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- PDB-7yui: Crystal structure of HOIL-1L(195-423) in complex with the linear ... -

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Basic information

Entry
Database: PDB / ID: 7yui
TitleCrystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin
Components
  • Polyubiquitin-C
  • RanBP-type and C3HC4-type zinc finger-containing protein 1
KeywordsPROTEIN BINDING / E3 / ubiquitination
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / 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 / Maturation of protein E / Maturation of protein E ...protein linear polyubiquitination / LUBAC complex / 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 / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / protein sequestering activity / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / ubiquitin binding / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Stabilization of p53 / Hh mutants are degraded by ERAD / Negative regulation of FGFR4 signaling / Activation of NF-kappaB in B cells / Downregulation of SMAD2/3:SMAD4 transcriptional activity
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 superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / RanBP-type and C3HC4-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,7257
Polymers61,3982
Non-polymers3275
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-32 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.500, 90.304, 117.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polyubiquitin-C


Mass: 34551.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein RanBP-type and C3HC4-type zinc finger-containing protein 1


Mass: 26846.248 Da / Num. of mol.: 1
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
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium chloride, 0.1 M Tris(pH 8), 20 %(w/v)PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL17B / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.599→71.59 Å / Num. obs: 19702 / % possible obs: 99.5 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 13.7
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 1.151 / Num. unique obs: 929

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R71, 3B08

7r71

3b08


Resolution: 2.599→71.587 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2575 942 4.78 %
Rwork0.2026 18748 -
obs0.2052 19690 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.64 Å2 / Biso mean: 57.7576 Å2 / Biso min: 22.12 Å2
Refinement stepCycle: final / Resolution: 2.599→71.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4267 0 5 74 4346
Biso mean--51.31 46.65 -
Num. residues----537
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.599-2.73570.36051380.2948257097
2.7357-2.90710.34951440.26482634100
2.9071-3.13160.33121230.25452645100
3.1316-3.44670.29361520.23492656100
3.4467-3.94550.26691280.18932682100
3.9455-4.97070.19471260.16692720100
4.9707-71.5870.21031310.1769284199
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)
13.5009-0.6974-0.48291.711-0.08642.1060.1723-0.1681-0.0503-0.1285-0.06740.1777-0.0605-0.0911-0.06750.28630.018-0.01290.3032-00.2142-27.756214.9979-2.035
23.8342-0.0218-1.49170.6116-0.08211.7761-0.08690.1188-0.2895-0.0655-0.0769-0.11750.18620.05650.10590.34470.0086-0.00860.2781-0.00750.2824-6.617312.7325-16.149
32.317-0.859-1.80461.07550.76432.8698-0.08690.23620.1349-0.0735-0.19680.5879-0.1221-0.81820.23350.51570.14530.040.5838-0.06480.697516.76085.5905-47.6788
43.1992-0.5638-0.03571.97970.45882.43740.12520.49580.7867-0.2466-0.08450.1174-0.4939-0.212-0.11790.50170.04530.0210.40690.11860.65142.763214.8549-62.6222
56.45180.7419-1.38983.7641-0.21834.4790.4840.97670.4567-0.6437-0.05540.13310.075-0.0597-0.29790.36290.10980.00020.47720.02340.2752-19.967321.367-22.9291
63.5966-2.4398-4.01334.1413.00924.46230.43680.33380.7614-0.4982-0.0421-0.4527-0.2668-0.0823-0.34970.408-0.02460.02510.39530.02850.40979.503620.5349-29.9803
73.75030.2159-1.39522.5962-0.53395.05150.0306-0.42720.03110.53370.07870.0675-0.13880.1482-0.03390.4107-0.0280.09940.4271-0.08510.362931.9452-4.2218-38.2002
83.94630.9318-2.06490.7975-0.27862.59240.1208-0.00360.2804-0.00530.01430.1311-0.08590.0559-0.11880.33610.00630.00070.23430.00130.389545.8791-0.4042-58.6577
98.4214-6.6287-1.81976.67251.77675.42030.49340.393-0.011-0.5333-0.4116-0.4362-0.05190.5918-0.12650.3630.004-0.00540.45130.08570.430969.4131-2.4271-80.8469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 54 )A0 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 153 )A55 - 153
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 234 )A154 - 234
4X-RAY DIFFRACTION4chain 'A' and (resid 235 through 304 )A235 - 304
5X-RAY DIFFRACTION5chain 'B' and (resid 193 through 233 )B193 - 233
6X-RAY DIFFRACTION6chain 'B' and (resid 234 through 270 )B234 - 270
7X-RAY DIFFRACTION7chain 'B' and (resid 271 through 300 )B271 - 300
8X-RAY DIFFRACTION8chain 'B' and (resid 301 through 399 )B301 - 399
9X-RAY DIFFRACTION9chain 'B' and (resid 400 through 424 )B400 - 424

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