[English] 日本語
Yorodumi
- PDB-9fj3: Structure of ubiquitin bound of coiled-coil UIM form 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fj3
TitleStructure of ubiquitin bound of coiled-coil UIM form 2
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
  • Polyubiquitin-C
KeywordsSIGNALING PROTEIN / Ubiquitin / coiled-coil peptide / UIM
Function / homology
Function and homology information


Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion ...Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Endosomal Sorting Complex Required For Transport (ESCRT) / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / PINK1-PRKN Mediated Mitophagy / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / InlB-mediated entry of Listeria monocytogenes into host cell / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / 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 / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Degradation of AXIN / Peroxisomal protein import / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Degradation of GLI1 by the proteasome / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR2 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Stabilization of p53 / EGFR downregulation / Hedgehog ligand biogenesis / Negative regulation of FGFR4 signaling / Defective CFTR causes cystic fibrosis / Termination of translesion DNA synthesis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Negative regulation of FGFR1 signaling
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: 1.4 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
D: Polyubiquitin-C
E: GLU-GLN-GLU-ILE-GLU-GLU-LEU-GLU-ILE-GLU-ILE-ALA-ILE-LEU-LEU-SER-GLU-ILE-GLU-GLY
F: LYS-GLN-LYS-ILE-ALA-ALA-LEU-LYS-TYR-LYS-ILE-ALA-ALA-LEU-LYS-GLN-LYS-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3378
Polymers26,9396
Non-polymers3982
Water3,639202
1
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
hetero molecules


  • defined by author
  • Evidence: assay for oligomerization, Fluorescence polarization
  • 13.7 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)13,6694
Polymers13,4693
Non-polymers1991
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-20 kcal/mol
Surface area6440 Å2
2
D: Polyubiquitin-C
E: GLU-GLN-GLU-ILE-GLU-GLU-LEU-GLU-ILE-GLU-ILE-ALA-ILE-LEU-LEU-SER-GLU-ILE-GLU-GLY
F: LYS-GLN-LYS-ILE-ALA-ALA-LEU-LYS-TYR-LYS-ILE-ALA-ALA-LEU-LYS-GLN-LYS-ILE
hetero molecules


  • defined by author
  • 13.7 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)13,6694
Polymers13,4693
Non-polymers1991
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-18 kcal/mol
Surface area6670 Å2
Unit cell
Length a, b, c (Å)42.450, 50.090, 52.200
Angle α, β, γ (deg.)90.00, 101.26, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Polyubiquitin-C


Mass: 8922.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Contain GSGGS at the N-terminus resulted from cloning and cleavage of tag. C-terminal RGG are not modeled 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.: 2 / Source method: obtained synthetically
Details: Synthetic coiled-coil peptide. N-terminus of Chains B and E are covalently linked to the N-terminus of Chains C and F, respectively, 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


Mass: 2247.806 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic coiled-coil peptide. N-terminus of Chain C is covalently linked to the N-terminus of Chain B by a triazole crosslinker (A1IDH). C-terminal QG are not modeled due to absence of electron density.
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.: 2 / Source method: obtained synthetically / Formula: C7H9N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.12 %
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)

-
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 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.4→41.63 Å / Num. obs: 58645 / % possible obs: 97 % / Redundancy: 3.4 % / CC1/2: 0.999 / Net I/σ(I): 10.5
Reflection shellResolution: 1.4→1.44 Å / Num. unique obs: 3872 / CC1/2: 0.781

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→41.63 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2377 2016 4.93 %
Rwork0.2169 --
obs0.2179 40902 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 24 202 1991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.721
X-RAY DIFFRACTIONf_dihedral_angle_d14.942725
X-RAY DIFFRACTIONf_chiral_restr0.066303
X-RAY DIFFRACTIONf_plane_restr0.005325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.44261400.4152719X-RAY DIFFRACTION94
1.44-1.470.39041290.37592712X-RAY DIFFRACTION94
1.47-1.520.44381360.34642740X-RAY DIFFRACTION95
1.52-1.570.34081530.31592716X-RAY DIFFRACTION96
1.57-1.620.3521500.28542712X-RAY DIFFRACTION96
1.62-1.690.2721520.26322782X-RAY DIFFRACTION96
1.69-1.760.27121380.23862761X-RAY DIFFRACTION97
1.76-1.860.27541550.22982783X-RAY DIFFRACTION97
1.86-1.970.24181340.21742791X-RAY DIFFRACTION97
1.97-2.130.21471240.19042830X-RAY DIFFRACTION97
2.13-2.340.22021510.20542814X-RAY DIFFRACTION98
2.34-2.680.25871400.2122806X-RAY DIFFRACTION98
2.68-3.370.23261500.21132827X-RAY DIFFRACTION97
3.37-41.630.19571640.18742893X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -42.0029 Å / Origin y: -41.6726 Å / Origin z: -14.3957 Å
111213212223313233
T0.2037 Å2-0.0023 Å20.0057 Å2-0.2063 Å20.0108 Å2--0.2129 Å2
L0.3027 °20.2247 °20.2125 °2-0.208 °20.1443 °2--0.3041 °2
S0.0255 Å °-0.0031 Å °-0.0367 Å °-0.045 Å °-0.0255 Å °-0.0649 Å °0.0154 Å °0.0054 Å °0 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more