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- PDB-2uyz: Non-covalent complex between Ubc9 and SUMO1 -

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Basic information

Entry
Database: PDB / ID: 2uyz
TitleNon-covalent complex between Ubc9 and SUMO1
Components
  • SMALL UBIQUITIN-RELATED MODIFIER 1
  • SUMO-CONJUGATING ENZYME UBC9
KeywordsLIGASE / SUMOYLATION / CELL DIVISION / NUCLEAR PROTEIN / UBIQUITIN-LIKE MODIFIER / UBL CONJUGATION PATHWAY / CONJUGATING ENZYME / CHROMOSOME PARTITION / E2 / UBC9 / SUMO1 / MITOSIS / CELL CYCLE
Function / homology
Function and homology information


SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMOylation of nuclear envelope proteins / Vitamin D (calciferol) metabolism / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / SUMOylation of RNA binding proteins ...SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMOylation of nuclear envelope proteins / Vitamin D (calciferol) metabolism / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / SUMOylation of RNA binding proteins / SUMOylation of DNA methylation proteins / SUMOylation of DNA damage response and repair proteins / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / SUMOylation of immune response proteins / Formation of Incision Complex in GG-NER / SUMO conjugating enzyme activity / Processing of DNA double-strand break ends / Transcriptional and post-translational regulation of MITF-M expression and activity / RING-like zinc finger domain binding / SUMO ligase complex / negative regulation of potassium ion transmembrane transporter activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / HLH domain binding / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of delayed rectifier potassium channel activity / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of DNA binding / negative regulation of action potential / PML body organization / nuclear stress granule / small protein activating enzyme binding / SUMOylation of immune response proteins / SUMOylation of DNA methylation proteins / SUMOylation of SUMOylation proteins / regulation of calcium ion transmembrane transport / XY body / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / nuclear export / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / transcription factor binding / cellular response to cadmium ion / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / roof of mouth development / SUMOylation of DNA replication proteins / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / nuclear pore / : / transporter activator activity / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / transcription coregulator binding / SUMOylation of intracellular receptors / chromosome segregation / positive regulation of protein-containing complex assembly / PKR-mediated signaling / PML body / modulation of chemical synaptic transmission / protein modification process / regulation of protein stability / Schaffer collateral - CA1 synapse / protein tag activity / Formation of Incision Complex in GG-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of protein localization / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / protein stabilization / nuclear speck / nuclear body / positive regulation of cell migration / cell division / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding
Similarity search - Function
Small ubiquitin-related modifier 1, Ubl domain / 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 / Ubiquitin-conjugating enzyme ...Small ubiquitin-related modifier 1, Ubl domain / 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 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 1 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKnipscheer, P. / van Dijk, W.J. / Olsen, J.V. / Mann, M. / Sixma, T.K.
CitationJournal: EMBO J. / Year: 2007
Title: Noncovalent interaction between Ubc9 and SUMO promotes SUMO chain formation.
Authors: Knipscheer, P. / van Dijk, W.J. / Olsen, J.V. / Mann, M. / Sixma, T.K.
History
DepositionApr 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: SMALL UBIQUITIN-RELATED MODIFIER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2683
Polymers27,2452
Non-polymers231
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.481, 35.030, 72.915
Angle α, β, γ (deg.)90.00, 93.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SUMO-CONJUGATING ENZYME UBC9 / SUMO-PROTEIN LIGASE / UBIQUITIN-CONJUGATING ENZYME E2 I / UBIQUITIN-PROTEIN LIGASE I / UBIQUITIN ...SUMO-PROTEIN LIGASE / UBIQUITIN-CONJUGATING ENZYME E2 I / UBIQUITIN-PROTEIN LIGASE I / UBIQUITIN CARRIER PROTEIN I / UBIQUITIN CARRIER PROTEIN 9 / MUBC9


Mass: 18014.750 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: START METHIONINE (1) AND SECOND SERINE (2) ARE MISSING IN STRUCTURE
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63280, ubiquitin-protein ligase
#2: Protein SMALL UBIQUITIN-RELATED MODIFIER 1 / SUMO-1 / SENTRIN / UBIQUITIN-LIKE PROTEIN SMT3C / SMT3 HOMOLOG 3 / UBIQUITIN-HOMOLOGY DOMAIN ...SUMO-1 / SENTRIN / UBIQUITIN-LIKE PROTEIN SMT3C / SMT3 HOMOLOG 3 / UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1 / UBIQUITIN-LIKE PROTEIN UBL1 / GAP-MODIFYING PROTEIN 1 / GMP1 / SUMO1


Mass: 9230.559 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63165
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 93 TO SER
Sequence detailsC93S MUTANT

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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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growpH: 5.5
Details: 16.5 % (W/V) PEG3350 100 MM BISTRIS PH 5.5 15 % (W/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 18, 2007 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. obs: 49557 / % possible obs: 99.2 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 1.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U9A, 2BF8

1u9a

2bf8


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.668 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2482 5 %RANDOM
Rwork0.141 ---
obs0.143 46681 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.2 Å2
2--0.4 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 1 408 2302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222206
X-RAY DIFFRACTIONr_bond_other_d0.0010.021596
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9763014
X-RAY DIFFRACTIONr_angle_other_deg0.93733927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28424.455101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38615429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9911514
X-RAY DIFFRACTIONr_chiral_restr0.10.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022539
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02435
X-RAY DIFFRACTIONr_nbd_refined0.2350.2468
X-RAY DIFFRACTIONr_nbd_other0.1930.21685
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21050
X-RAY DIFFRACTIONr_nbtor_other0.0820.21121
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2530.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4121.51336
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1722207
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9933895
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3824.5804
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.216 163
Rwork0.168 3398

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