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- PDB-6s98: Crystal structure of the catalytic domain of UBE2S WT. -

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Basic information

Entry
Database: PDB / ID: 6s98
TitleCrystal structure of the catalytic domain of UBE2S WT.
ComponentsUbiquitin-conjugating enzyme E2 S
KeywordsTRANSFERASE / human E2 / catalytic domain
Function / homology
Function and homology information


protein K29-linked ubiquitination / protein K27-linked ubiquitination / free ubiquitin chain polymerization / 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 / Phosphorylation of the APC/C ...protein K29-linked ubiquitination / protein K27-linked ubiquitination / free ubiquitin chain polymerization / 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 / Phosphorylation of the APC/C / anaphase-promoting complex binding / protein K6-linked ubiquitination / positive regulation of ubiquitin protein ligase activity / exit from mitosis / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / Regulation of APC/C activators between G1/S and early anaphase / 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 / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / 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
ACETATE ION / Ubiquitin-conjugating enzyme E2 S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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

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)35,1859
Polymers34,8742
Non-polymers3117
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-46 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.812, 49.050, 71.926
Angle α, β, γ (deg.)90.000, 106.031, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 17436.957 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M sodium-acetate-trihydrate; 0.1 M Tris; 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / 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: 1.55→42.15 Å / Num. obs: 43484 / % possible obs: 99.4 % / Redundancy: 1.8 % / Biso Wilson estimate: 18.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02539 / Rpim(I) all: 0.02539 / Rrim(I) all: 0.03591 / Net I/σ(I): 14.5
Reflection shellResolution: 1.55→1.605 Å / Rmerge(I) obs: 0.4299 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 4292 / CC1/2: 0.638 / Rpim(I) all: 0.4299 / Rrim(I) all: 0.608 / % possible all: 98.89

