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- PDB-2lq7: E2 binding surface on Uba3 beta-grasp domain undergoes a conforma... -

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Basic information

Entry
Database: PDB / ID: 2lq7
TitleE2 binding surface on Uba3 beta-grasp domain undergoes a conformational transition
ComponentsNEDD8-activating enzyme E1 catalytic subunit
KeywordsLIGASE / E1 enzyme / beta grasp domain
Function / homology
Function and homology information


E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / NEDD8 transferase activity / protein neddylation / post-translational protein modification / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / protein modification process / Antigen processing: Ubiquitination & Proteasome degradation ...E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / NEDD8 transferase activity / protein neddylation / post-translational protein modification / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / protein modification process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / regulation of cell cycle / protein heterodimerization activity / protein-containing complex / proteolysis / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / E2 binding / NEDD8-activating enzyme E1 catalytic subunit / E2 binding domain / E2_bind / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme ...Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / E2 binding / NEDD8-activating enzyme E1 catalytic subunit / E2 binding domain / E2_bind / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Roll / Alpha Beta
Similarity search - Domain/homology
NEDD8-activating enzyme E1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsElgin, E.S. / Peterson, F.C. / Volkman, B.F.
CitationJournal: Proteins / Year: 2012
Title: E2-binding surface on Uba3 beta-grasp domain undergoes a conformational transition.
Authors: Elgin, E.S. / Sokmen, N. / Peterson, F.C. / Volkman, B.F. / Dag, C. / Haas, A.L.
History
DepositionFeb 27, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEDD8-activating enzyme E1 catalytic subunit


Theoretical massNumber of molelcules
Total (without water)10,6581
Polymers10,6581
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NEDD8-activating enzyme E1 catalytic subunit / NEDD8-activating enzyme E1C / Ubiquitin-activating enzyme E1C / Ubiquitin-like modifier-activating ...NEDD8-activating enzyme E1C / Ubiquitin-activating enzyme E1C / Ubiquitin-like modifier-activating enzyme 3 / Ubiquitin-activating enzyme 3


Mass: 10658.067 Da / Num. of mol.: 1
Fragment: Interaction with UBE2M core domain residues 368-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA3, UBE1C / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009[pREP4]
References: UniProt: Q8TBC4, 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
1113D 1H-15N NOESY
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.4 mM [U-100% 13C; U-100% 15N] Uba3, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMUba3-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
0.02 %sodium azide-41
Sample conditionsIonic strength: 127 / pH: 6.0 / Pressure: ambient / 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
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
XEASYBartels et al.chemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TopSpinBruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1214 / NOE intraresidue total count: 179 / NOE long range total count: 411 / NOE medium range total count: 233 / NOE sequential total count: 391 / Protein phi angle constraints total count: 76 / Protein psi angle constraints total count: 80
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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