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- PDB-8z30: Crystal structure of HOIP PUB domain in complex with tolfenamic a... -

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Basic information

Entry
Database: PDB / ID: 8z30
TitleCrystal structure of HOIP PUB domain in complex with tolfenamic acid complex
ComponentsE3 ubiquitin-protein ligase RNF31
KeywordsLIGASE / E3 ubiquitin-protein ligase HOIP / sertraline
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / RBR-type E3 ubiquitin transferase / CD40 signaling pathway / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion ...protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / RBR-type E3 ubiquitin transferase / CD40 signaling pathway / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / ubiquitin protein ligase binding / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : / HOIP UBA domain pair ...E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / : / : / : / : / : / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / PUB domain / PUB-like domain superfamily / PUB domain / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 2-[(3-chloro-2-methylphenyl)amino]benzoic acid / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhong, F. / Ruan, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22377119 China
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Repurposing Tolfenamic Acid to Anchor the Uncharacterized Pocket of the PUB Domain for Proteolysis of the Atypical E3 Ligase HOIP.
Authors: Zhong, F. / Zhou, Y. / Liu, M. / Wang, L. / Li, F. / Zhang, J. / Han, Z. / Shi, Y. / Gao, J. / Ruan, K.
History
DepositionApr 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31
C: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,84611
Polymers60,2243
Non-polymers1,6228
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.039, 114.758, 66.186
Angle α, β, γ (deg.)90.00, 109.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-329-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / RING-type E3 ubiquitin transferase RNF31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 20074.553 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31, ZIBRA / Production host: Escherichia coli (E. coli)
References: UniProt: Q96EP0, RBR-type E3 ubiquitin transferase

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Non-polymers , 5 types, 194 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-TLF / 2-[(3-chloro-2-methylphenyl)amino]benzoic acid / Tolfenamic acid


Mass: 261.704 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H12ClNO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, inhibitor*YM
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20 mM Tris, 150 mM NaCl, pH 7.5, 10% w/v PEG1000, 10% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.3→19.53 Å / Num. obs: 29296 / % possible obs: 99.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.43 / Num. unique obs: 2885