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Processing

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

1zdn


Resolution: 1.55→42.15 Å / SU ML: 0.1518 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8522
RfactorNum. reflection% reflection
Rfree0.1839 2091 4.81 %
Rwork0.1614 --
obs0.1626 43482 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.83 Å2
Refinement stepCycle: LAST / Resolution: 1.55→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 19 171 2531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332431
X-RAY DIFFRACTIONf_angle_d1.34073314
X-RAY DIFFRACTIONf_chiral_restr0.067376
X-RAY DIFFRACTIONf_plane_restr0.0099430
X-RAY DIFFRACTIONf_dihedral_angle_d13.96181470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.29171160.26792735X-RAY DIFFRACTION98.79
1.59-1.630.26511400.23982723X-RAY DIFFRACTION98.86
1.63-1.670.24531220.21322770X-RAY DIFFRACTION99.21
1.67-1.720.18931260.19582725X-RAY DIFFRACTION99.2
1.72-1.770.23461130.19592758X-RAY DIFFRACTION99.1
1.77-1.840.21931340.18322764X-RAY DIFFRACTION99.55
1.84-1.910.18321320.17742738X-RAY DIFFRACTION99.72
1.91-20.20661270.16972798X-RAY DIFFRACTION99.59
2-2.10.19081520.15512750X-RAY DIFFRACTION99.79
2.1-2.240.17691460.15072778X-RAY DIFFRACTION99.66
2.24-2.410.20471400.14862732X-RAY DIFFRACTION99.86
2.41-2.650.18911320.15212793X-RAY DIFFRACTION99.46
2.65-3.030.17211720.16022754X-RAY DIFFRACTION99.76
3.03-3.820.1761800.14692735X-RAY DIFFRACTION99.15
3.82-42.150.15861590.1492838X-RAY DIFFRACTION99.4
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)
17.99582257522.03016739358-0.7458583748454.315644529962.082276968856.39141296505-0.3052864953080.718000242997-0.717266489279-0.524198964460.00176669732912-0.3578111850481.32293281071-0.2128123994330.3089536787080.569693541185-0.05409978143910.1076030314880.252361404403-0.003981409526650.45522191068-3.52772905923-9.43609801236-23.63369083
22.302021108120.090556781505-1.213513380412.442633757561.086430510453.071672090190.03123520746520.101703112887-0.1190274152790.0381248784292-0.07059485941830.06012778302250.187792994024-0.2254246014650.04094541232670.106650814045-0.00203779101579-0.01205728730720.1716310607690.004496870012840.159066778614-7.16357673346.03804628448-19.0338996102
38.897834198115.19066336048-2.656595268286.751523124640.2001135137617.88940480084-0.007978303944770.1284447554670.393687084911-0.131973439828-0.088958069408-0.00139955556759-0.32878474021-0.2001255512340.07296630979440.0880287497289-0.0105540406492-0.01206866250310.137240757465-0.03856533424810.1039862714214.05462359246.14988972102-29.2867508246
43.296202219751.21297803937-1.432462545191.34864205643-0.4751624583092.998627810730.308583958485-0.0358810659060.6898188436060.0929517358465-0.01812575480360.0963135111665-0.557601672169-0.157230372907-0.1958153676530.1855818502470.02746187669240.03737787181030.13703601454-0.004146160333630.21968642607-3.1535169541819.2443686521-17.2577883467
54.8444646503-0.6988327670281.241759418027.724827175515.01944461526.50417602973-0.309850361926-0.5342708832290.397266737580.728899186520.456223356575-0.149857141180.7891017050520.191532964227-0.1982214728760.3752926878710.1350871075330.02410372915660.4315074302420.04979513568680.22082429771814.900818866910.7683494976.9220958613
65.895093384551.91219249418-5.838152558956.9812774634-0.8975912438147.85347502938-0.109676113315-1.04741295113-1.037746250640.2048520673910.108193410322-0.2139766989761.44889156788-0.385664660380.09454393780780.34433437521-0.0598914567785-6.01576909958E-60.3658146745310.1320208807940.24481026145613.99330550622.15084092435-6.61740563497
72.774323947140.6972400476451.926423135863.291140216122.084078528844.977762602010.0952929551299-0.552214050281-0.1713576859460.4393384704830.0675662147357-0.2151533863810.550578562582-0.0127681688579-0.2034785765980.1058246562290.0275130149884-0.008296907514980.2402177681710.03388007232690.16163357043918.55743488547.70667344522-10.1247784518
81.302817311771.354691800420.9565135448277.966733167176.601741533185.42650629714-0.0356609322335-0.410060738346-0.228880920910.5644358607030.231349419863-0.06777462946640.4043049735880.231390550253-0.3910349864790.1914001775070.0480071343354-0.01898157274750.2701221752880.02934729561920.21857882095721.400628125110.6667143656-10.3502701048
93.01374197548-0.593333152906-1.378463982751.824117290791.316665752787.40164290519-0.0597531102115-0.5507431616530.4500729258840.2397250294170.192353149419-0.0930722344334-0.3431455208590.267779354361-0.2329243706030.154382213714-0.000673034681785-0.01550689641870.219054412915-0.06300905694560.20017598036518.474377833718.4671129981-7.31718956562
105.42344720681-4.838907246972.162806228485.01665946217-2.261979294538.3215816222-0.251298160042-0.1754563767750.5575839394820.258064171652-0.0492675397194-0.215454878432-0.3195875634250.1114263130140.1584931604830.128409659805-0.0428593734650.01319838256540.1182713861910.01782064745620.16984569116819.525786603920.1326053774-17.4814932569
114.00941468301-2.756163792854.140259731996.39123723543-1.011198029555.09143903051-0.185197645498-0.116551275772-0.0250365527475-0.03142579030760.469902677304-0.0788908756467-0.415566037876-0.124028629232-0.2364701789290.2368807309620.02268934969010.005032571960030.310139830681-0.04494361297730.2115761502167.3263705598621.4634340232-5.94561928534
124.80375514898-1.232834362892.500875805073.312137009270.2160293396167.73915523045-0.0944725575708-0.563263194775-0.1469989808220.2616807437670.105333196564-0.0005945396428620.11482417499-0.1565350564570.01998875269170.0865321315404-0.001532412930810.00676188863840.1510964368690.02382459312630.1327929172429.8532210803811.6801726983-10.8641802382
133.09083481045-0.8542036124560.1712163527441.53957978486-0.48281433983.269695727830.03457582350050.1752719699480.193060603785-0.104504038142-0.0155971633793-0.0851764437972-0.1901433324690.169252223345-0.0372342110590.104246518843-0.04376828217480.01464240828590.1011150210830.025060143920.13214065591416.260189081116.4900141636-27.535343717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 108 )
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 156 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 25 )
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 34 )
7X-RAY DIFFRACTION7chain 'B' and (resid 35 through 58 )
8X-RAY DIFFRACTION8chain 'B' and (resid 59 through 65 )
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 84 )
10X-RAY DIFFRACTION10chain 'B' and (resid 85 through 94 )
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 108 )
12X-RAY DIFFRACTION12chain 'B' and (resid 109 through 121 )
13X-RAY DIFFRACTION13chain 'B' and (resid 122 through 156 )

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