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- PDB-9fj3: Structure of ubiquitin bound of coiled-coil UIM form 2 -

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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 / 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 / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / 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 / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / 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 / Regulation of TNFR1 signaling / Hh mutants are degraded by ERAD / 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: 1.4 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
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
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


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


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

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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
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: 2.02 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)

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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 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

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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: 1.4→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

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