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- PDB-6qhk: PAO-linked dimer of the catalytic domain of the human ubiquitin-c... -

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Basic information

Entry
Database: PDB / ID: 6qhk
TitlePAO-linked dimer of the catalytic domain of the human ubiquitin-conjugating enzyme UBE2S
ComponentsUbiquitin-conjugating enzyme E2 S
KeywordsTRANSFERASE / human E2 / catalytic domain / PAO
Function / homology
Function and homology information


protein K27-linked ubiquitination / free ubiquitin chain polymerization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / protein K29-linked ubiquitination / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / anaphase-promoting complex-dependent catabolic process / anaphase-promoting complex binding ...protein K27-linked ubiquitination / free ubiquitin chain polymerization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / protein K29-linked ubiquitination / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / anaphase-promoting complex-dependent catabolic process / anaphase-promoting complex binding / Phosphorylation of the APC/C / protein K6-linked ubiquitination / positive regulation of ubiquitin protein ligase activity / protein K11-linked ubiquitination / exit from mitosis / E2 ubiquitin-conjugating enzyme / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / Transcriptional Regulation by VENTX / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / protein modification process / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / CDK-mediated phosphorylation and removal of Cdc6 / protein polyubiquitination / ubiquitin-protein transferase activity / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cell division / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
: / 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
Similarity search - Domain/homology
Phenylarsine oxide / Ubiquitin-conjugating enzyme E2 S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLiess, A.K.L. / Lorenz, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationEmmy Noether LO2003/1-1 Germany
German Research FoundationGRK 2243 Germany
CitationJournal: Structure / Year: 2019
Title: Autoinhibition Mechanism of the Ubiquitin-Conjugating Enzyme UBE2S by Autoubiquitination.
Authors: Liess, A.K.L. / Kucerova, A. / Schweimer, K. / Yu, L. / Roumeliotis, T.I. / Diebold, M. / Dybkov, O. / Sotriffer, C. / Urlaub, H. / Choudhary, J.S. / Mansfeld, J. / Lorenz, S.
History
DepositionJan 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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: Ubiquitin-conjugating enzyme E2 S
B: Ubiquitin-conjugating enzyme E2 S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1687
Polymers34,7782
Non-polymers3905
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-9 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.150, 83.150, 83.125
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 S / E2 ubiquitin-conjugating enzyme S / E2-EPF / Ubiquitin carrier protein S / Ubiquitin-conjugating ...E2 ubiquitin-conjugating enzyme S / E2-EPF / Ubiquitin carrier protein S / Ubiquitin-conjugating enzyme E2-24 kDa / Ubiquitin-conjugating enzyme E2-EPF5 / Ubiquitin-protein ligase S


Mass: 17388.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2S, E2EPF, OK/SW-cl.73 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q16763, E2 ubiquitin-conjugating enzyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PA0 / Phenylarsine oxide / oxo(phenyl)arsane


Mass: 168.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5AsO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1 mM TCEP, 11.74 mg/ml PAO, 0.2 M magnesium chloride, 0.1 M Tris pH 8.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.96→19.417 Å / Num. obs: 23393 / % possible obs: 99.72 % / Redundancy: 2 % / Biso Wilson estimate: 32.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02321 / Rpim(I) all: 0.02321 / Rrim(I) all: 0.03282 / Net I/σ(I): 20.05
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 2 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 2317 / CC1/2: 0.787 / Rpim(I) all: 0.281 / Rrim(I) all: 0.3973 / % possible all: 99.44

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZDN

1zdn


Resolution: 1.96→19.417 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.78
RfactorNum. reflection% reflection
Rfree0.2231 1159 4.95 %
Rwork0.1893 --
obs0.1909 23393 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→19.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 20 84 2357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032336
X-RAY DIFFRACTIONf_angle_d0.6993179
X-RAY DIFFRACTIONf_dihedral_angle_d14.0581387
X-RAY DIFFRACTIONf_chiral_restr0.043367
X-RAY DIFFRACTIONf_plane_restr0.004413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9603-2.04940.31771640.25692699X-RAY DIFFRACTION100
2.0494-2.15730.26961390.22952796X-RAY DIFFRACTION100
2.1573-2.29230.27461410.20542769X-RAY DIFFRACTION100
2.2923-2.46890.29511140.21662777X-RAY DIFFRACTION100
2.4689-2.71680.26171610.21482798X-RAY DIFFRACTION100
2.7168-3.10850.24591420.19972766X-RAY DIFFRACTION100
3.1085-3.91120.19531500.18132803X-RAY DIFFRACTION100
3.9112-19.41770.18031480.15912826X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1722-0.03311.15273.2984-0.03443.09070.16380.0582-0.104-0.20730.0185-0.1286-0.06850.1431-0.17450.2620.00780.00420.15850.03840.1944-33.037811.77576.7166
24.6025-0.60130.66122.5838-0.36622.6478-0.0514-0.117-0.02050.0818-0.06020.04230.1471-0.08450.10140.2727-0.02610.06590.1057-0.01690.2084-38.3112-8.246713.4936
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 10 through 156)
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 156)

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