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- PDB-3k9o: The crystal structure of E2-25K and UBB+1 complex -

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Basic information

Entry
Database: PDB / ID: 3k9o
TitleThe crystal structure of E2-25K and UBB+1 complex
Components
  • Ubiquitin-conjugating enzyme E2 K
  • Ubiquitin
KeywordsLIGASE / E2-25K / UBB+1 / complex structure / ATP-binding / Isopeptide bond / Nucleotide-binding / Ubl conjugation pathway
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 / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / cellular response to interferon-beta ...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 / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / cellular response to interferon-beta / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / 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 BACH1 activity / Regulation of PTEN localization / Translesion synthesis by POLK / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 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 / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Degradation of DVL / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Recognition of DNA damage by PCNA-containing replication complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Termination of translesion DNA synthesis / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Degradation of AXIN / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis
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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase, Ruva Protein; domain 3 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / 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-C / Ubiquitin-conjugating enzyme E2 K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKang, G.B. / Ko, S. / Song, S.M. / Lee, W. / Eom, S.H.
CitationJournal: To be Published
Title: Structural Basis of E2-25K/UBB+1 Interaction for Neurotoxicity of Alzheimer Disease by Proteasome Inhibition
Authors: Kang, G.B. / Ko, S. / Song, S.M. / Lee, W. / Eom, S.M.
History
DepositionOct 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,3152
Polymers33,3152
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-7 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.480, 50.547, 71.323
Angle α, β, γ (deg.)90.00, 125.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 K / Ubiquitin-conjugating enzyme E2-25 kDa / E2(25K) / E2-25K / Ubiquitin-protein ligase / Ubiquitin ...Ubiquitin-conjugating enzyme E2-25 kDa / E2(25K) / E2-25K / Ubiquitin-protein ligase / Ubiquitin carrier protein / Huntingtin-interacting protein 2 / HIP-2


Mass: 22487.643 Da / Num. of mol.: 1
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, ubiquitin-protein ligase
#2: Protein Ubiquitin / / UBB+1


Mass: 10827.129 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: P0CG48*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THE CHAIN B DOES NOT CURRENTLY EXIST. N-TERMINAL GLY RESIDUE IN ...A SEQUENCE DATABASE REFERENCE FOR THE CHAIN B DOES NOT CURRENTLY EXIST. N-TERMINAL GLY RESIDUE IN THE CHAIN B IS EXPRESSION TAG

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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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris-HCl (pH 8.5), 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2009
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→58.42 Å / Num. all: 26832 / Num. obs: 26832 / % possible obs: 99.1 %
Reflection shellResolution: 1.8→1.83 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.395 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23325 1387 5 %RANDOM
Rwork0.18704 ---
all0.206 26828 --
obs0.18933 26181 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.055 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å2-0.98 Å2
2---0.27 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 0 165 2326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222201
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.9752986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3115271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.68925.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32215402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2681512
X-RAY DIFFRACTIONr_chiral_restr0.1610.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211634
X-RAY DIFFRACTIONr_mcbond_it1.4551.51367
X-RAY DIFFRACTIONr_mcangle_it2.64222225
X-RAY DIFFRACTIONr_scbond_it3.9793834
X-RAY DIFFRACTIONr_scangle_it6.724.5761
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 96 -
Rwork0.252 1881 -
obs--97.34 %

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