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- PDB-5y3t: Crystal structure of hetero-trimeric core of LUBAC: HOIP double-U... -

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Basic information

Entry
Database: PDB / ID: 5y3t
TitleCrystal structure of hetero-trimeric core of LUBAC: HOIP double-UBA complexed with HOIL-1L UBL and SHARPIN UBL
Components
  • E3 ubiquitin-protein ligase RNF31
  • RanBP-type and C3HC4-type zinc finger-containing protein 1
  • Sharpin
KeywordsLIGASE / HOIP / HOIL-1L / SHARPIN / Linear-Ubiquitin Assembly Complex / NF-KB Activation / LUBAC Tethering Motif / LUBAC Stabilization
Function / homology
Function and homology information


TNFR1-induced proapoptotic signaling / apoptotic nuclear changes / regulation of CD40 signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein linear polyubiquitination / Regulation of TNFR1 signaling / LUBAC complex / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / CD40 receptor complex ...TNFR1-induced proapoptotic signaling / apoptotic nuclear changes / regulation of CD40 signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein linear polyubiquitination / Regulation of TNFR1 signaling / LUBAC complex / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / CD40 receptor complex / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase activator activity / negative regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / keratinization / epidermis development / polyubiquitin modification-dependent protein binding / ubiquitin ligase complex / tumor necrosis factor-mediated signaling pathway / mitochondrion organization / ubiquitin binding / protein kinase C binding / brain development / cytoplasmic side of plasma membrane / negative regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of NF-kappaB transcription factor 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 / postsynaptic density / protein ubiquitination / defense response to bacterium / positive regulation of apoptotic process / ubiquitin protein ligase binding / dendrite / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / identical protein binding / metal ion binding / cytosol
Similarity search - Function
RanBP-type and C3HC4-type zinc finger-containing protein 1/SHARPIN / Sharpin, PH domain / Sharpin PH domain / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal ...RanBP-type and C3HC4-type zinc finger-containing protein 1/SHARPIN / Sharpin, PH domain / Sharpin PH domain / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / PUB-like domain superfamily / PUB domain / PUB domain / IBR domain, a half RING-finger domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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 domain profile. / Ubiquitin-like domain / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Sharpin / E3 ubiquitin-protein ligase RNF31 / RanBP-type and C3HC4-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTokunaga, A. / Fujita, H. / Ariyoshi, M. / Ohki, I. / Tochio, H. / Iwai, K. / Shirakawa, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP26119004 Japan
Japan Society for the Promotion of Science15H01182 Japan
CitationJournal: Cell Rep / Year: 2018
Title: Cooperative Domain Formation by Homologous Motifs in HOIL-1L and SHARPIN Plays A Crucial Role in LUBAC Stabilization.
Authors: Fujita, H. / Tokunaga, A. / Shimizu, S. / Whiting, A.L. / Aguilar-Alonso, F. / Takagi, K. / Walinda, E. / Sasaki, Y. / Shimokawa, T. / Mizushima, T. / Ohki, I. / Ariyoshi, M. / Tochio, H. / ...Authors: Fujita, H. / Tokunaga, A. / Shimizu, S. / Whiting, A.L. / Aguilar-Alonso, F. / Takagi, K. / Walinda, E. / Sasaki, Y. / Shimokawa, T. / Mizushima, T. / Ohki, I. / Ariyoshi, M. / Tochio, H. / Bernal, F. / Shirakawa, M. / Iwai, K.
History
DepositionJul 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: E3 ubiquitin-protein ligase RNF31
C: Sharpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7724
Polymers53,6803
Non-polymers921
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Presence of all the protein components in eluted fraction were verified by mass spectrometry., native gel electrophoresis, Formation of a single complex was confirmed.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-61 kcal/mol
Surface area21410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.902, 59.732, 58.554
Angle α, β, γ (deg.)90.00, 97.42, 90.00
Int Tables number5
Space group name H-MC121

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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: 15762.995 Da / Num. of mol.: 1 / Fragment: UNP residues 1-140
Source method: isolated from a genetically manipulated source
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, RING-type E3 ubiquitin transferase
#2: Protein E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / Putative Ariadne-like ubiquitin ligase / PAUL / RING finger ...HOIL-1-interacting protein / HOIP / Putative Ariadne-like ubiquitin ligase / PAUL / RING finger protein 31 / RING-type E3 ubiquitin transferase RNF31


Mass: 17995.115 Da / Num. of mol.: 1 / Fragment: UNP residues 474-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnf31, Paul / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q924T7, RING-type E3 ubiquitin transferase
#3: Protein Sharpin / Shank-associated RH domain-interacting protein / Shank-interacting protein-like 1 / mSIPL1


Mass: 19921.514 Da / Num. of mol.: 1 / Fragment: UNP residues 163-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sharpin, Cpdm, Sipl1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q91WA6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Magnesium sulfate, MES

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 7, 2017
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19275 / % possible obs: 99.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.9 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DBG

4dbg


Resolution: 2.4→48.19 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.857 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23961 1413 7.3 %RANDOM
Rwork0.18567 ---
obs0.18971 17862 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.224 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.03 Å2
2--0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.4→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 6 21 3342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193391
X-RAY DIFFRACTIONr_bond_other_d0.0020.023227
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9574597
X-RAY DIFFRACTIONr_angle_other_deg1.00437415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0865421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71223.789161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93515568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1271529
X-RAY DIFFRACTIONr_chiral_restr0.0870.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213859
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02782
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6946.1531693
X-RAY DIFFRACTIONr_mcbond_other4.6946.1511692
X-RAY DIFFRACTIONr_mcangle_it6.4669.2242111
X-RAY DIFFRACTIONr_mcangle_other6.4659.2252112
X-RAY DIFFRACTIONr_scbond_it5.736.8221698
X-RAY DIFFRACTIONr_scbond_other5.736.8211698
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5519.9662487
X-RAY DIFFRACTIONr_long_range_B_refined10.33148.9083653
X-RAY DIFFRACTIONr_long_range_B_other10.3348.9133654
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 113 -
Rwork0.279 1219 -
obs--92.89 %

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