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- PDB-5elu: Isoform-specific inhibition of SUMO-dependent protein-protein int... -

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Basic information

Entry
Database: PDB / ID: 5elu
TitleIsoform-specific inhibition of SUMO-dependent protein-protein interactions
Components
  • SUMO-Affirmer-S2B3
  • Small ubiquitin-related modifier 2
KeywordsSIGNALING PROTEIN / Ubiquitin / Sumoylation
Function / homology
Function and homology information


SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins ...SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / postsynaptic cytosol / protein sumoylation / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / hippocampal mossy fiber to CA3 synapse / GABA-ergic synapse / Regulation of endogenous retroelements by KRAB-ZFP proteins / SUMOylation of intracellular receptors / PML body / protein tag activity / Formation of Incision Complex in GG-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / ubiquitin protein ligase binding / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear Transport Factor 2; Chain: A, - #10 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Nuclear Transport Factor 2; Chain: A, / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 2
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHughes, D.J. / Tiede, C. / Hall, N. / Tang, A.A.S. / Trinh, C.H. / Zajac, K. / Mandal, U. / Howell, G. / Edwards, T.A. / McPherson, M.J. ...Hughes, D.J. / Tiede, C. / Hall, N. / Tang, A.A.S. / Trinh, C.H. / Zajac, K. / Mandal, U. / Howell, G. / Edwards, T.A. / McPherson, M.J. / Tomlinson, D.C. / Whitehouse, A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust089330 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/K000306/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M006557/1 United Kingdom
CitationJournal: Sci Signal / Year: 2017
Title: Generation of specific inhibitors of SUMO-1- and SUMO-2/3-mediated protein-protein interactions using Affimer (Adhiron) technology.
Authors: Hughes, D.J. / Tiede, C. / Penswick, N. / Tang, A.A. / Trinh, C.H. / Mandal, U. / Zajac, K.Z. / Gaule, T. / Howell, G. / Edwards, T.A. / Duan, J. / Feyfant, E. / McPherson, M.J. / Tomlinson, ...Authors: Hughes, D.J. / Tiede, C. / Penswick, N. / Tang, A.A. / Trinh, C.H. / Mandal, U. / Zajac, K.Z. / Gaule, T. / Howell, G. / Edwards, T.A. / Duan, J. / Feyfant, E. / McPherson, M.J. / Tomlinson, D.C. / Whitehouse, A.
History
DepositionNov 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 7, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / struct
Item: _citation.title / _entity.pdbx_description ..._citation.title / _entity.pdbx_description / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _struct.pdbx_descriptor
Revision 1.3Apr 18, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUMO-Affirmer-S2B3
B: Small ubiquitin-related modifier 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7635
Polymers22,4752
Non-polymers2883
Water1,838102
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-33 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.975, 42.264, 113.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SUMO-Affirmer-S2B3


Mass: 13509.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MASAATGVRAVPGNENSLEIEELARFAVDEHNKKENALLEFVRVVKAKEQVDLTRFPVTTMYYLTLEAKDGGKKKLYEAKVWVKGYLLEELKHNFKELQEFKPVGDAAAAHHHHHHHH
Source: (gene. exp.) synthetic construct (others) / Gene: PHYTOCYSTATIN / Plasmid: PET11 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Small ubiquitin-related modifier 2 / SUMO-2 / HSMT3 / SMT3 homolog 2 / SUMO-3 / Sentrin-2 / Ubiquitin-like protein SMT3B / Smt3B


Mass: 8965.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO2, SMT3B, SMT3H2 / Plasmid: PET11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61956
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 0.2 M sodium chloride and 2.0 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2014
RadiationMonochromator: SAGITALLY FOCUSED Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→28.4 Å / Num. obs: 8893 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 29.4
Reflection shellResolution: 2.35→2.44 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 11.1 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
REFMAC5.8.0049refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1WM3 and 5ELJ

1wm3

5elj


Resolution: 2.35→28.393 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.79 / Phase error: 0.217 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 725 4.48 %Random selection
Rwork0.172 ---
obs0.1737 16171 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→28.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 15 102 1461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081371
X-RAY DIFFRACTIONf_angle_d1.0281847
X-RAY DIFFRACTIONf_dihedral_angle_d14.072516
X-RAY DIFFRACTIONf_chiral_restr0.039203
X-RAY DIFFRACTIONf_plane_restr0.004239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.53140.25881230.2023060X-RAY DIFFRACTION98
2.5314-2.78590.25651720.19123096X-RAY DIFFRACTION100
2.7859-3.18860.23781290.18243097X-RAY DIFFRACTION100
3.1886-4.01550.18361680.15663074X-RAY DIFFRACTION100
4.0155-28.39510.1731330.16043119X-RAY DIFFRACTION100

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