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- PDB-2px9: The intrinsic affinity between E2 and the Cys domain of E1 in Ubi... -

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Basic information

Entry
Database: PDB / ID: 2px9
TitleThe intrinsic affinity between E2 and the Cys domain of E1 in Ubiquitin-like modifications
Components
  • SUMO-activating enzyme subunit 2
  • SUMO-conjugating enzyme UBC9
KeywordsPROTEIN BINDING / Ubiquitination / SUMO / E1 / E2 / Ubc9 / SAE2 / protein-protein interaction / paramagnetic spin-labeling
Function / homology
Function and homology information


SUMO activating enzyme activity / SUMO activating enzyme complex / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / transferase complex / SUMOylation of nuclear envelope proteins / HLH domain binding / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) ...SUMO activating enzyme activity / SUMO activating enzyme complex / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / transferase complex / SUMOylation of nuclear envelope proteins / HLH domain binding / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / synaptonemal complex / SUMO binding / positive regulation of protein sumoylation / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / nuclear export / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / ubiquitin-like protein conjugating enzyme binding / SUMOylation of ubiquitinylation proteins / transcription factor binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / postsynaptic cytosol / nuclear pore / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Transcriptional and post-translational regulation of MITF-M expression and activity / Meiotic synapsis / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / chromosome segregation / SUMOylation of intracellular receptors / Formation of Incision Complex in GG-NER / modulation of chemical synaptic transmission / protein modification process / PML body / PKR-mediated signaling / Schaffer collateral - CA1 synapse / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / Processing of DNA double-strand break ends / transferase activity / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / magnesium ion binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 ...SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Arc Repressor Mutant, subunit A / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SUMO-conjugating enzyme UBC9 / SUMO-activating enzyme subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsWang, J.H. / Hu, W.D. / Cai, S. / Lee, B. / Song, J. / Chen, Y.
CitationJournal: Mol.Cell / Year: 2007
Title: The intrinsic affinity between E2 and the Cys domain of E1 in ubiquitin-like modifications.
Authors: Wang, J. / Hu, W. / Cai, S. / Lee, B. / Song, J. / Chen, Y.
History
DepositionMay 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUMO-activating enzyme subunit 2
B: SUMO-conjugating enzyme UBC9


Theoretical massNumber of molelcules
Total (without water)42,8652
Polymers42,8652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
Representative

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Components

#1: Protein SUMO-activating enzyme subunit 2 / Ubiquitin-like 1- activating enzyme E1B / Anthracycline-associated resistance ARX


Mass: 24833.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9UBT2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein SUMO-conjugating enzyme UBC9 / SUMO-protein ligase / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / Ubiquitin ...SUMO-protein ligase / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / Ubiquitin carrier protein I / Ubiquitin carrier protein 9 / p18


Mass: 18030.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TROSY-HSQC
121TROSY-HN(CA)CB
131TROSY-HNCA
141TROSY-HN(CO)CACB

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Sample preparation

DetailsContents: 0.15-0.6mM E1 Cys domain, 0.15-0.7mM Ubc9, 50mM Phosphate buffer
Solvent system: 50mM Phosphate buffer
Sample conditionsIonic strength: 50mM Phosphate / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, F. et al.data analysis
HADDOCKDominguez, C. et al.refinement
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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