[English] 日本語
Yorodumi
- PDB-5elj: Isoform-specific inhibition of SUMO-dependent protein-protein int... -

+
Open data


ID or keywords:

Loading...

-
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 / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / 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 / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / septin ring / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / 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 / Maturation of nucleoprotein / negative regulation of protein import into nucleus / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / Formation of Incision Complex in GG-NER / protein tag activity / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / nuclear body / protein stabilization / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more