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- PDB-1y8x: Structural basis for recruitment of Ubc12 by an E2-binding domain... -

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Basic information

Entry
Database: PDB / ID: 1y8x
TitleStructural basis for recruitment of Ubc12 by an E2-binding domain in NEDD8's E1
Components
  • Ubiquitin-activating enzyme E1C
  • Ubiquitin-conjugating enzyme E2 M
KeywordsLIGASE / Ubiquitin-conjugating enzyme E2 M
Function / homology
Function and homology information


E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / NEDD8 transferase activity / protein neddylation / TGF-beta receptor signaling activates SMADs / post-translational protein modification / NIK-->noncanonical NF-kB signaling ...E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / NEDD8 transferase activity / protein neddylation / TGF-beta receptor signaling activates SMADs / post-translational protein modification / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / protein modification process / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / regulation of cell cycle / protein heterodimerization activity / protein-containing complex / proteolysis / nucleoplasm / 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 / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
NEDD8-conjugating enzyme Ubc12 / NEDD8-activating enzyme E1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsHuang, D.T. / Paydar, A. / Zhuang, M. / Waddell, M.B. / Holton, J.M. / Schulman, B.A.
CitationJournal: Mol.Cell / Year: 2005
Title: Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1.
Authors: Huang, D.T. / Paydar, A. / Zhuang, M. / Waddell, M.B. / Holton, J.M. / Schulman, B.A.
History
DepositionDec 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: 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: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 M
B: Ubiquitin-activating enzyme E1C


Theoretical massNumber of molelcules
Total (without water)29,3432
Polymers29,3432
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-6 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.606, 61.518, 125.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 M / Ubiquitin-protein ligase M / Ubiquitin carrier protein M / Nedd8-conjugating enzyme Ubc12


Mass: 18485.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2M, UBC12 / Production host: Escherichia coli (E. coli) / References: UniProt: P61081, ubiquitin-protein ligase
#2: Protein Ubiquitin-activating enzyme E1C / Nedd8-activating enzyme E1C / Ubiquitin-activating enzyme 3 homolog


Mass: 10856.974 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE1C, UBA3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TBC4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.11 %

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Data collection

Diffraction
IDCrystal-ID
11
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.3.110.9790.979,0.9792,0.95
SYNCHROTRONNSLS X12B20.9790.979,0.9792,0.95
SYNCHROTRONNSLS X2530.9790.979,0.9792,0.95
SYNCHROTRONAPS 19-ID40.9790.979,0.9792,0.95
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97921
30.951
ReflectionResolution: 2.4→50 Å / Num. all: 12655 / Num. obs: 12655 / Redundancy: 11.4 % / Rsym value: 0.099 / Net I/σ(I): 38.3

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Processing

RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.259 638 Random
Rwork0.242 --
all-12655 -
obs-12655 -
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 0 112 2114

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