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- PDB-3znz: Crystal structure of OTULIN OTU domain (C129A) in complex with Me... -

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Basic information

Entry
Database: PDB / ID: 3znz
TitleCrystal structure of OTULIN OTU domain (C129A) in complex with Met1- di ubiquitin
Components
  • POLYUBIQUITIN-C
  • PROTEIN FAM105B
KeywordsHYDROLASE
Function / homology
Function and homology information


protein linear deubiquitination / LUBAC complex / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / Maturation of protein E / Maturation of protein E / cysteine-type peptidase activity ...protein linear deubiquitination / LUBAC complex / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / Maturation of protein E / Maturation of protein E / cysteine-type peptidase activity / 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) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Defective CFTR causes cystic fibrosis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Stabilization of p53
Similarity search - Function
Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues ...Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Polyubiquitin-C / Ubiquitin thioesterase otulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKeusekotten, K. / Elliott, P.R. / Glockner, L. / Kulathu, Y. / Wauer, T. / Krappmann, D. / Hofmann, K. / Komander, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Otulin Antagonizes Lubac Signaling by Specifically Hydrolyzing met1-Linked Polyubiquitin.
Authors: Keusekotten, K. / Elliott, P.R. / Glockner, L. / Fiil, B.K. / Damgaard, R.B. / Kulathu, Y. / Wauer, T. / Hospenthal, M.K. / Gyrd-Hansen, M. / Krappmann, D. / Hofmann, K. / Komander, D.
History
DepositionFeb 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN FAM105B
B: POLYUBIQUITIN-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7039
Polymers49,0302
Non-polymers6727
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-88 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.020, 100.020, 280.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2031-

HOH

21A-2057-

HOH

31A-2191-

HOH

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Components

#1: Protein PROTEIN FAM105B


Mass: 31894.590 Da / Num. of mol.: 1 / Fragment: OTU DOMAIN, RESIDUES 80-352 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLACI / References: UniProt: Q96BN8, ubiquitinyl hydrolase 1
#2: Protein POLYUBIQUITIN-C / MET1-DI UBIQUITIN


Mass: 17135.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLACI / References: UniProt: F5H265, UniProt: P0CG48*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN B: THE LAST THREE RESIDUES (RGG) ARE PART OF THE SECOND UBIQUITIN SEQUENCE. THE UNIPROT ENTRY ...CHAIN B: THE LAST THREE RESIDUES (RGG) ARE PART OF THE SECOND UBIQUITIN SEQUENCE. THE UNIPROT ENTRY REFERS TO A GENE PRODUCT OF UB WHICH IS CLEAVED WITHIN CELLS TO YIELD MONO UB (FIRST HALF OF THE SEQUENCE). THE AUTHORS ENGINEERED A DI-UB MOLECULE FROM THE FUSION OF TWO UB ORFS. MET1-DI UBIQUITIN IS FORMED FROM THE FUSION OF A SECOND UBIQUITIN TO THE 3' CDNA OF UBIQUITIN. CHAIN A: CYS129 MUTATED TO ALA TO PERMIT CO-CRYSTALLISATION WITH MET1-DIUB.

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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: 2.81 Å3/Da / Density % sol: 56.2 % / Description: NONE
Crystal growpH: 6.5 / Details: 100 MM BIS-TRIS, 2M (NH4)2SO4, PH 6.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 29, 2012 / Details: MIRROR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→42.8 Å / Num. obs: 42974 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 27.36 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZNV

3znv


Resolution: 1.9→42.802 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: ML
Details: RESIDUES 93,94,153,160,187,197,222 FROM CHAIN A AND RESIDUES 48,63 FROM CHAIN B HAVE DISORDERED SIDE CHAINS AND WERE TRIMMED TO THE CORRESPONDING ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.222 2168 5.1 %
Rwork0.1839 --
obs0.1857 42965 99.97 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.949 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4091 Å20 Å20 Å2
2--4.4091 Å20 Å2
3----8.8181 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 35 370 3699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073447
X-RAY DIFFRACTIONf_angle_d1.0184680
X-RAY DIFFRACTIONf_dihedral_angle_d14.8641319
X-RAY DIFFRACTIONf_chiral_restr0.07524
X-RAY DIFFRACTIONf_plane_restr0.004599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94420.33161470.25872674X-RAY DIFFRACTION100
1.9442-1.99280.28871570.23372687X-RAY DIFFRACTION100
1.9928-2.04670.28771480.21352661X-RAY DIFFRACTION100
2.0467-2.10690.27161500.20742694X-RAY DIFFRACTION100
2.1069-2.17490.27271230.19282728X-RAY DIFFRACTION100
2.1749-2.25270.26091410.19482672X-RAY DIFFRACTION100
2.2527-2.34290.23791340.192720X-RAY DIFFRACTION100
2.3429-2.44950.28491400.19042697X-RAY DIFFRACTION100
2.4495-2.57860.22741510.18992684X-RAY DIFFRACTION100
2.5786-2.74010.24991450.19352722X-RAY DIFFRACTION100
2.7401-2.95160.24631670.19522698X-RAY DIFFRACTION100
2.9516-3.24860.20941410.19182735X-RAY DIFFRACTION100
3.2486-3.71840.19791490.16662749X-RAY DIFFRACTION100
3.7184-4.68390.18211490.14582757X-RAY DIFFRACTION100
4.6839-42.81270.1781260.18622919X-RAY DIFFRACTION100

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