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- PDB-9eyh: Ubiquitin conjugating enzyme Ubc6 UBC domain with isopeptide-link... -

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Basic information

Entry
Database: PDB / ID: 9eyh
TitleUbiquitin conjugating enzyme Ubc6 UBC domain with isopeptide-linked ubiquitin
Components
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-conjugating enzyme E2 6
KeywordsTRANSFERASE / ubiquitin / Endoplasmic Reticulum Associated Degradation
Function / homology
Function and homology information


maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues ...S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / Ubiquitin-ribosomal protein eS31 fusion protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSwarnkar, A. / Stein, A.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)677770European Union
German Research Foundation (DFG)SFB1190 Germany
CitationJournal: Embo J. / Year: 2024
Title: Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes.
Authors: Swarnkar, A. / Leidner, F. / Rout, A.K. / Ainatzi, S. / Schmidt, C.C. / Becker, S. / Urlaub, H. / Griesinger, C. / Grubmuller, H. / Stein, A.
History
DepositionApr 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 25, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 6
B: Ubiquitin-conjugating enzyme E2 6
C: Ubiquitin-40S ribosomal protein S31
D000: Ubiquitin-40S ribosomal protein S31


Theoretical massNumber of molelcules
Total (without water)57,8844
Polymers57,8844
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.753, 53.490, 111.798
Angle α, β, γ (deg.)90.000, 103.152, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 6 / E2 ubiquitin-conjugating enzyme 6 / Ubiquitin carrier protein UBC6 / Ubiquitin-protein ligase UBC6


Mass: 20373.053 Da / Num. of mol.: 2 / Mutation: C87K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBC6, GI527_G0001907 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8H8ULW7, E2 ubiquitin-conjugating enzyme
#2: Protein Ubiquitin-40S ribosomal protein S31


Mass: 8568.769 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPS31, RPS37, UBI3, YLR167W, L9470.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P05759
Has protein modificationN

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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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG smear, sodium acetate, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.01 Å / Num. obs: 19017 / % possible obs: 99.67 % / Redundancy: 12.1 % / Biso Wilson estimate: 63.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0848 / Net I/σ(I): 17.41
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 11.8 % / Num. unique obs: 1903 / CC1/2: 0.945 / % possible all: 99.53

