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- PDB-8im5: Solution structure of the mouse HOIL1-L NZF domain in the free form -

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Basic information

Entry
Database: PDB / ID: 8im5
TitleSolution structure of the mouse HOIL1-L NZF domain in the free form
ComponentsRanBP-type and C3HC4-type zinc finger-containing protein 1
KeywordsIMMUNE SYSTEM / Ubiquitin-binding
Function / homology
Function and homology information


TNFR1-induced proapoptotic signaling / TNFR1-induced NF-kappa-B signaling pathway / protein linear polyubiquitination / Regulation of TNFR1 signaling / LUBAC complex / RBR-type E3 ubiquitin transferase / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway ...TNFR1-induced proapoptotic signaling / TNFR1-induced NF-kappa-B signaling pathway / protein linear polyubiquitination / Regulation of TNFR1 signaling / LUBAC complex / RBR-type E3 ubiquitin transferase / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / ubiquitin binding / protein kinase C binding / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / ubiquitin-protein transferase activity / T cell receptor signaling pathway / double-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / positive regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / identical protein binding / metal ion binding
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 RanBP2-type signature. ...: / : / : / 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
RanBP-type and C3HC4-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWalinda, E. / Morimoto, D.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K15756 Japan
Japan Society for the Promotion of Science (JSPS)22K06161 Japan
Japan Society for the Promotion of Science (JSPS)18K14665 Japan
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Solution structure of the HOIL-1L NZF domain reveals a conformational switch regulating linear ubiquitin affinity.
Authors: Walinda, E. / Sugase, K. / Ishii, N. / Shirakawa, M. / Iwai, K. / Morimoto, D.
History
DepositionMar 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 27, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,5653
Polymers7,4341
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 250structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein RanBP-type and C3HC4-type zinc finger-containing protein 1 / Heme-oxidized IRP2 ubiquitin ligase 1 homolog / HOIL-1 / RING-type E3 ubiquitin transferase HOIL-1 ...Heme-oxidized IRP2 ubiquitin ligase 1 homolog / HOIL-1 / RING-type E3 ubiquitin transferase HOIL-1 / UbcM4-interacting protein 28 / Ubiquitin-conjugating enzyme 7-interacting protein 3


Mass: 7434.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ZN / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rbck1, Rbck, Ubce7ip3, Uip28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9WUB0, RBR-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aliphatic
121isotropic13D 1H-13C NOESY aromatic
131isotropic13D 1H-15N NOESY
241anisotropic1HSQC-DSSE (IPAP)
351anisotropic1HSQC-DSSE (IPAP)
161isotropic1HSQC-DSSE (IPAP)

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] HOIL-1L NZF domain, 20 mM HEPES pH 7.0, 1 mM TCEP, 50 mM sodium chloride, 95% H2O/5% D2O
Details: NMR sample for structure determination 13C- and 15N-NOESY measurements in isotropic liquid
Label: 15N_13C_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHOIL-1L NZF domain[U-100% 13C; U-100% 15N]1
20 mMHEPES pH 7.0natural abundance1
1 mMTCEPnatural abundance1
50 mMsodium chloridenatural abundance1
Sample conditions

pH: 7.0 / PH err: 0.05 / Pressure: 1013.2 mbar / Temperature: 298 K / Temperature err: 0.2

Conditions-IDDetailsIonic strengthLabel
1Buffer conditions for structure determination 13C- and 15N-NOESY measurements in isotropic liquid as described before in Ishii, Naoki, et al. "NMR resonance assignments of the NZF domain of mouse HOIL-1L free and bound to linear di-ubiquitin." Biomolecular NMR Assignments 13.1 (2019): 149-153.70 mMconditions_1
2PEG bicelle nematic phase was obtained by mixing Pentaethylene glycol monododecyl ether (C12E5 PEG, Sigma Aldrich) with NMR buffer (as defined in condition_1) and then stepwise adding small aliquots (1 microliterl) of hexanol (Sigma Aldrich) according to the detailed protocol given on: http://www.nmr2.buffalo.edu/nesg.wiki/Alignment_Media_Preparation70 mManisotropic_1
3Pf1 phage from ASLA biotech was mixed with condition_1 to achieve a final concentration of Pf1 phage of 10 mg/ml.40 mManisotropic_2

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz
Details: 5-mm 15N/13C/1H z-gradient triple resonance cryogenic probe

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Processing

NMR softwareName: CYANA / Version: 3.98.13 / Developer: Peter Guentert / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 250 / Conformers submitted total number: 10

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