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- PDB-9fj4: Structure of ubiquitin bound to coiled coil-UIM form 1 -

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Basic information

Entry
Database: PDB / ID: 9fj4
TitleStructure of ubiquitin bound to coiled coil-UIM form 1
Components
  • GLU-GLN-GLU-ILE-GLU-GLU-LEU-GLU-ILE-GLU-ILE-ALA-ILE-LEU-LEU-SER-GLU-ILE-GLU-GLY
  • LYS-GLN-LYS-ILE-ALA-ALA-LEU-LYS-TYR-LYS-ILE-ALA-ALA-LEU-LYS-GLN-LYS-ILE-GLN
  • Polyubiquitin-C
KeywordsSIGNALING PROTEIN / Ubiquitin / Ubiquitin-interacting motif / coiled-coil peptide
Function / homology
Function and homology information


Maturation of protein E / Maturation of protein E / 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 ...Maturation of protein E / Maturation of protein E / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Hh mutants are degraded by ERAD / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / EGFR downregulation / Termination of translesion DNA synthesis / Degradation of GLI1 by the proteasome / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Iron uptake and transport / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Assembly Of The HIV Virion
Similarity search - Function
: / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsParedes Vergara, P. / Huang, D.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKA23278 United Kingdom
CitationJournal: Chem Sci / Year: 2024
Title: An engineered ubiquitin binding coiled coil peptide.
Authors: Vosbein, P. / Vergara, P.P. / Huang, D.T. / Thomson, A.R.
History
DepositionMay 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 2.0Oct 2, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 16, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-C
B: GLU-GLN-GLU-ILE-GLU-GLU-LEU-GLU-ILE-GLU-ILE-ALA-ILE-LEU-LEU-SER-GLU-ILE-GLU-GLY
C: LYS-GLN-LYS-ILE-ALA-ALA-LEU-LYS-TYR-LYS-ILE-ALA-ALA-LEU-LYS-GLN-LYS-ILE-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6694
Polymers13,4693
Non-polymers1991
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Fluorescence polarization was used to verify interaction
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-20 kcal/mol
Surface area6420 Å2
Unit cell
Length a, b, c (Å)61.360, 49.710, 42.290
Angle α, β, γ (deg.)90.00, 123.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Polyubiquitin-C


Mass: 8922.141 Da / Num. of mol.: 1 / Mutation: contain GSGGS at the N-terminus
Source method: isolated from a genetically manipulated source
Details: Contain GSGGS at the N-terminus resulted from cloning and cleavage of tag. C-terminal GG is not modelled due to the absence of electron density
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein/peptide GLU-GLN-GLU-ILE-GLU-GLU-LEU-GLU-ILE-GLU-ILE-ALA-ILE-LEU-LEU-SER-GLU-ILE-GLU-GLY


Mass: 2299.524 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic coiled-coil peptide. N-terminus is covalently linked to the N-terminus of Chain C by a triazole crosslinker (A1IDH).
Source: (synth.) synthetic construct (others)
#3: Protein/peptide LYS-GLN-LYS-ILE-ALA-ALA-LEU-LYS-TYR-LYS-ILE-ALA-ALA-LEU-LYS-GLN-LYS-ILE-GLN


Mass: 2247.806 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic coiled coil peptide. The N-terminus is covalently linked to the N-terminus of Chain B by a triazole crosslinker (A1IDH). The electron density of C-terminal Gly is absent and ...Details: Synthetic coiled coil peptide. The N-terminus is covalently linked to the N-terminus of Chain B by a triazole crosslinker (A1IDH). The electron density of C-terminal Gly is absent and therefore it is not modeled.
Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-A1IDH / 3-[1-(2-oxidanylideneethyl)-1,2,3-triazol-4-yl]propanal


Mass: 199.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M amino acids, 0.1 M buffer system 1, pH 6.6-6.7 and 36-38 %(v/v) precipitant mix 1 (Molecular Dimension)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.54→35.6 Å / Num. obs: 15709 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Net I/σ(I): 12.9
Reflection shellResolution: 1.54→1.59 Å / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1340 / CC1/2: 0.618

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→35.6 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2664 785 5 %
Rwork0.2251 --
obs0.2271 15709 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 12 45 940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.777
X-RAY DIFFRACTIONf_dihedral_angle_d16.302356
X-RAY DIFFRACTIONf_chiral_restr0.051149
X-RAY DIFFRACTIONf_plane_restr0.005153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.640.36971180.29242486X-RAY DIFFRACTION100
1.64-1.760.27091350.28272477X-RAY DIFFRACTION100
1.76-1.940.25271420.24682453X-RAY DIFFRACTION100
1.94-2.220.30531350.23522465X-RAY DIFFRACTION100
2.22-2.80.25821270.24932510X-RAY DIFFRACTION100
2.8-35.60.25691280.20272533X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 34.2355 Å / Origin y: -28.9531 Å / Origin z: -27.4086 Å
111213212223313233
T0.2255 Å2-0.0115 Å2-0.0151 Å2-0.2507 Å2-0.0407 Å2--0.1988 Å2
L2.2118 °20.777 °2-0.5905 °2-1.2998 °20.1261 °2--0.9382 °2
S0.097 Å °-0.5299 Å °0.079 Å °0.1523 Å °-0.0962 Å °0.0247 Å °0.0589 Å °0.2555 Å °-0.0027 Å °
Refinement TLS groupSelection details: all

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