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.01 Å / SU ML: 0.3587 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6574
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2656 895 4.72 %
Rwork0.2341 18073 -
obs0.2356 18968 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.87 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 0 0 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224031
X-RAY DIFFRACTIONf_angle_d0.50625472
X-RAY DIFFRACTIONf_chiral_restr0.0368611
X-RAY DIFFRACTIONf_plane_restr0.0039704
X-RAY DIFFRACTIONf_dihedral_angle_d12.4141544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.760.34781600.31922962X-RAY DIFFRACTION99.49
2.76-2.980.3321700.31882970X-RAY DIFFRACTION99.59
2.98-3.280.35271300.28682982X-RAY DIFFRACTION99.65
3.28-3.750.30041420.2593019X-RAY DIFFRACTION99.62
3.75-4.720.22721420.20913024X-RAY DIFFRACTION99.81
4.72-48.010.23211510.23116X-RAY DIFFRACTION99.97
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)
11.00271406623-0.08379544244020.1311288614511.046953061850.1764620568251.33473193209-0.2000348185670.7495525982990.0899494308492-0.2057498914930.164657492209-0.103284073298-0.420764709693-0.161437029643-7.05240795896E-50.751207002913-0.1189034115380.009596018631750.888626180586-0.05234841317440.725433051676-33.0960043904-14.5998892573-12.1004991454
22.737183438480.49933318602-0.3392071434651.358170321390.9697612269932.36691131575-0.4438493012150.2349961075250.391212357376-0.2812633331810.305979104562-0.264150984352-0.569170300599-0.0658712331837-0.0002031417341250.755383819711-0.118535695095-0.09625825673280.6292064555570.01727124939250.75476785756-28.462069693-7.68177532765-1.45791545737
31.238806287182.268353778120.1984020341281.601388679690.2988531838280.9301900081960.1252677543520.4704649461310.1108323680530.155502973360.277251326744-0.290410766827-0.2265741519631.277116729550.001139654640210.772406405488-0.0605195776356-0.04704397881940.721444961974-0.04361018451520.699294235794-21.7751213628-9.510436816990.410991061478
41.154870493271.0262461190.1118375007990.988730893621-0.7837428237990.739943105553-0.002839680818930.130274858626-0.333597055999-0.07473329512460.07405123360620.1157710435560.289769047536-0.04764099402284.44029140296E-50.676265920404-0.06354938995310.008403659727290.653674651917-0.07497808297910.750708913591-35.4621640736-25.5842788415.96155397027
52.70769783379-1.405545869741.485840311011.80704488593-0.7378335700624.42568163111-0.185120842125-0.2583638568620.2511241044870.1480467086760.183084799022-0.227707042761-0.5654574278-0.3636327912718.91334980181E-50.6839613902350.0410389160306-0.02307596989890.623382888050.06517788928990.729437036597-43.2262740736-23.485730261124.6791780487
61.14473055868-1.530264445571.463956819581.8272570835-1.509630970921.523020490971.556150600531.562765441470.363337810138-1.567113554980.06506591913350.04570048407411.04473525004-1.142169562930.1693415348291.138324144770.360223238660.02805981323270.9773022928180.2255883195331.12153121744-42.5052185617-6.7084004071630.7762068822
73.169002177360.805508960266-0.59741999832.57857174037-1.123429062994.3394805875-0.0263450200768-0.227163107743-0.5802604534770.2609730988830.502397945050.4318467931240.482438030216-1.409144866142.27032051335E-50.836434522814-0.0298165568502-0.1600191307110.9247299809870.1765604275930.777979603436-54.2120163361-30.197521807320.0122552495
80.2246350990550.273761253826-0.199791190790.988774255878-0.05751570607780.170832924676-0.3316638887181.33168185257-0.684274177656-0.5653125302390.777432643524-0.478797798393-0.3081835248771.21544349010.0004483998431980.95204809572-0.05966881036270.1668667334461.40291163029-0.17942692880.989568555653-7.95041736848-16.3917552343-15.6928079718
9-0.00731926741709-0.0246924439356-0.11718086978-0.01040686052250.007135597273120.05668401699720.244635724146-0.1314469923381.139212409610.188744680884-0.453506622191-0.496108908295-1.112712003120.63604299468-0.001160427716461.47232339628-0.391571990989-0.1235529528691.319191176980.05167724802181.34988401199-6.23216844652-6.81292491941-15.1103159291
100.5268632509120.351103722820.1257697744840.2502716620370.1380975297690.180036298972-0.881575696141-0.527791267430.496471299725-0.123804120290.61839779939-0.806509676151-0.756123110334-0.2414792831690.0004010935245030.683944769944-0.03866751130710.1006638089350.952069188019-0.08993374704240.972850492734-8.07546939597-15.4715978219-3.98064720073
111.521076158430.945996312194-0.5925517143660.945077158863-1.089791051121.23978303693-0.60797575103-0.01886981853760.3622056398090.890761173460.505232135925-1.138068637960.117839753040.7401714000090.001780224153380.860381876103-0.0833965645878-0.03846613948911.13956496001-0.05359545774960.804407120043-12.0825598995-14.1925161377-8.58027240723
120.5131810342540.518272600086-0.08783632130670.329366155657-0.09663147542140.0514224891258-0.368187762406-0.6858479645050.7654868757291.105121667910.953843753247-0.210612489462-0.41049078492-0.972618204569-9.94573326332E-51.817206044510.4586315193960.09407213681561.400653772220.2187996213350.983622050456-52.0835026617-14.731839562349.8884720268
130.366240930390.0670119042577-0.4473956853870.1499245064030.2307621941630.632278947325-0.789376847259-0.9264078210.814112137976-0.8473405685320.2951633548740.878684583018-1.62706648899-1.22769847599-0.001028075995591.718604637780.6586398365970.05830207539161.300176204570.04686997301111.19916398922-52.2393520318-10.380704573642.2502872891
140.0697420426975-0.0923461928282-0.05866575015190.07455059122170.05414306365140.0287590207299-0.0270942361198-0.7186865087331.08097818097-0.0637210693297-1.052301686521.45001754872-0.5044684320690.0403850172265-0.001304908966652.118692585850.2919621372970.2587604354491.844391405570.3572904146761.68507762325-63.3955364276-9.6829463468342.8545772538
150.3340884145170.1185597856990.1875027071070.01203440666810.2299022596730.387345511698-0.168960528366-1.138086968320.128431634165-0.44518736010.2970493157870.4835434445050.720962314454-0.8190301461240.000643783872371.564976216330.3142854665840.02508208277511.344902944350.2503894053910.78996386775-55.451921956-15.750439895841.4507168637
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 2:44)AA2 - 441 - 43
22(chain A and resid 45:98)AA45 - 9844 - 97
33(chain A and resid 99:130)AA99 - 13098 - 129
44(chain A and resid 131:170)AA131 - 170130 - 169
55(chain B and resid 2:88)BB3 - 881 - 86
66(chain B and resid 89:103)BB89 - 10387 - 101
77(chain B and resid 104:171)BB104 - 171102 - 169
88(chain C and resid 1:24)CC1 - 241 - 24
99(chain C and resid 25:40)CC25 - 4025 - 40
1010(chain C and resid 41:59)CC41 - 5941 - 59
1111(chain C and resid 60:76)CC60 - 7660 - 76
1212(chain D and resid 1:22)D000D2 - 221 - 21
1313(chain D and resid 23:49)D000D23 - 4922 - 48
1414(chain D and resid 50:59)D000D50 - 5949 - 58
1515(chain D and resid 60:76)D000D60 - 7659 - 75

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