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- PDB-5f6w: Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment... -

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Basic information

Entry
Database: PDB / ID: 5f6w
TitleCrystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol)
ComponentsSUMO-conjugating enzyme UBC9
KeywordsLIGASE/LIGASE inhibitor / Ubc9 / Fragment drug design / sumoylation / LIGASE-LIGASE inhibitor complex
Function / homology
Function and homology information


: / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / transferase complex / SUMOylation of nuclear envelope proteins / 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 ...: / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / transferase complex / SUMOylation of nuclear envelope proteins / 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 / synaptonemal complex / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / nuclear export / Transferases; Acyltransferases; Aminoacyltransferases / Postmitotic nuclear pore complex (NPC) reformation / SUMO transferase activity / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / nuclear pore / SUMOylation of DNA damage response and repair proteins / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Transcriptional and post-translational regulation of MITF-M expression and activity / Meiotic synapsis / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / chromosome segregation / SUMOylation of intracellular receptors / PKR-mediated signaling / protein modification process / PML body / Formation of Incision Complex in GG-NER / nuclear envelope / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / 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
2-(2-hydroxyphenyl)phenol / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.699 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 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUMO-conjugating enzyme UBC9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9122
Polymers17,7251
Non-polymers1861
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.160, 35.377, 57.810
Angle α, β, γ (deg.)90.00, 112.23, 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-5VL / 2-(2-hydroxyphenyl)phenol


Mass: 186.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.699→50 Å / Num. obs: 20956 / % possible obs: 97.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 44.5
Reflection shellResolution: 1.699→1.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.4 / % possible all: 79

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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: 1.699→30.239 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2004 1993 9.52 %
Rwork0.1718 --
obs0.1745 20942 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→30.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 14 244 1499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061348
X-RAY DIFFRACTIONf_angle_d1.0741845
X-RAY DIFFRACTIONf_dihedral_angle_d11.53519
X-RAY DIFFRACTIONf_chiral_restr0.045189
X-RAY DIFFRACTIONf_plane_restr0.007244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6988-1.74130.2551170.23561094X-RAY DIFFRACTION81
1.7413-1.78830.27561400.23511273X-RAY DIFFRACTION93
1.7883-1.8410.24511400.19871351X-RAY DIFFRACTION98
1.841-1.90040.20611380.17991359X-RAY DIFFRACTION99
1.9004-1.96830.19721470.17681379X-RAY DIFFRACTION99
1.9683-2.04710.20991430.17091361X-RAY DIFFRACTION99
2.0471-2.14020.21581440.16861380X-RAY DIFFRACTION100
2.1402-2.2530.22121470.1691362X-RAY DIFFRACTION100
2.253-2.39410.19671390.18171390X-RAY DIFFRACTION100
2.3941-2.57890.23261480.18121382X-RAY DIFFRACTION100
2.5789-2.83820.23841450.18811390X-RAY DIFFRACTION100
2.8382-3.24850.19821500.17841390X-RAY DIFFRACTION100
3.2485-4.09120.20561470.15371398X-RAY DIFFRACTION100
4.0912-30.24390.15091480.16171440X-RAY DIFFRACTION99

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