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- PDB-6s96: Crystal structure of the catalytic domain of UBE2S C118A. -

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Basic information

Entry
Database: PDB / ID: 6s96
TitleCrystal structure of the catalytic domain of UBE2S C118A.
ComponentsUbiquitin-conjugating enzyme E2 S
KeywordsTRANSFERASE / human E2 / catalytic domain
Function / homology
Function and homology information


protein K27-linked ubiquitination / free ubiquitin chain polymerization / protein K29-linked ubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / 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 / protein K29-linked ubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / 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 / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / 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 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein modification process / CDK-mediated phosphorylation and removal of Cdc6 / protein polyubiquitination / Separation of Sister Chromatids / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / Senescence-Associated Secretory Phenotype (SASP) / 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, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
FORMIC ACID / Ubiquitin-conjugating enzyme E2 S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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: Sci.Signal. / Year: 2020
Title: Dimerization regulates the human APC/C-associated ubiquitin-conjugating enzyme UBE2S.
Authors: Liess, A.K.L. / Kucerova, A. / Schweimer, K. / Schlesinger, D. / Dybkov, O. / Urlaub, H. / Mansfeld, J. / Lorenz, S.
History
DepositionJul 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
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)35,1336
Polymers34,9722
Non-polymers1614
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-22 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.927, 120.927, 45.344
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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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: 17486.008 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 (E. coli)
References: UniProt: Q16763, E2 ubiquitin-conjugating enzyme
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5 / Details: 2.5 M potassium formate, 0.1 M sodium cacodylate

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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: P13 (MX1) / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.18→34.91 Å / Num. all: 39533 / Num. obs: 19810 / % possible obs: 98.76 % / Redundancy: 2 % / Biso Wilson estimate: 44.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04402 / Rpim(I) all: 0.04402 / Rrim(I) all: 0.06225 / Net I/σ(I): 8.58
Reflection shellResolution: 2.18→2.258 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4077 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 1898 / CC1/2: 0.741 / Rpim(I) all: 0.4077 / Rrim(I) all: 0.5765 / % possible all: 95.14

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZDN

1zdn


Resolution: 2.18→34.91 Å / SU ML: 0.2652 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.0142
RfactorNum. reflection% reflection
Rfree0.2461 1042 5.26 %
Rwork0.2036 --
obs0.2059 19802 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.13 Å2
Refinement stepCycle: LAST / Resolution: 2.18→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 10 32 2283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01362305
X-RAY DIFFRACTIONf_angle_d1.20613154
X-RAY DIFFRACTIONf_chiral_restr0.0691370
X-RAY DIFFRACTIONf_plane_restr0.0087410
X-RAY DIFFRACTIONf_dihedral_angle_d10.25871370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.30.32041410.26392603X-RAY DIFFRACTION96.38
2.3-2.440.29251370.25352642X-RAY DIFFRACTION98.76
2.44-2.630.25961360.23682688X-RAY DIFFRACTION99.02
2.63-2.890.27861620.23152647X-RAY DIFFRACTION98.67
2.89-3.310.28011540.21262691X-RAY DIFFRACTION99.41
3.31-4.170.21741590.18762700X-RAY DIFFRACTION99.62
4.17-34.910.22871530.18322789X-RAY DIFFRACTION99.86
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)
17.934956179621.81103652469-0.7158598069353.13394650151-0.931185457172.67559712586-0.045853121650.0962697246630.0528666066506-0.3193177964830.1219729484220.1815284520270.196007400523-0.119201231373-0.07247270430970.3456519763260.01893847670740.03940504065690.3014955436020.03196148890750.254653373851-17.182510599438.8962368044-8.30613908023
24.11562057391-0.166673750541-1.711945364497.369413837820.1021300483674.847496178390.0496830797408-0.4107770603920.128791964782-0.0847880965184-0.055506128609-0.2993552739810.06445370723420.374691368275-0.003155420502730.234844809295-0.0167125010221-0.001220663001220.5059484252660.03935586896810.233843965986-12.096678588746.234185916811.9362269024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 9 through 156)
2X-RAY DIFFRACTION2(chain 'A' and resid 8 through 156)

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