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- PDB-5f6d: Crystal structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 6 -

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Basic information

Entry
Database: PDB / ID: 5f6d
TitleCrystal structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 6
ComponentsSUMO-conjugating enzyme UBC9
KeywordsLIGASE/LIGASE inhibitor / Ubc9 / Fragment drug design / sumoylation / LIGASE-LIGASE inhibitor complex
Function / homology
Function and homology information


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) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly ...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) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / small protein activating enzyme binding / synaptonemal complex / 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 / transcription factor binding / SUMOylation of ubiquitinylation proteins / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / nuclear pore / SUMOylation of DNA damage response and repair proteins / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Meiotic synapsis / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of endogenous retroelements by KRAB-ZFP proteins / transcription coregulator binding / chromosome segregation / SUMOylation of intracellular receptors / protein modification process / 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
: / 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 ...: / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
6~{H}-benzo[c][1,2]benzothiazine 5,5-dioxide / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.553 Å
AuthorsLountos, G.T. / Hewitt, W.M. / Zlotkowski, K. / Dahlhauser, S. / Saunders, L.B. / Needle, D. / Tropea, J.E. / Zhan, C. / Wei, G. / Ma, B. ...Lountos, G.T. / Hewitt, W.M. / Zlotkowski, K. / Dahlhauser, S. / Saunders, L.B. / Needle, D. / Tropea, J.E. / Zhan, C. / Wei, G. / Ma, B. / Nussinov, R. / Schneekloth, J.S.Jr. / Waugh, D.S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.
Authors: Hewitt, W.M. / Lountos, G.T. / Zlotkowski, K. / Dahlhauser, S.D. / Saunders, L.B. / Needle, D. / Tropea, J.E. / Zhan, C. / Wei, G. / Ma, B. / Nussinov, R. / Waugh, D.S. / Schneekloth, J.S.
History
DepositionDec 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Mar 15, 2017Group: Structure summary
Revision 1.3Sep 27, 2023Group: 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-conjugating enzyme UBC9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9572
Polymers17,7251
Non-polymers2311
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.734, 35.452, 57.979
Angle α, β, γ (deg.)90.00, 111.63, 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: 17725.375 Da / Num. of mol.: 1 / Mutation: K48A,K49A,E54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Plasmid: pDN2405 / Production host: Escherichia coli (E. coli)
References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-5VJ / 6~{H}-benzo[c][1,2]benzothiazine 5,5-dioxide


Mass: 231.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9NO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.74 Å3/Da / Density % sol: 55.08 % / Description: rods
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 26685 / % possible obs: 95.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 34.9
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3.1 / % possible all: 70.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9B

1u9b


Resolution: 1.553→26.949 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1962 1999 7.5 %
Rwork0.1706 --
obs0.1725 26670 95.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.553→26.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 16 266 1523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061402
X-RAY DIFFRACTIONf_angle_d1.1221928
X-RAY DIFFRACTIONf_dihedral_angle_d11.137556
X-RAY DIFFRACTIONf_chiral_restr0.046198
X-RAY DIFFRACTIONf_plane_restr0.006255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5529-1.59170.29661160.2341324X-RAY DIFFRACTION73
1.5917-1.63470.25831060.21341523X-RAY DIFFRACTION82
1.6347-1.68280.24271410.19461643X-RAY DIFFRACTION90
1.6828-1.73720.25391430.20031747X-RAY DIFFRACTION96
1.7372-1.79920.24911470.19551801X-RAY DIFFRACTION98
1.7992-1.87120.21461480.19041858X-RAY DIFFRACTION99
1.8712-1.95640.21961390.18061818X-RAY DIFFRACTION100
1.9564-2.05950.21081470.1791843X-RAY DIFFRACTION99
2.0595-2.18850.22911500.17221830X-RAY DIFFRACTION99
2.1885-2.35740.20631560.17831837X-RAY DIFFRACTION100
2.3574-2.59440.21741490.17891827X-RAY DIFFRACTION100
2.5944-2.96940.20231570.17621868X-RAY DIFFRACTION100
2.9694-3.73960.16551430.15631866X-RAY DIFFRACTION100
3.7396-26.95280.15471570.14671886X-RAY DIFFRACTION98

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