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.53 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 2000 6.83 %
Rwork0.1963 --
obs0.1994 29282 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 110 186 4419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024317
X-RAY DIFFRACTIONf_angle_d0.4525853
X-RAY DIFFRACTIONf_dihedral_angle_d7.999631
X-RAY DIFFRACTIONf_chiral_restr0.034653
X-RAY DIFFRACTIONf_plane_restr0.005775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.30661420.24541946X-RAY DIFFRACTION100
2.36-2.420.26151410.22841922X-RAY DIFFRACTION100
2.42-2.490.30321440.2391956X-RAY DIFFRACTION100
2.49-2.570.33271410.24671937X-RAY DIFFRACTION100
2.57-2.660.28951450.23451954X-RAY DIFFRACTION100
2.66-2.770.27841400.22071928X-RAY DIFFRACTION100
2.77-2.90.28781420.22641929X-RAY DIFFRACTION100
2.9-3.050.27251450.22511977X-RAY DIFFRACTION100
3.05-3.240.29171420.21581946X-RAY DIFFRACTION100
3.24-3.490.25451420.21781945X-RAY DIFFRACTION100
3.49-3.840.221430.18851943X-RAY DIFFRACTION100
3.84-4.390.24981450.16571973X-RAY DIFFRACTION100
4.39-5.50.19781430.16321955X-RAY DIFFRACTION100
5.51-19.530.17951450.17131971X-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)
10.0014-0.00440.0181-0.0413-0.0218-0.012-0.27880.5506-0.3176-0.34670.2549-0.23550.3971-0.1220.05210.50850.0720.42040.9496-0.56150.1249-38.5436-4.658514.0133
20.1161-0.02190.03490.2160.09540.2223-0.29130.4984-0.1283-0.57350.4275-0.63280.1185-0.17410.26120.4277-0.07010.19051.0894-0.02020.054-36.13263.834816.9964
30.25610.077-0.03230.1104-0.10660.1091-0.18110.46970.0628-0.07780.07450.3832-0.1444-0.12580.00190.2851-0.03390.01650.3301-0.04160.295-51.99394.552525.7754
4-0.0183-0.05030.0479-0.04950.08310.2264-0.1675-0.05160.12010.23180.3307-0.0533-0.24270.35450.01380.24030.0361-0.03870.3029-0.01450.2741-41.18064.902732.6363
5-0.00110.00810.0212-0.0183-0.00260.00820.2381-0.6285-0.42920.01010.1436-0.34940.0130.10680.00020.72250.20880.07760.6293-0.01460.5953-33.1211-12.376237.7772
60.02810.045-00.02180.0145-0.0026-0.1531-0.6158-0.12650.3135-0.02110.38050.03310.2865-0.00010.4109-0.02010.04370.40610.03460.3987-43.0909-1.031544.8909
70.0455-0.06350.0861-0.012-0.06870.0936-0.0658-0.1067-0.2287-0.24370.10620.2105-0.0433-0.10290.00020.3318-0.02140.00480.24540.00180.3258-48.1518-5.744738.1586
80.03230.0599-0.01360.0936-0.02790.02730.2116-0.0618-0.15450.07550.1208-0.07920.03270.01360.05331.2280.5828-0.0341-1.4534-0.57850.3625-41.0549-18.806734.6865
90.6338-0.10150.08450.0950.00210.12010.00190.79470.0312-0.07630.0743-0.19560.14580.26240.03050.3085-0.0068-0.01330.4424-0.09480.2808-41.02461.393224.2879
100.0237-0.0476-0.0330.09490.04220.06710.01880.28970.1823-0.0606-0.09770.1066-0.057-0.0005-00.3663-0.05360.02250.56670.13240.3764-46.649216.815718.9542
110.02380.02670.18730.09650.26390.87240.0258-0.05820.3877-0.10510.11410.1356-0.9533-0.40620.04110.8105-0.0831-0.03120.2353-0.0210.637-38.09737.482244.2824
12-0.0017-0.0139-0.00270.00040.01220.0019-0.12430.2042-0.1032-0.01420.1236-0.4522-0.15220.2507-0.00030.6958-0.1736-0.04480.58790.03720.6509-27.89531.768545.4214
130.36240.01910.08970.10940.03720.0004-0.0341-0.2329-0.04890.29970.0092-0.01230.08670.4166-0.01210.3583-0.0019-0.07750.2858-0.04040.298-35.160517.710750.9382
140.16830.3223-0.05360.2247-0.11690.05020.13140.1092-0.2972-0.0449-0.13130.1543-0.0950.083200.3180.0232-0.06990.2432-0.02740.3325-49.193323.209143.1429
150.012-0.00810.0481-0.0030.0010.0363-0.07060.2760.00550.09750.36280.0478-0.05410.1658-00.38260.0234-0.00520.3342-0.03810.3653-55.519814.019945.1427
160.10150.01910.0473-0.0108-0.0104-0.01430.0548-0.2578-0.22920.4407-0.1889-0.1109-0.1058-0.0927-0.00010.3747-0.0104-0.02770.2988-0.01110.2977-47.369517.395950.8375
170.0230.0373-0.01650.0203-0.02370.0343-0.2858-0.3566-0.0840.1278-0.02080.2166-0.2862-0.0457-0.0010.57030.00350.13690.4954-0.06830.3879-57.047718.62655.9012
180.0086-0.01410.00460.00650.00060.0253-0.2277-0.11940.30.17060.04920.0588-0.1467-0.0478-0.0030.57720.06250.13280.4067-0.21990.6821-58.216231.465156.0071
190.1398-0.05370.090.0583-0.10130.21610.0075-0.13140.2215-0.1601-0.17560.0046-0.42250.3162-0.08210.5345-0.0262-0.07470.2726-0.03720.4067-39.623127.287945.1814
200.03240.00080.00180.02220.03490.02310.38-0.1924-0.2656-0.42980.1959-0.41190.04460.5163-00.5034-0.09370.05930.61290.03770.6317-25.103619.64440.1684
210.01530.02-0.00880.6068-0.02480.02410.131-0.2675-0.27440.6699-0.00850.40820.1882-0.12950.07570.3247-0.03780.11950.68220.27390.6793-47.2052-7.20874.0521
220.47190.1692-0.1061.03470.91471.05580.1716-0.0694-0.278-0.1432-0.0690.0253-0.1014-0.34430.11660.19610.0161-0.04730.33190.10280.3487-39.0523-3.144464.1293
230.37680.24010.1060.457-0.15950.11910.1452-0.1595-0.1723-0.04970.0364-0.1711-0.1896-0.12920.02020.22060.01550.0040.39420.06930.2497-30.37974.140273.3204
240.0270.0053-0.00860.03330.00850.0126-0.02330.14970.10240.15560.112-0.1235-0.3679-0.0745-00.43870.0490.00130.3406-0.04060.3917-26.248212.836168.8747
250.7049-0.03550.58650.6043-0.18890.80710.1833-0.2892-0.0634-0.1688-0.210.2028-0.19-0.75250.15940.23420.080.08170.4180.03940.3263-37.51787.593972.5556
260.1909-0.1823-0.18290.15170.12870.1509-0.1863-0.0441-0.933-0.64-0.06530.0901-0.0268-0.0604-0.01710.38710.0026-0.0260.25190.04310.6758-34.8941-9.57853.6028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 64 )
4X-RAY DIFFRACTION4chain 'A' and (resid 65 through 86 )
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 96 )
6X-RAY DIFFRACTION6chain 'A' and (resid 97 through 107 )
7X-RAY DIFFRACTION7chain 'A' and (resid 108 through 133 )
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 142 )
9X-RAY DIFFRACTION9chain 'A' and (resid 143 through 164 )
10X-RAY DIFFRACTION10chain 'A' and (resid 165 through 179 )
11X-RAY DIFFRACTION11chain 'B' and (resid 4 through 34 )
12X-RAY DIFFRACTION12chain 'B' and (resid 35 through 43 )
13X-RAY DIFFRACTION13chain 'B' and (resid 44 through 64 )
14X-RAY DIFFRACTION14chain 'B' and (resid 65 through 96 )
15X-RAY DIFFRACTION15chain 'B' and (resid 97 through 107 )
16X-RAY DIFFRACTION16chain 'B' and (resid 108 through 122 )
17X-RAY DIFFRACTION17chain 'B' and (resid 123 through 133 )
18X-RAY DIFFRACTION18chain 'B' and (resid 134 through 142 )
19X-RAY DIFFRACTION19chain 'B' and (resid 143 through 164 )
20X-RAY DIFFRACTION20chain 'B' and (resid 165 through 179 )
21X-RAY DIFFRACTION21chain 'C' and (resid 4 through 23 )
22X-RAY DIFFRACTION22chain 'C' and (resid 24 through 64 )
23X-RAY DIFFRACTION23chain 'C' and (resid 65 through 96 )
24X-RAY DIFFRACTION24chain 'C' and (resid 97 through 114 )
25X-RAY DIFFRACTION25chain 'C' and (resid 115 through 164 )
26X-RAY DIFFRACTION26chain 'C' and (resid 165 through 179 )

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