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- PDB-2lgy: Ubiquitin-like domain from HOIL-1 -

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Basic information

Entry
Database: PDB / ID: 2lgy
TitleUbiquitin-like domain from HOIL-1
ComponentsRanBP-type and C3HC4-type zinc finger-containing protein 1
KeywordsLIGASE / ubiquitin / HOIP / E3 ligase / UBLD
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 / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / protein polyubiquitination / positive regulation of non-canonical NF-kappaB signal transduction / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / 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 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
RanBP-type and C3HC4-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 4
AuthorsBeasley, S.A. / Shaw, G.S.
CitationJournal: Protein Sci. / Year: 2012
Title: Solution structure of the E3 ligase HOIL-1 Ubl domain.
Authors: Beasley, S.A. / Safadi, S.S. / Barber, K.R. / Shaw, G.S.
History
DepositionAug 3, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)10,3541
Polymers10,3541
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein RanBP-type and C3HC4-type zinc finger-containing protein 1 / HBV-associated factor 4 / Heme-oxidized IRP2 ubiquitin ligase 1 / HOIL-1 / Hepatitis B virus X- ...HBV-associated factor 4 / Heme-oxidized IRP2 ubiquitin ligase 1 / HOIL-1 / Hepatitis B virus X-associated protein 4 / RING finger protein 54 / Ubiquitin-conjugating enzyme 7-interacting protein 3


Mass: 10353.765 Da / Num. of mol.: 1 / Fragment: sequence database residues 51-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBCK1, C20orf18, RNF54, UBCE7IP3, XAP3, XAP4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Codon Plus RIL
References: UniProt: Q9BYM8, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: HOIL-1 UBL
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCO
1323D HN(CA)CO
1423D HNCA
1523D HN(CO)CA
1623D HN(CA)CB
1723D CBCA(CO)NH
1823D C(CO)NH
1923D H(CCO)NH
11033D (H)CCH-TOCSY
11133D (H)CCH-COSY aromatic
11232D 1H-13C HSQC aromatic
11332D 1H-13C HSQC aliphatic
11433D 1H-13C NOESY aliphatic
11533D 1H-13C NOESY aromatic
11613D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM potassium phosphate, 1 mM EDTA, 50 mM potassium chloride, 30 uM DSS, 0.2 mM [U-15N] HOIL-1 Ubl, 90% H2O/10% D2O90% H2O/10% D2O
210 mM potassium phosphate, 1 mM EDTA, 50 mM potassium chloride, 30 uM DSS, 0.2 mM [U-13C; U-15N] HOIL-1 Ubl, 90% H2O/10% D2O90% H2O/10% D2O
310 mM potassium phosphate, 1 mM EDTA, 50 mM potassium chloride, 30 uM DSS, 0.2 mM [U-13C; U-15N] HOIL-1 Ubl, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMpotassium phosphate-11
1 mMEDTA-21
50 mMpotassium chloride-31
30 uMDSS-41
0.2 mMHOIL-1 Ubl-5[U-15N]1
10 mMpotassium phosphate-62
1 mMEDTA-72
50 mMpotassium chloride-82
30 uMDSS-92
0.2 mMHOIL-1 Ubl-10[U-13C; U-15N]2
10 mMpotassium phosphate-113
1 mMEDTA-123
50 mMpotassium chloride-133
30 uMDSS-143
0.2 mMHOIL-1 Ubl-15[U-13C; U-15N]3
Sample conditionsIonic strength: 61 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDraw5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.11.0Schwieters, Kuszewski, Tjandra and Clorerefinement
TALOStalosplusCornilescu, Delaglio and Baxgeometry optimization
NMRView8.0.rc47Johnson, One Moon Scientificchemical shift assignment
NMRView8.0.rc47Johnson, One Moon Scientificpeak picking
NMRView8.0.rc47Johnson, One Moon Scientificdata analysis
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thostructure verification
VnmrJ2.1BVariancollection
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: based on modified RECOORD scripts
NMR constraintsNOE constraints total: 1194 / Protein phi angle constraints total count: 65 / Protein psi angle constraints total count: 65
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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