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- PDB-8bvl: Crystal structure of the IBR-RING2 domain of HOIL-1 -

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Basic information

Entry
Database: PDB / ID: 8bvl
TitleCrystal structure of the IBR-RING2 domain of HOIL-1
ComponentsRanBP-type and C3HC4-type zinc finger-containing protein 1
KeywordsLIGASE / LUBAC / ubiquitin / RBCK1 / HOIP / SHARPIN / RBR ligase / E3 ligase
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / 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 / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / 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 / 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 / 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. / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 Å
AuthorsStieglitz, B. / Koliopoulos, M.G. / Rittinger, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteCC2075 United Kingdom
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural basis for ubiquitylation by HOIL-1.
Authors: Wu, Q. / Koliopoulos, M.G. / Rittinger, K. / Stieglitz, B.
History
DepositionDec 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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


Theoretical massNumber of molelcules
Total (without water)33,32612
Polymers32,6722
Non-polymers65410
Water1,36976
1
A: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6636
Polymers16,3361
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6636
Polymers16,3361
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.908, 59.263, 57.206
Angle α, β, γ (deg.)90.00, 90.31, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 / RING-type E3 ubiquitin transferase HOIL-1 / Ubiquitin-conjugating enzyme 7-interacting protein 3


Mass: 16335.819 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBCK1, C20orf18, RNF54, UBCE7IP3, XAP3, XAP4 / Plasmid: PET49B / Production host: Escherichia coli BL21 (bacteria)
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 mM magnesium chloride hexahydrate 100mM Tris-HCl pH 7.0 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2829 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2012
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2829 Å / Relative weight: 1
ReflectionResolution: 2.24→41.16 Å / Num. obs: 16782 / % possible obs: 95.79 % / Redundancy: 2.8 % / Biso Wilson estimate: 25.91 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.08046 / Net I/σ(I): 10.14
Reflection shellResolution: 2.24→2.32 Å / Rmerge(I) obs: 0.2176 / Mean I/σ(I) obs: 3.75 / Num. unique obs: 1651 / CC1/2: 0.914

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
ARP/wARPmodel building
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.24→41.16 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 33.65 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2961 847 5.06 %
Rwork0.2341 --
obs0.2371 16740 95.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→41.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 10 76 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.007
X-RAY DIFFRACTIONf_dihedral_angle_d8.347308
X-RAY DIFFRACTIONf_chiral_restr0.061324
X-RAY DIFFRACTIONf_plane_restr0.012418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.380.35021270.29042632X-RAY DIFFRACTION95
2.38-2.560.30571440.2722633X-RAY DIFFRACTION96
2.56-2.820.31091540.25912624X-RAY DIFFRACTION96
2.82-3.230.36311480.26832635X-RAY DIFFRACTION96
3.23-4.070.2671470.22282671X-RAY DIFFRACTION96
4.07-41.160.26191270.19082698X-RAY DIFFRACTION95

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