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- PDB-6lp2: Structure of Lpg2148/UBE2N-Ub complex -

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Basic information

Entry
Database: PDB / ID: 6lp2
TitleStructure of Lpg2148/UBE2N-Ub complex
Components
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 N
  • Uncharacterized protein lpg2148
KeywordsTRANSFERASE / complex / deamidase / transglutaminase
Function / homology
Function and homology information


UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / hypothalamus gonadotrophin-releasing hormone neuron development / DNA damage tolerance / female meiosis I / positive regulation of protein monoubiquitination / fat pad development ...UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / hypothalamus gonadotrophin-releasing hormone neuron development / DNA damage tolerance / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / E2 ubiquitin-conjugating enzyme / female gonad development / positive regulation of double-strand break repair / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / regulation of DNA repair / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / negative regulation of TORC1 signaling / 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 / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / antiviral innate immune response / 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 / positive regulation of DNA repair / 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 / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / ubiquitin binding / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of protein ubiquitination / 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 / regulation of mitochondrial membrane potential / 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 / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling
Similarity search - Function
: / MvcA insertion domain / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...: / MvcA insertion domain / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 N / MvcA insertion domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.479 Å
AuthorsFeng, Y. / Wang, Y. / Huang, Y. / Li, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31822012 China
CitationJournal: To Be Published
Title: Structure of Lpg2148/UBE2N-Ub complex
Authors: Feng, Y. / Wang, Y. / Huang, Y. / Li, D.
History
DepositionJan 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein lpg2148
C: Ubiquitin
D: Ubiquitin-conjugating enzyme E2 N


Theoretical massNumber of molelcules
Total (without water)69,8923
Polymers69,8923
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-21 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.953, 71.266, 75.111
Angle α, β, γ (deg.)90.000, 90.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein lpg2148


Mass: 44157.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2148 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTL3
#2: 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
#3: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17157.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, potassium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.479→50 Å / Num. obs: 25834 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.987 / Net I/σ(I): 21.4
Reflection shellResolution: 2.479→2.568 Å / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2132 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SUJ, 1UBQ, 1J7D

5suj

1ubq

1j7d


Resolution: 2.479→31.872 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 23.84
RfactorNum. reflection% reflection
Rfree0.2326 1306 5.07 %
Rwork0.1751 --
obs0.1781 25834 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.03 Å2 / Biso mean: 39.0475 Å2 / Biso min: 16.89 Å2
Refinement stepCycle: final / Resolution: 2.479→31.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4844 0 0 142 4986
Biso mean---37.67 -
Num. residues----606
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.479-2.52630.3348990.2237203275
2.5263-2.57780.31741100.2085246791
2.5778-2.63390.31261520.2123267097
2.6339-2.69510.24851100.1983273099
2.6951-2.76250.27631410.20452673100
2.7625-2.83710.23481560.20482730100
2.8371-2.92060.28291430.20992719100
2.9206-3.01480.33171500.20972695100
3.0148-3.12240.25491530.2012748100
3.1224-3.24730.24391380.19772692100
3.2473-3.39490.23621280.1972741100
3.3949-3.57370.27841480.17682719100
3.5737-3.79730.23181460.17862686100
3.7973-4.08990.22951350.16142724100
4.0899-4.50050.20211560.13712704100
4.5005-5.14930.17381690.13972687100
5.1493-6.47870.23651470.16422727100
6.4787-31.8720.16641690.1433260998

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