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- PDB-6qh3: Catalytic domain of the human ubiquitin-conjugating enzyme UBE2S C118M -

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Basic information

Entry
Database: PDB / ID: 6qh3
TitleCatalytic domain of the human ubiquitin-conjugating enzyme UBE2S C118M
ComponentsUbiquitin-conjugating enzyme E2 S
KeywordsTRANSFERASE / human E2 / catalytic domain / C118M
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
Ubiquitin-conjugating enzyme E2 S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
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 15, 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

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Assembly

Deposited unit
B: Ubiquitin-conjugating enzyme E2 S
A: Ubiquitin-conjugating enzyme E2 S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0826
Polymers34,8342
Non-polymers2484
Water00
1
B: Ubiquitin-conjugating enzyme E2 S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6034
Polymers17,4171
Non-polymers1863
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ubiquitin-conjugating enzyme E2 S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4792
Polymers17,4171
Non-polymers621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.619, 84.619, 87.832
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-EPF / Ubiquitin carrier protein S / Ubiquitin-conjugating enzyme E2-24 kDa / Ubiquitin- ...E2-EPF / Ubiquitin carrier protein S / Ubiquitin-conjugating enzyme E2-24 kDa / Ubiquitin-conjugating enzyme E2-EPF5 / Ubiquitin-protein ligase S


Mass: 17417.012 Da / Num. of mol.: 2 / Mutation: C118M
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2

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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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium chloride, 0.1 M hepes pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.9→42.309 Å / Num. obs: 7984 / % possible obs: 99.94 % / Redundancy: 2 % / Biso Wilson estimate: 63.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02634 / Rpim(I) all: 0.02634 / Rrim(I) all: 0.03725 / Net I/σ(I): 21.4
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1729 / Mean I/σ(I) obs: 4.19 / Num. unique obs: 795 / CC1/2: 0.896 / Rpim(I) all: 0.1729 / Rrim(I) all: 0.2445 / % possible all: 100

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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: 2.9→42.309 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.93
RfactorNum. reflection% reflection
Rfree0.23 439 5.5 %
Rwork0.1843 --
obs0.187 7984 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→42.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 16 0 2270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032323
X-RAY DIFFRACTIONf_angle_d0.7043163
X-RAY DIFFRACTIONf_dihedral_angle_d15.8941390
X-RAY DIFFRACTIONf_chiral_restr0.044365
X-RAY DIFFRACTIONf_plane_restr0.005408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.31960.29221130.21742518X-RAY DIFFRACTION100
3.3196-4.18180.22621770.19192495X-RAY DIFFRACTION100
4.1818-42.3090.21851490.16962532X-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)
15.91650.9954-1.13517.98040.04445.4084-0.37470.3813-0.3574-0.48790.2177-0.32260.2547-0.00120.11350.3076-0.14320.04640.3955-0.00580.4029120.3938-37.8424-4.8241
24.7323-0.93380.94617.6026-2.84015.9694-0.1009-0.01690.10520.1458-0.05210.18630.0395-0.43280.16180.2267-0.10310.06590.4997-0.02780.331299.2848-43.61811.8454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 10 through 156)
2X-RAY DIFFRACTION2(chain 'A' and resid 9 through 156)

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