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- PDB-7p47: Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO th... -

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Basic information

Entry
Database: PDB / ID: 7p47
TitleStructure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic
Components
  • E3 SUMO-protein ligase MMS21
  • SUMO-conjugating enzyme UBC9
  • Structural maintenance of chromosomes protein 5
  • Ubiquitin-like protein SMT3
KeywordsLIGASE / SUMO E3 ligase activity / DNA repair
Function / homology
Function and homology information


Smc5-Smc6 complex / SUMO conjugating enzyme activity / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / mitotic spindle elongation / chromosome separation / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...Smc5-Smc6 complex / SUMO conjugating enzyme activity / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / mitotic spindle elongation / chromosome separation / 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 / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin looping / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / SUMOylation of chromatin organization proteins / regulation of telomere maintenance / recombinational repair / ubiquitin-like protein ligase binding / protein sumoylation / protein serine/threonine kinase inhibitor activity / condensed nuclear chromosome / double-strand break repair via homologous recombination / protein tag activity / nuclear envelope / single-stranded DNA binding / damaged DNA binding / chromosome, telomeric region / cell division / DNA repair / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / E3 SUMO-protein ligase MMS21, N-terminal domain / E3 SUMO-protein ligase Nse2 (Mms21) / Zinc-finger of the MIZ type in Nse subunit / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like ...: / E3 SUMO-protein ligase MMS21, N-terminal domain / E3 SUMO-protein ligase Nse2 (Mms21) / Zinc-finger of the MIZ type in Nse subunit / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / : / 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 / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E3 SUMO-protein ligase MMS21 / SUMO-conjugating enzyme UBC9 / Structural maintenance of chromosomes protein 5 / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.314 Å
AuthorsLascorz, J. / Varejao, N. / Reverter, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098423-B-I00 Spain
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for the E3 ligase activity enhancement of yeast Nse2 by SUMO-interacting motifs.
Authors: Varejao, N. / Lascorz, J. / Codina-Fabra, J. / Belli, G. / Borras-Gas, H. / Torres-Rosell, J. / Reverter, D.
History
DepositionJul 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Structural maintenance of chromosomes protein 5
C: SUMO-conjugating enzyme UBC9
A: E3 SUMO-protein ligase MMS21
E: Ubiquitin-like protein SMT3
D: Ubiquitin-like protein SMT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7126
Polymers80,6465
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-29 kcal/mol
Surface area30130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.144, 103.240, 115.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Structural maintenance of chromosomes protein 5


Mass: 9978.620 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SMC5, YOL034W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08204
#2: Protein SUMO-conjugating enzyme UBC9 / RING-type E3 SUMO transferase UBC9 / Ubiquitin carrier protein 9 / Ubiquitin-conjugating enzyme E2- ...RING-type E3 SUMO transferase UBC9 / Ubiquitin carrier protein 9 / Ubiquitin-conjugating enzyme E2-18 kDa / Ubiquitin-protein ligase


Mass: 19071.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Point mutants A129K, K153R Isopeptidic bond between K129 (chain A) and G98 (chain D)
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBC9, YDL064W / Production host: Escherichia coli (E. coli)
References: UniProt: P50623, Transferases; Acyltransferases; Aminoacyltransferases
#3: Protein E3 SUMO-protein ligase MMS21 / E3 SUMO-protein transferase MMS21 / Methyl methanesulfonate-sensitivity protein 21 / Non-structural ...E3 SUMO-protein transferase MMS21 / Methyl methanesulfonate-sensitivity protein 21 / Non-structural maintenance of chromosome element 2 / Non-SMC element 2


Mass: 24117.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MMS21, NSE2, YEL019C / Production host: Escherichia coli (E. coli)
References: UniProt: P38632, Transferases; Acyltransferases; Aminoacyltransferases
#4: Protein Ubiquitin-like protein SMT3


Mass: 13739.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SMT3, YDR510W, D9719.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12306
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 311 K / Method: vapor diffusion, hanging drop
Details: 12% PEG8000, 0.2M dimethyl-2-hydroxyethylammoniumpropane sulfonate (NDSB 211), 8% ethylene glycol, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.31→47.14 Å / Num. obs: 13097 / % possible obs: 99.2 % / Redundancy: 5.4 % / CC1/2: 0.99 / Net I/σ(I): 9.7
Reflection shellResolution: 3.31→3.58 Å / Num. unique obs: 2585 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HTK

3htk


Resolution: 3.314→47.135 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2932 652 4.99 %
Rwork0.2357 12404 -
obs0.2386 13056 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.58 Å2 / Biso mean: 98.82 Å2 / Biso min: 57.74 Å2
Refinement stepCycle: final / Resolution: 3.314→47.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 1 0 4561
Biso mean--81.67 --
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094641
X-RAY DIFFRACTIONf_angle_d1.5176248
X-RAY DIFFRACTIONf_chiral_restr0.095678
X-RAY DIFFRACTIONf_plane_restr0.006816
X-RAY DIFFRACTIONf_dihedral_angle_d17.8491824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3144-3.57020.40721300.3252236897
3.5702-3.92930.37761200.28092453100
3.9293-4.49750.28441330.25112472100
4.4975-5.66480.2821320.22612488100
5.6648-47.130.2521370.19822623100
Refinement TLS params.Method: refined / Origin x: 19.2457 Å / Origin y: -12.4467 Å / Origin z: -20.4649 Å
111213212223313233
T0.6538 Å20.0104 Å20.0018 Å2-0.7404 Å2-0.0053 Å2--0.7881 Å2
L0.2365 °2-0.0063 °20.3016 °2-0.5552 °2-0.1803 °2--1.7554 °2
S0.0079 Å °0.0648 Å °-0.0027 Å °-0.0266 Å °-0.0942 Å °0.0271 Å °-0.0292 Å °-0.0567 Å °0.0762 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB329 - 773
2X-RAY DIFFRACTION1allC3 - 157
3X-RAY DIFFRACTION1allA23 - 270
4X-RAY DIFFRACTION1allE22 - 94
5X-RAY DIFFRACTION1allD21 - 98

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