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- PDB-7yuj: Crystal structure of HOIL-1L(365-510) -

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Basic information

Entry
Database: PDB / ID: 7yuj
TitleCrystal structure of HOIL-1L(365-510)
ComponentsRanBP-type and C3HC4-type zinc finger-containing protein 1
KeywordsLIGASE / E3 / ubiquitination / RBR
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / cytoplasmic sequestering of protein / RBR-type E3 ubiquitin transferase / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / negative regulation of NF-kappaB transcription factor activity / protein sequestering activity ...protein linear polyubiquitination / LUBAC complex / cytoplasmic sequestering of protein / RBR-type E3 ubiquitin transferase / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / negative regulation of NF-kappaB transcription factor activity / protein sequestering activity / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / defense response to bacterium / identical protein binding / metal ion binding / cytosol
Similarity search - Function
: / : / : / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Zinc finger RanBP2 type profile. ...: / : / : / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / 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. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / RanBP-type and C3HC4-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.865 Å
AuthorsXiao, L. / Pan, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21621002 China
CitationJournal: Sci Adv / Year: 2023
Title: Mechanistic insights into the enzymatic activity of E3 ligase HOIL-1L and its regulation by the linear ubiquitin chain binding.
Authors: Xu, X. / Wang, Y. / Zhang, Y. / Wang, Y. / Yin, Y. / Peng, C. / Gong, X. / Li, M. / Zhang, Y. / Zhang, M. / Tang, Y. / Zhou, X. / Liu, H. / Pan, L.
History
DepositionAug 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RanBP-type and C3HC4-type zinc finger-containing protein 1
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,33113
Polymers33,5712
Non-polymers76011
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-11 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.252, 59.870, 57.818
Angle α, β, γ (deg.)90.000, 90.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RanBP-type and C3HC4-type zinc finger-containing protein 1 / HOIL-1


Mass: 16785.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBCK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BYM8, RBR-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 22 % w/v Poly(acrylic acid sodium salt) 5,100, 100 mM HEPES(pH 7.5), 20 mM Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.865→57.81 Å / Num. obs: 27779 / % possible obs: 91.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 12
Reflection shellResolution: 1.87→1.97 Å / Rmerge(I) obs: 0.39 / Num. unique obs: 2558

