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- PDB-6jb6: Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopep... -

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Basic information

Entry
Database: PDB / ID: 6jb6
TitleCrystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A resolution
Components
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 K
KeywordsLIGASE / complex
Function / homology
Function and homology information


free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / ubiquitin-ubiquitin ligase activity / mitochondrion transport along microtubule ...free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / ubiquitin-ubiquitin ligase activity / mitochondrion transport along microtubule / fat pad development / E2 ubiquitin-conjugating enzyme / female gonad development / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to interferon-beta / regulation of neuron apoptotic process / protein K48-linked ubiquitination / regulation of proteasomal protein catabolic process / energy homeostasis / 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 / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / neuron projection morphogenesis / 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 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / 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 / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex
Similarity search - Function
Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily ...Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Helicase, Ruva Protein; domain 3 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLee, J.-G. / Youn, H.-S. / Lee, Y. / An, J.Y. / Park, K.R. / Kang, J.Y. / Mun, S.A. / Park, J. / Park, T. / Jin, M.W. ...Lee, J.-G. / Youn, H.-S. / Lee, Y. / An, J.Y. / Park, K.R. / Kang, J.Y. / Mun, S.A. / Park, J. / Park, T. / Jin, M.W. / Yang, J. / Eom, S.H.
CitationJournal: To Be Published
Title: Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A resolution
Authors: Lee, J.-G. / Eom, S.H.
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Ubiquitin
A: Ubiquitin-conjugating enzyme E2 K


Theoretical massNumber of molelcules
Total (without water)31,3792
Polymers31,3792
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint2 kcal/mol
Surface area14360 Å2
Unit cell
Length a, b, c (Å)145.798, 38.200, 56.180
Angle α, β, γ (deg.)90.000, 93.551, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Protein Ubiquitin-conjugating enzyme E2 K / Ube2K / E2 ubiquitin-conjugating enzyme K / Huntingtin-interacting protein 2 / HIP-2 / Ubiquitin ...Ube2K / E2 ubiquitin-conjugating enzyme K / Huntingtin-interacting protein 2 / HIP-2 / Ubiquitin carrier protein / Ubiquitin-conjugating enzyme E2-25 kDa / Ubiquitin-conjugating enzyme E2-25K / Ubiquitin-protein ligase


Mass: 22801.982 Da / Num. of mol.: 1 / Mutation: C92K, K97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2K, HIP2, LIG / Production host: Escherichia coli (E. coli)
References: UniProt: P61086, E2 ubiquitin-conjugating enzyme
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, PEG 400, magnesium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 9091 / % possible obs: 99.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 37.22 Å2 / Net I/σ(I): 8.9
Reflection shellResolution: 2.67→2.72 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.81 Å / SU ML: 0.2961 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3699
RfactorNum. reflection% reflection
Rfree0.2845 752 9.75 %
Rwork0.2436 --
obs0.2477 7713 88.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.89 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 0 15 2198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00452223
X-RAY DIFFRACTIONf_angle_d0.71233015
X-RAY DIFFRACTIONf_chiral_restr0.0481348
X-RAY DIFFRACTIONf_plane_restr0.0055389
X-RAY DIFFRACTIONf_dihedral_angle_d22.0782845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.3338990.2948943X-RAY DIFFRACTION61.11
2.91-3.20.33061390.2891288X-RAY DIFFRACTION82.49
3.2-3.660.35041700.26851535X-RAY DIFFRACTION98.5
3.66-4.620.271710.22241579X-RAY DIFFRACTION99.66
4.62-45.810.23021730.21911616X-RAY DIFFRACTION98.79

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