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- PDB-4y1l: Ubc9 Homodimer The Missing Link in Poly-SUMO Chain Formation -

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Basic information

Entry
Database: PDB / ID: 4y1l
TitleUbc9 Homodimer The Missing Link in Poly-SUMO Chain Formation
Components
  • RWD domain-containing protein 3
  • SUMO-conjugating enzyme UBC9
Keywordsligase/nuclear protein / UBC9 / RWD / SUMOylation / Homodimer / SUMO / ligase-nuclear protein complex
Function / homology
Function and homology information


positive regulation of hypoxia-inducible factor-1alpha signaling pathway / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic nuclear membrane reassembly ...positive regulation of hypoxia-inducible factor-1alpha signaling pathway / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism / synaptonemal complex / small protein activating enzyme binding / positive regulation of protein sumoylation / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / nuclear export / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of NF-kappaB transcription factor activity / SUMOylation of ubiquitinylation proteins / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / SUMOylation of DNA damage response and repair proteins / nuclear pore / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Meiotic synapsis / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / chromosome segregation / transcription coregulator binding / protein modification process / SUMOylation of intracellular receptors / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RWD domain-containing protein 3 / RWD domain / RWD domain / RWD domain profile. / RWD / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues ...RWD domain-containing protein 3 / RWD domain / RWD domain / RWD domain profile. / RWD / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
SUMO-conjugating enzyme UBC9 / RWD domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAileen, Y.A. / Ambaye, N.D. / Li, Y.J. / Vega, R. / Bzymek, K. / Williams, J.C. / Hu, W. / Chen, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102538 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086171 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: RWD Domain as an E2 (Ubc9)-Interaction Module.
Authors: Alontaga, A.Y. / Ambaye, N.D. / Li, Y.J. / Vega, R. / Chen, C.H. / Bzymek, K.P. / Williams, J.C. / Hu, W. / Chen, Y.
History
DepositionFeb 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-conjugating enzyme UBC9
B: SUMO-conjugating enzyme UBC9
C: RWD domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)48,9223
Polymers48,9223
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.230, 34.860, 114.510
Angle α, β, γ (deg.)90.00, 98.53, 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 carrier protein 9 / Ubiquitin carrier protein I / Ubiquitin- ...SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin carrier protein I / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / p18


Mass: 18030.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Production host: Escherichia coli (E. coli)
References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein RWD domain-containing protein 3 / RWD domain-containing sumoylation enhancer / RSUME


Mass: 12860.683 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RWDD3, RSUME / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3V2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 10% (w/v) PEG8000, 100 mM HEPES, pH 8.0, 8% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→33.32 Å / Num. obs: 13980 / % possible obs: 99.56 % / Redundancy: 3.2 % / Biso Wilson estimate: 54.21 Å2 / Net I/σ(I): 8.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Aimlessdata scaling
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→33.317 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2782 699 5 %
Rwork0.2252 --
obs0.2278 13980 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→33.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 0 149 3531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053475
X-RAY DIFFRACTIONf_angle_d1.1694720
X-RAY DIFFRACTIONf_dihedral_angle_d15.0091318
X-RAY DIFFRACTIONf_chiral_restr0.043506
X-RAY DIFFRACTIONf_plane_restr0.008615
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7001-2.90850.38671390.29762642100
2.9085-3.2010.31071370.27792596100
3.201-3.66370.30371390.23812641100
3.6637-4.61390.25351390.1962657100
4.61390.24711450.2087274599
Refinement TLS params.Method: refined / Origin x: 76.046 Å / Origin y: -11.1362 Å / Origin z: 80.2615 Å
111213212223313233
T0.4141 Å20.168 Å20.0151 Å2-0.4365 Å2-0.0457 Å2--0.3967 Å2
L0.3039 °2-0.0659 °20.9404 °2-0.7215 °2-1.3084 °2--2.4028 °2
S-0.0603 Å °0.16 Å °-0.0271 Å °-0.043 Å °-0.1782 Å °-0.2931 Å °0.167 Å °0.4918 Å °0.2253 Å °
Refinement TLS groupSelection details: all

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