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.865→26.623 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1868 1355 4.89 %
Rwork0.1531 26370 -
obs0.1547 27725 91.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.1 Å2 / Biso mean: 39.5712 Å2 / Biso min: 17.75 Å2
Refinement stepCycle: final / Resolution: 1.865→26.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 17 220 2551
Biso mean--43.39 43.54 -
Num. residues----299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8655-1.93210.2735760.2315153954
1.9321-2.00950.23841190.197202971
2.0095-2.10090.23241090.1839256088
2.1009-2.21160.21681590.175285199
2.2116-2.35010.21071390.15942872100
2.3501-2.53140.24071310.16142899100
2.5314-2.78590.20181540.16492884100
2.7859-3.18850.20282080.17142839100
3.1885-4.01490.16981130.14262936100
4.0149-26.6230.1391470.1245296199
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)
12.0393-1.26690.84191.45291.54746.723-0.0920.13220.3461-0.33130.0267-0.1758-0.25550.372-0.00860.3644-0.0101-0.05690.23620.02520.24324.45.9387-20.1421
21.2226-1.1750.18715.55552.67842.440.101-0.3021-0.3790.4982-0.28170.23520.6932-0.0130.1120.5133-0.0042-0.05960.22530.02180.2274-1.8974-3.7947-15.6643
35.5131-3.02070.22445.5013-0.46576.3750.18850.1671-0.1762-0.6539-0.23380.43720.3361-0.08060.02570.39360.0242-0.08410.2282-0.01070.1998-2.68881.0027-26.3267
45.423-0.8753-0.454.3491.67963.94040.00940.57780.3082-0.40.0298-0.183-0.51620.3256-0.03770.5048-0.0307-0.00040.30650.03930.22659.3302-8.2017-32.2153
53.51531.781-0.93185.6725-2.23583.05960.053-0.20410.16870.106-0.2069-0.8292-0.58340.87370.11870.3901-0.13260.00310.3816-0.02070.345216.7138-10.9677-22.8537
61.6613-0.7667-1.18611.8481-1.26834.6025-0.01220.0681-0.0028-0.4032-0.00220.088-0.111-0.0260.00910.2537-0.011-0.06070.1875-0.0030.17733.9176-17.6452-15.5374
76.61791.878-2.41255.20992.91223.7737-0.1379-0.3221-0.25660.3791-0.08760.14270.81520.22890.19620.33190.0401-0.00370.2020.04980.22543.7374-26.6091-4.1032
88.158-0.42842.41534.8091-0.18977.8921-0.2401-0.50730.32830.03220.02260.2589-0.4721-0.18220.18290.2344-0.0017-0.04740.2089-0.00160.23374.8071-17.062-2.9422
95.7674-4.70533.48165.3246-1.74354.6112-0.0824-0.5172-0.7445-0.33690.66410.76950.1608-0.6009-0.35620.3585-0.0088-0.13860.30630.14040.52668.2802-5.8456-4.4647
104.35762.31421.22451.9792-1.10434.43210.16580.0471-0.3137-0.2-0.12260.09860.0098-0.07230.02340.1648-0.0032-0.08180.22890.02380.383417.5367-6.9616-0.8577
116.2045-1.78180.17746.3966-3.45165.5473-0.16990.02660.46780.33450.0085-0.7547-0.0948-0.00380.12490.2294-0.0095-0.09670.21310.04270.418923.7497-6.96332.9806
124.0772-0.3871-0.03024.0993-2.0283.5720.21310.4124-0.6394-0.0513-0.1886-0.8249-0.03270.4787-0.01170.21650.0153-0.01430.2994-0.0570.548830.83372.1046-8.6503
133.1605-2.85010.08716.81541.13824.73180.13181.0125-0.4772-0.9876-0.3738-0.12050.12470.05370.12510.3739-0.01210.06490.4909-0.14810.488422.36335.1268-16.5396
145.24530.1762-0.41561.2279-1.00281.6054-0.0251-0.10320.16290.0432-0.038-0.4238-0.11260.08370.09680.2261-0.0014-0.05460.1971-0.00530.258713.499511.7984-4.8552
153.04371.6649-3.32263.521.37218.7662-0.06890.26210.88760.2512-0.03390.0107-0.2034-0.6650.06970.2740.0576-0.09160.2610.01140.341.794119.9852-5.0239
163.11210.05610.68283.8510.37094.67210.0418-0.08480.07990.1679-0.1177-0.22480.2746-0.34810.02580.2359-0.0072-0.01060.2391-0.0060.19371.36311.09-6.9251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 362 through 378 )A362 - 378
2X-RAY DIFFRACTION2chain 'A' and (resid 379 through 387 )A379 - 387
3X-RAY DIFFRACTION3chain 'A' and (resid 388 through 399 )A388 - 399
4X-RAY DIFFRACTION4chain 'A' and (resid 400 through 425 )A400 - 425
5X-RAY DIFFRACTION5chain 'A' and (resid 426 through 451 )A426 - 451
6X-RAY DIFFRACTION6chain 'A' and (resid 452 through 488 )A452 - 488
7X-RAY DIFFRACTION7chain 'A' and (resid 489 through 499 )A489 - 499
8X-RAY DIFFRACTION8chain 'A' and (resid 500 through 510 )A500 - 510
9X-RAY DIFFRACTION9chain 'B' and (resid 361 through 370 )B361 - 370
10X-RAY DIFFRACTION10chain 'B' and (resid 371 through 387 )B371 - 387
11X-RAY DIFFRACTION11chain 'B' and (resid 388 through 399 )B388 - 399
12X-RAY DIFFRACTION12chain 'B' and (resid 400 through 425 )B400 - 425
13X-RAY DIFFRACTION13chain 'B' and (resid 426 through 452 )B426 - 452
14X-RAY DIFFRACTION14chain 'B' and (resid 453 through 488 )B453 - 488
15X-RAY DIFFRACTION15chain 'B' and (resid 489 through 499 )B489 - 499
16X-RAY DIFFRACTION16chain 'B' and (resid 500 through 510 )B500 - 510

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