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- PDB-2eke: Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: con... -

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Basic information

Entry
Database: PDB / ID: 2eke
TitleStructure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a noncovalent Ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway
Components
  • SUMO-conjugating enzyme UBC9
  • Ubiquitin-like protein SMT3
KeywordsLIGASE/PROTEIN BINDING / Ubc9 / Smt3 / SUMO binding motif / SBM / LIGASE-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


SUMO conjugating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / mitotic spindle elongation / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins ...SUMO conjugating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / mitotic spindle elongation / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of chromatin organization proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / PML body / protein tag activity / cell division / ATP binding / identical protein binding / nucleus
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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. ...Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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
SUMO-conjugating enzyme UBC9 / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDuda, D.M. / Schulman, B.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of a SUMO-binding-motif Mimic Bound to Smt3p-Ubc9p: Conservation of a Non-covalent Ubiquitin-like Protein-E2 Complex as a Platform for Selective Interactions within a SUMO Pathway
Authors: Duda, D.M. / van Waardenburg, R.C.A.M. / Borg, L.A. / McGarity, S. / Nourse, A. / Waddell, M.B. / Bjornsti, M.A. / Schulman, B.A.
History
DepositionMar 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUMO-conjugating enzyme UBC9
B: SUMO-conjugating enzyme UBC9
C: Ubiquitin-like protein SMT3
D: Ubiquitin-like protein SMT3


Theoretical massNumber of molelcules
Total (without water)60,2544
Polymers60,2544
Non-polymers00
Water6,756375
1
A: SUMO-conjugating enzyme UBC9
C: Ubiquitin-like protein SMT3


Theoretical massNumber of molelcules
Total (without water)30,1272
Polymers30,1272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SUMO-conjugating enzyme UBC9
D: Ubiquitin-like protein SMT3


Theoretical massNumber of molelcules
Total (without water)30,1272
Polymers30,1272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.891, 84.578, 80.141
Angle α, β, γ (deg.)90.00, 124.31, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains 2 biological units. Each unit is comprised of chain A and C or B and D. The biological unit is the non-covalent interaction between yUbc9 and smt3p.

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Components

#1: Protein SUMO-conjugating enzyme UBC9 / Ubiquitin-conjugating enzyme E2-18 kDa / Ubiquitin-protein ligase / Ubiquitin carrier protein 9


Mass: 17936.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBC9 / Plasmid: pRSF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P50623, ubiquitin-protein ligase
#2: Protein Ubiquitin-like protein SMT3


Mass: 12190.697 Da / Num. of mol.: 2 / Mutation: thrombin site, Ubiquitin-like
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SMT3 / Plasmid: pRSF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: Q12306
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% PEG 3350, 0.2M magnesium chloride, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 56611 / Num. obs: 54517 / % possible obs: 96.3 % / Observed criterion σ(I): 5 / Redundancy: 6.5 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 56
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 10.1 / Num. unique all: 4273 / % possible all: 78.5

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GJD

2gjd


Resolution: 1.9→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Geometry errors for proline D106 and D1020 are due to poor density over this region.
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 2521 -RANDOM
Rwork0.2247 ---
all0.244 52530 --
obs0.244 50250 95.7 %-
Displacement parametersBiso mean: 44.8266 Å2
Baniso -1Baniso -2Baniso -3
1-3.875 Å20 Å21.319 Å2
2--2.539 Å20 Å2
3----6.414 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 0 375 4290
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00582
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.57545
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→1.949 Å
RfactorNum. reflection% reflection
Rfree0.302 171 -
Rwork0.324 --
obs-3023 82.3 %

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