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

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Basic information

Entry
Database: PDB / ID: 5elj
TitleIsoform-specific inhibition of SUMO-dependent protein-protein interactions
Components
  • SUMO-Affirmer-S2D5
  • Small ubiquitin-related modifier 1
KeywordsSIGNALING PROTEIN / Ubiquitin / Sumoylation
Function / homology
Function and homology information


protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / small protein activating enzyme binding / negative regulation of action potential / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / regulation of calcium ion transmembrane transport / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of DNA binding / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / cellular response to cadmium ion / ubiquitin-specific protease binding / transcription factor binding / roof of mouth development / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / potassium channel regulator activity / Regulation of IFNG signaling / nuclear pore / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / nuclear membrane / protein stabilization / nuclear speck / nuclear body / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Small ubiquitin-related modifier 1, Ubl domain / 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 1
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.983 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
Biotechnology and Biological Sciences Research CouncilBB/M006557/1
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 4, 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_gene_src_gene / _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-S2D5
B: Small ubiquitin-related modifier 1


Theoretical massNumber of molelcules
Total (without water)22,9382
Polymers22,9382
Non-polymers00
Water1,35175
1
A: SUMO-Affirmer-S2D5


Theoretical massNumber of molelcules
Total (without water)13,2521
Polymers13,2521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Small ubiquitin-related modifier 1


Theoretical massNumber of molelcules
Total (without water)9,6861
Polymers9,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-4 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.230, 70.720, 83.630
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-S2D5


Mass: 13252.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: PET11 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Small ubiquitin-related modifier 1 / SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain ...SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein SMT3C / Smt3C / Ubiquitin-like protein UBL1


Mass: 9686.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Plasmid: PET11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63165
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes sodium salt, 10% w/v polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013
RadiationMonochromator: SAGITALLY FOCUSED Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.98→70.7 Å / Num. obs: 15526 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.3 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.3
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 13 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 5.2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
REFMAC5.8.0049refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2UYZ and 4N6T

2uyz

4n6t


Resolution: 1.983→54.001 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 658 5.05 %Random Selection
Rwork0.1884 ---
obs0.1906 13029 83.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.983→54.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 0 75 1436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071386
X-RAY DIFFRACTIONf_angle_d1.0121857
X-RAY DIFFRACTIONf_dihedral_angle_d14.652531
X-RAY DIFFRACTIONf_chiral_restr0.043200
X-RAY DIFFRACTIONf_plane_restr0.004234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9826-2.13570.2485600.20261168X-RAY DIFFRACTION40
2.1357-2.35060.29941270.23312281X-RAY DIFFRACTION79
2.3506-2.69070.26071610.23322893X-RAY DIFFRACTION99
2.6907-3.38990.27791620.20532932X-RAY DIFFRACTION100
3.3899-54.02070.19231480.16133097X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4358-0.3577-0.18323.891-1.17056.63410.11630.27620.177-0.2944-0.31040.1312-0.0292-0.26780.24580.28670.0244-0.08830.32190.01870.2836-5.112933.9871-37.9857
24.0185-2.22650.93935.8559-1.59725.29190.0151-0.0479-0.08650.1017-0.10950.10820.1065-0.13230.0770.2998-0.0796-0.05120.2158-0.00720.2821-1.06918.0672-19.8382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 32 through 121)
2X-RAY DIFFRACTION2(chain 'B' and resid 19 through 93)

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