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- PDB-1zgu: Solution structure of the human Mms2-Ubiquitin complex -

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Basic information

Entry
Database: PDB / ID: 1zgu
TitleSolution structure of the human Mms2-Ubiquitin complex
Components
  • Ubiquitin-conjugating enzyme E2 variant 2
  • Ubiquitin
KeywordsLIGASE/SIGNALING PROTEIN / UEV domain / ubiquitin binding motif / LIGASE-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


: / : / Metalloprotease DUBs / : / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Negative regulators of DDX58/IFIH1 signaling ...: / : / Metalloprotease DUBs / : / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Negative regulators of DDX58/IFIH1 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / : / UCH proteinases / Regulation of PTEN stability and activity / Aggrephagy / Regulation of TP53 Degradation / Translesion synthesis by REV1 / CDK-mediated phosphorylation and removal of Cdc6 / error-free postreplication DNA repair / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Endosomal Sorting Complex Required For Transport (ESCRT) / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Peroxisomal protein import / UBC13-MMS2 complex / Orc1 removal from chromatin / ABC-family proteins mediated transport / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / MAPK6/MAPK4 signaling / DNA double-strand break processing / positive regulation of protein K63-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / postreplication repair / positive regulation of double-strand break repair / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Formation of TC-NER Pre-Incision Complex / Ub-specific processing proteases / Dual incision in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / protein K63-linked ubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / regulation of DNA repair / 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)
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e ...Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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 / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 / Ubiquitin-conjugating enzyme E2 variant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / protein-protein docking
AuthorsLewis, M.J. / Saltibus, L.F. / Hau, D.D. / Xiao, W. / Spyracopoulos, L.
CitationJournal: J.Biomol.Nmr / Year: 2006
Title: Structural Basis for Non-Covalent Interaction Between Ubiquitin and the Ubiquitin Conjugating Enzyme Variant Human MMS2.
Authors: Lewis, M.J. / Saltibus, L.F. / Hau, D.D. / Xiao, W. / Spyracopoulos, L.
History
DepositionApr 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Remark 999Sequence Yeast Ubiquitin was used to obtain restraint information, while human Ubiquitin was used ...Sequence Yeast Ubiquitin was used to obtain restraint information, while human Ubiquitin was used to model the interaction. The sequence differences between yeast and human Ubiquitin are absent from the protein-protein binding interface.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 variant 2
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)24,4392
Polymers24,4392
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #10lowest energy

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 variant 2 / MMS2 / Enterocyte differentiation associated factor EDAF-1 / Enterocyte differentiation promoting ...MMS2 / Enterocyte differentiation associated factor EDAF-1 / Enterocyte differentiation promoting factor / EDPF-1 / Vitamin D3 inducible protein / DDVit 1


Mass: 15834.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2V2, MMS2 / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q15819
#2: Protein Ubiquitin /


Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K48R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P61864, UniProt: P0CG48*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
112F1-filtered, F3-edited NOESY
123F1-filtered, F3-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1[U-15N; U-10% 13C]-hMms2 + Ubiquitin (1:4 ratio) 90% H20 : 10% D2090% H20 : 10% D20
2[U-13C; U-15N]-Ubiquitin + hMms2 (4:1 ratio) 90% H20 : 10% D2090% H20 : 10% D20
3[U-13C; U-15N]-hMms2 + Ubiquitin (1:4 ratio) 90% H20 : 10% D2090% H20 : 10% D20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1150 mM NaCl 7.5 1 atm293 K
2150 mM NaCl 7.5 1 atm303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVarian, Inc.collection
NMRPipe2.3Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.processing
Sparky3.11Goddard, T.D., Kneller, D.G.data analysis
HADDOCK1.3Dominguez, C., Boelens, R., Bonvin, A.M.J.J.structure solution
HADDOCK1.3Dominguez, C., Boelens, R., Bonvin, A.M.J.J.refinement
RefinementMethod: protein-protein docking / Software ordinal: 1 / Details: HADDOCK algorithm
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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