 )AA361 - 37451 - 64
55chain 'A' and (resid 375 through 400 )AA375 - 40065 - 92
66chain 'A' and (resid 401 through 410 )AA401 - 41093 - 104
77chain 'A' and (resid 411 through 436 )AA411 - 436105 - 132
88chain 'A' and (resid 437 through 466 )AA437 - 466133 - 162
99chain 'A' and (resid 467 through 478 )AA467 - 478163 - 174
1010chain 'A' and (resid 479 through 502 )AA479 - 502175 - 198
1111chain 'C' and (resid 319 through 371 )CE319 - 3711 - 53
1212chain 'C' and (resid 372 through 502 )CE372 - 50254 - 184
1313chain 'B' and (resid 315 through 343 )BG315 - 3431 - 31
1414chain 'B' and (resid 344 through 502 )BG344 - 50232 - 197

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