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- PDB-7ahf: Dimeric structure of the catalytic domain of the human ubiquitin-... -

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Basic information

Entry
Database: PDB / ID: 7ahf
TitleDimeric structure of the catalytic domain of the human ubiquitin-conjugating enzyme UBE2S L114E varaiant
ComponentsUbiquitin-conjugating enzyme E2 S
KeywordsTRANSFERASE / E2 / UBE2S / dimer / cell cycle
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 / molecular replacement / Resolution: 2.15 Å
AuthorsLiess, A.K.L. / Feiler, C.G. / Lorenz, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Emmy Noether LO 2003/1-1 Germany
CitationJournal: To Be Published
Title: Structural analyses of the ubiquitin-conjugating enzyme UBE2S in different crystal forms
Authors: Liess, A.K.L. / Feiler, C.G. / Lorenz, S.
History
DepositionSep 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)35,1507
Polymers34,8102
Non-polymers3405
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-1 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.317, 48.411, 70.127
Angle α, β, γ (deg.)90.000, 107.070, 90.000
Int Tables number4
Space group name H-MP1211

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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: 17404.914 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.33 M magnesium formate dihydrate, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.148→43.322 Å / Num. obs: 15974 / % possible obs: 99.96 % / Redundancy: 2 % / Biso Wilson estimate: 32.23 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0447 / Rpim(I) all: 0.0447 / Rrim(I) all: 0.06321 / Net I/σ(I): 11.83
Reflection shellResolution: 2.148→2.2828 Å / Rmerge(I) obs: 0.3028 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 1561 / CC1/2: 0.841 / CC star: 0.956 / Rpim(I) all: 0.3028 / Rrim(I) all: 0.4282 / % possible all: 99.49

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zdn

1zdn


Resolution: 2.15→43.32 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 798 5 %
Rwork0.1911 15176 -
obs0.1936 15974 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.85 Å2 / Biso mean: 50.1927 Å2 / Biso min: 20.27 Å2
Refinement stepCycle: final / Resolution: 2.15→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 22 79 2437
Biso mean--52.06 47.09 -
Num. residues----297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.280.30261310.23162489262098
2.28-2.460.27941310.215425122643100
2.46-2.710.25391320.205325132645100
2.71-3.10.24971330.196125262659100
3.1-3.90.22531340.170225492683100
3.9-43.320.21761370.1862587272499
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)
12.55260.1671-1.48026.4521-3.23532.60790.1547-0.81440.07340.00360.45150.90521.49140.0832-0.4850.68650.06090.06130.5020.08670.7084-9.1668-10.6437-10.4287
23.8212-0.62430.44516.3794-2.38646.6250.01150.1548-0.7497-0.1086-0.0009-0.050.76570.1671-0.10360.28380.00820.06150.2197-0.05880.3093-4.95711.9101-19.6287
33.39020.7927-0.25193.6518-1.31123.9065-0.1146-0.4198-0.11280.34260.14040.2680.0313-0.229-0.03380.2380.03060.06510.23540.00650.218-9.49028.5498-10.4364
47.0744-3.6267-0.87025.6667-0.10037.15050.26430.44390.97170.3084-0.2021-0.3375-1.28350.1845-0.08250.3993-0.0340.05260.27150.09580.3555-4.563823.746-21.3199
57.2824-3.67013.53385.0652-6.6619.0421-0.041-0.22920.6322-0.60310.2702-0.26330.15580.1333-0.20550.39960.01560.01710.2962-0.08460.3352-26.803110.831-41.874
62.9551-0.7381-0.56533.90980.1286.65890.00070.33860.096-0.37040.0102-0.0620.1094-0.03950.01280.163-0.03460.00150.22110.02250.2213-30.688111.2275-24.8874
73.58132.54772.3525.05012.10241.6026-0.5771-0.06860.5597-0.29420.2868-0.831-0.29551.33610.36520.5911-0.06130.09990.6630.13730.8483-19.249721.5375-29.1662
84.5726-0.0544-2.1193.34010.50427.6960.0991-0.09860.4738-0.23090.0821-0.2064-0.62330.0939-0.19960.1975-0.0097-0.02940.1711-0.01760.238-24.18516.7222-15.2268
95.9625.93215.97345.91545.91725.9663-0.0027-0.2446-0.17290.64720.13370.12390.7105-0.07060.07410.32550.02480.02620.3369-0.02410.2813-32.06559.0129-5.962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 9 through 25 )B9 - 25
2X-RAY DIFFRACTION2chain 'B' and (resid 26 through 65 )B26 - 65
3X-RAY DIFFRACTION3chain 'B' and (resid 66 through 130 )B66 - 130
4X-RAY DIFFRACTION4chain 'B' and (resid 131 through 156 )B131 - 156
5X-RAY DIFFRACTION5chain 'A' and (resid 8 through 25 )A8 - 25
6X-RAY DIFFRACTION6chain 'A' and (resid 26 through 96 )A26 - 96
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 108 )A97 - 108
8X-RAY DIFFRACTION8chain 'A' and (resid 109 through 140 )A109 - 140
9X-RAY DIFFRACTION9chain 'A' and (resid 141 through 156 )A141 - 156

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