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- PDB-7cap: Cyclic Lys48-linked triubiquitin -

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Basic information

Entry
Database: PDB / ID: 7cap
TitleCyclic Lys48-linked triubiquitin
ComponentsUbiquitin
KeywordsSIGNALING PROTEIN / UBIQUITIN / TRIUBIQUITIN / ISOPEPTIDE BOND / NUCLEUS
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / seminiferous tubule development / female gonad development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / neuron projection morphogenesis ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / seminiferous tubule development / female gonad development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / neuron projection morphogenesis / energy homeostasis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / 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 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / regulation of neuron apoptotic process / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Downregulation of ERBB2:ERBB3 signaling / Regulation of PTEN localization / positive regulation of protein ubiquitination / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / regulation of mitochondrial membrane potential / Josephin domain DUBs / 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) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Regulation of signaling by CBL / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ubiquitin-dependent degradation of Cyclin D / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Fanconi Anemia Pathway / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulation of FGFR3 signaling / Peroxisomal protein import / TNFR2 non-canonical NF-kB pathway / Deactivation of the beta-catenin transactivating complex / Stabilization of p53 / Assembly of the pre-replicative complex / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Vpu mediated degradation of CD4 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR1 signaling / Termination of translesion DNA synthesis
Similarity search - Function
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsHiranyakorn, M. / Yanaka, S. / Satoh, T. / Wilasri, T. / Jityuti, B. / Yagi-Utsumi, T. / Kato, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H05229 Japan
CitationJournal: Int J Mol Sci / Year: 2020
Title: NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains.
Authors: Hiranyakorn, M. / Yanaka, S. / Satoh, T. / Wilasri, T. / Jityuti, B. / Yagi-Utsumi, M. / Kato, K.
History
DepositionJun 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: Ubiquitin
B: Ubiquitin
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1239
Polymers25,7303
Non-polymers3926
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-175 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.429, 54.820, 60.954
Angle α, β, γ (deg.)90.00, 121.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: PT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CG47
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.43 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 20% PEG 3350, 200 mM zinc acetate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 22, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 56837 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 25.2
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2796 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 1.33→20 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.927 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.174 3010 5.3 %RANDOM
Rwork0.135 ---
obs0.137 53746 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.735 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20.23 Å2
2---0.4 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.33→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 6 301 2110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0141832
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171752
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.6672462
X-RAY DIFFRACTIONr_angle_other_deg1.0471.6384134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86723.54893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26715374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4491512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021994
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02278
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_it2.2641.939913
X-RAY DIFFRACTIONr_mcbond_other2.2651.938912
X-RAY DIFFRACTIONr_mcangle_it2.7582.9191137
X-RAY DIFFRACTIONr_mcangle_other2.7572.9191138
X-RAY DIFFRACTIONr_scbond_it5.0252.472919
X-RAY DIFFRACTIONr_scbond_other5.0232.472920
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6643.4931324
X-RAY DIFFRACTIONr_long_range_B_refined5.13825.5012006
X-RAY DIFFRACTIONr_long_range_B_other4.98824.8311940
X-RAY DIFFRACTIONr_rigid_bond_restr4.55633584
X-RAY DIFFRACTIONr_sphericity_free24.2285210
X-RAY DIFFRACTIONr_sphericity_bonded15.06553658
LS refinement shellResolution: 1.33→1.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 201 -
Rwork0.243 3973 -
obs--100 %

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