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- PDB-7bxg: MavC-UBE2N-Ub complex -

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Basic information

Entry
Database: PDB / ID: 7bxg
TitleMavC-UBE2N-Ub complex
Components
  • MavC
  • Polyubiquitin-C
  • Ubiquitin-conjugating enzyme E2 N
KeywordsTRANSFERASE / ubiquitination / deubiquitination / MavC / MvcA / Lpg2149 / UBE2N
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 / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction ...UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / regulation of DNA repair / negative regulation of TORC1 signaling / 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 / antiviral innate immune response / 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 / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / 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 / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / ubiquitin binding / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR3 signaling / Deactivation of the beta-catenin transactivating complex / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
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-C / Ubiquitin-conjugating enzyme E2 N / MvcA insertion domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.705 Å
AuthorsGao, P. / Wang, Y.
CitationJournal: Nat Commun / Year: 2020
Title: Insights into catalysis and regulation of non-canonical ubiquitination and deubiquitination by bacterial deamidase effectors.
Authors: Wang, Y. / Zhan, Q. / Wang, X. / Li, P. / Liu, S. / Gao, G. / Gao, P.
History
DepositionApr 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: MavC
B: Ubiquitin-conjugating enzyme E2 N
D: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)69,9093
Polymers69,9093
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-23 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.527, 150.527, 58.372
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein MavC


Mass: 43999.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: lpg2147 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTL4
#2: 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: 17244.848 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
#3: Protein Polyubiquitin-C


Mass: 8663.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M sodium malonate, pH 7.0, 12% PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 36277 / % possible obs: 100 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 29
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.541 / Num. unique obs: 1038

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TSC,5ZQ3,5EYA

5tsc

5zq3

5eya


Resolution: 2.705→25.111 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.8
RfactorNum. reflection% reflection
Rfree0.2432 --
Rwork0.1929 --
obs0.1977 36277 89.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.11 Å2 / Biso mean: 42.6374 Å2 / Biso min: 8.34 Å2
Refinement stepCycle: final / Resolution: 2.705→25.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4797 0 0 75 4872
Biso mean---33.64 -
Num. residues----601
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.705-2.7420.36951010.301795764
2.742-2.78110.32251020.2859104169
2.7811-2.82260.35561240.2935107178
2.8226-2.86660.3441410.2835122383
2.8666-2.91350.35791310.2765122785
2.9135-2.96370.38531470.2662131589
2.9637-3.01750.34091480.268133092
3.0175-3.07540.32911500.2688136492
3.0754-3.13810.32671390.2622140396
3.1381-3.20620.30011410.2455141597
3.2062-3.28060.31351560.2402144499
3.2806-3.36250.29131570.222142799
3.3625-3.45320.22391640.22131467100
3.4532-3.55450.27261520.22381423100
3.5545-3.66890.27611580.19881520100
3.6689-3.79960.2631440.18851416100
3.7996-3.95120.2431540.1847146699
3.9512-4.13030.23181440.1652139896
4.1303-4.3470.18781440.1517139396
4.347-4.61780.19081530.1452140195
4.6178-4.97170.19361340.1408132392
4.9717-5.46740.17781460.1398124886
5.4674-6.24790.16071250.1506110776
6.2479-7.83180.17991180.1454114279
7.8318-25.110.15871330.1311125085
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1522-0.0189-0.07970.04850.03060.03170.0192-0.0642-0.32790.09310.00610.09780.0757-0.03380.01880.1772-0.0342-0.02150.1463-0.00990.2162-31.741338.152621.9791
20.48650.13410.03780.1497-0.05180.31290.16060.12-0.18350.2593-0.0804-0.1118-0.11150.16690.5270.07660.03490.00020.1816-0.0350.1677-5.3946.52468.3021
30.3834-0.0590.07250.12540.07510.17920.04220.1755-0.0584-0.0444-0.0520.0254-0.04410.12390.00610.15390.0531-0.02210.3065-0.04570.2082-5.898950.0091-3.683
40.7092-0.06310.37790.40.24450.35260.01450.1408-0.92430.0881-0.1734-0.0179-0.0048-0.0002-0.04150.1960.0293-0.01520.0759-0.08430.2479-22.349533.211110.6159
5-0.001-0.00620.00880.0060.00880.0008-0.02810.14720.1001-0.07830.0015-0.06810.09110.07650.0190.2039-0.0146-0.25670.46360.3462-0.3039-18.187764.5363-18.3069
60.0542-0.05880.00370.09440.01790.1022-0.20120.08590.42350.00330.21010.53530.14080.2602-0.05970.1470.0103-0.1340.1525-0.1079-0.1693-32.262260.0561-9.1349
70.0075-0.01870.00320.012-0.02020.00110.00850.057-0.16460.0940.0425-0.2169-0.06170.106300.33420.1071-0.02190.40170.08950.2656-19.003252.6303-2.5865
80.0362-0.0383-0.05880.03370.06280.11320.0428-0.03790.08560.0313-0.2477-0.02020.1659-0.0449-0.07360.1780.13680.03250.3148-0.213-0.0297-28.925652.2951-10.8656
90.0053-0.0124-0.00430.0080.01160.04910.0926-0.11020.14580.17030.050.00960.00160.12050.00690.5792-0.03570.05620.20550.1505-0.6688-40.041645.79933.8567
100.0189-0.0365-0.00980.0434-0.01420.0343-0.2580.160.09360.0264-0.39310.32660.121-0.3259-0.00760.31610.0099-0.02090.1859-0.00680.2563-48.292452.1603-8.1259
110.0057-0.00840.00810.0035-0.00030.00250.0357-0.0918-0.0190.10290.13470.0335-0.08130.0032-0.00010.48970.0149-0.19450.4057-0.03950.3978-12.690652.455327.8768
120.04730.0156-0.0250.04410.02570.03210.019-0.2998-0.0666-0.0830.0671-0.1804-0.18710.24440.17310.3483-0.0196-0.15570.3193-0.02980.3043-10.910749.825920.9794
130.09130.0515-0.0930.0507-0.08080.13490.03140.03370.01860.01190.0250.1358-0.19120.03920.0470.30820.0132-0.12160.245-0.01320.3204-17.972453.416915.0702
140.00190.0009-0.00520.00410.00510.00370.1036-0.0760.03460.07950.1484-0.04070.01520.035400.5953-0.0655-0.09180.3482-0.05090.4726-14.120861.278724.8026
150.0183-0.01160.00760.0077-0.01190.0063-0.0149-0.0518-0.08460.086-0.13520.0294-0.02020.0199-0.01260.2683-0.0161-0.12370.2173-0.00140.2982-23.074347.712217.7591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 64 )A8 - 64
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 173 )A65 - 173
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 259 )A174 - 259
4X-RAY DIFFRACTION4chain 'A' and (resid 260 through 384 )A260 - 384
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 17 )B3 - 17
6X-RAY DIFFRACTION6chain 'B' and (resid 18 through 86 )B18 - 86
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 100 )B87 - 100
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 113 )B101 - 113
9X-RAY DIFFRACTION9chain 'B' and (resid 114 through 132 )B114 - 132
10X-RAY DIFFRACTION10chain 'B' and (resid 133 through 152 )B133 - 152
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 6 )D1 - 6
12X-RAY DIFFRACTION12chain 'D' and (resid 7 through 34 )D7 - 34
13X-RAY DIFFRACTION13chain 'D' and (resid 35 through 55 )D35 - 55
14X-RAY DIFFRACTION14chain 'D' and (resid 56 through 65 )D56 - 65
15X-RAY DIFFRACTION15chain 'D' and (resid 66 through 74 )D66 - 74

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