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- PDB-6jb7: Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopep... -

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Basic information

Entry
Database: PDB / ID: 6jb7
TitleCrystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.1 A resolution
Components
  • Ubiquitin-conjugating enzyme E2 K
  • Ubiquitin
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 / mitochondrion transport along microtubule / ubiquitin-ubiquitin ligase activity ...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 / mitochondrion transport along microtubule / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K48-linked ubiquitination / cellular response to interferon-beta / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / 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 / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / 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 / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / positive regulation of peptidyl-threonine phosphorylation / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication 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. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...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. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / UBA-like superfamily / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Helicase, Ruva Protein; domain 3 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / 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: 2.1 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), 2.1 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,9752
Polymers30,9752
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area14540 Å2
Unit cell
Length a, b, c (Å)146.088, 38.124, 60.266
Angle α, β, γ (deg.)90.000, 90.899, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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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: 22398.523 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 / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.56 Å3/Da / Density % sol: 54.59 %
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: 2.05→50 Å / Num. obs: 21798 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 24.47 Å2 / Net I/σ(I): 13.5
Reflection shellResolution: 2.05→2.09 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: 2.1→31.02 Å / SU ML: 0.239 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.203
RfactorNum. reflection% reflection
Rfree0.2503 1881 9.58 %
Rwork0.2148 --
obs0.2182 19642 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 0 52 2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282217
X-RAY DIFFRACTIONf_angle_d0.62043007
X-RAY DIFFRACTIONf_chiral_restr0.044347
X-RAY DIFFRACTIONf_plane_restr0.0041388
X-RAY DIFFRACTIONf_dihedral_angle_d20.5288843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.26051420.23741323X-RAY DIFFRACTION96.45
2.16-2.220.34081420.24011349X-RAY DIFFRACTION99.47
2.22-2.290.32541410.2741318X-RAY DIFFRACTION99.18
2.29-2.370.25371470.24631374X-RAY DIFFRACTION99.8
2.37-2.470.28411400.24271334X-RAY DIFFRACTION99.93
2.47-2.580.29961420.24371373X-RAY DIFFRACTION100
2.58-2.720.26281480.24231383X-RAY DIFFRACTION100
2.72-2.890.26231440.24251360X-RAY DIFFRACTION100
2.89-3.110.29221490.23341362X-RAY DIFFRACTION100
3.11-3.420.28571430.23621391X-RAY DIFFRACTION100
3.42-3.920.24441460.20321370X-RAY DIFFRACTION99.87
3.92-4.930.20721420.16941385X-RAY DIFFRACTION99.54
4.93-31.020.1761550.16771439X-RAY DIFFRACTION99.07

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