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- PDB-5f6v: Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment... -

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Basic information

Entry
Database: PDB / ID: 5f6v
TitleCrystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol from fragment cocktail screen)
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 / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / transferase complex / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism ...positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase 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) / transferase complex / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism / synaptonemal complex / small protein activating enzyme binding / 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 / SUMOylation of ubiquitinylation proteins / SUMOylation of DNA replication proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / 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 / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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
2-(2-hydroxyphenyl)phenol / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.492 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
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.757, 35.233, 57.951
Angle α, β, γ (deg.)90.00, 111.96, 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.: 228 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / 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-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 31125 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 31.9
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9B

1u9b


Resolution: 1.492→26.873 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1838 1991 6.4 %
Rwork0.1519 --
obs0.154 31105 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.492→26.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 14 228 1483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061436
X-RAY DIFFRACTIONf_angle_d1.0861981
X-RAY DIFFRACTIONf_dihedral_angle_d13.039582
X-RAY DIFFRACTIONf_chiral_restr0.08205
X-RAY DIFFRACTIONf_plane_restr0.006263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4918-1.52910.24961380.1981994X-RAY DIFFRACTION95
1.5291-1.57040.2321240.18322054X-RAY DIFFRACTION100
1.5704-1.61660.21761570.15132057X-RAY DIFFRACTION100
1.6166-1.66880.20631380.13762089X-RAY DIFFRACTION100
1.6688-1.72840.17611430.13672049X-RAY DIFFRACTION100
1.7284-1.79760.20061400.13552095X-RAY DIFFRACTION100
1.7976-1.87940.16611390.13522083X-RAY DIFFRACTION100
1.8794-1.97850.19021450.14392081X-RAY DIFFRACTION100
1.9785-2.10240.1851430.14442081X-RAY DIFFRACTION100
2.1024-2.26460.19351390.14722088X-RAY DIFFRACTION100
2.2646-2.49240.18751420.15382094X-RAY DIFFRACTION100
2.4924-2.85270.2011470.16042091X-RAY DIFFRACTION100
2.8527-3.59270.18021480.15922117X-RAY DIFFRACTION100
3.5927-26.8770.15921480.152141X-RAY DIFFRACTION98

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