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- PDB-6zhs: Uba1 bound to two E2 (Ubc13) molecules -

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Basic information

Entry
Database: PDB / ID: 6zhs
TitleUba1 bound to two E2 (Ubc13) molecules
Components
  • Ubiquitin-activating enzyme E1 1
  • Ubiquitin-conjugating enzyme E2 13
KeywordsLIGASE / Ubiquitin / E1 / Ubc13
Function / homology
Function and homology information


protein targeting to vacuolar membrane / Interleukin-1 signaling / Aggrephagy / PINK1-PRKN Mediated Mitophagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / E3 ubiquitin ligases ubiquitinate target proteins ...protein targeting to vacuolar membrane / Interleukin-1 signaling / Aggrephagy / PINK1-PRKN Mediated Mitophagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / fungal-type vacuole membrane / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / protein K63-linked ubiquitination / protein polyubiquitination / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain ...Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Elongation Factor Tu (Ef-tu); domain 3 / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-activating enzyme E1 1 / Ubiquitin-conjugating enzyme E2 13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMisra, M. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHI 425-6/1 Germany
CitationJournal: To Be Published
Title: ATP induced conformational changes facilitate E1-E2 disulfide bridging in the ubiquitin system.
Authors: Misra, M. / Schaefer, A. / Kuhn, M. / Pluska, L. / Tessmer, I. / Sommer, T. / Schindelin, H.
History
DepositionJun 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
A: Ubiquitin-activating enzyme E1 1
B: Ubiquitin-conjugating enzyme E2 13
C: Ubiquitin-conjugating enzyme E2 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,23311
Polymers149,4883
Non-polymers7458
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-66 kcal/mol
Surface area56510 Å2
Unit cell
Length a, b, c (Å)177.710, 72.900, 139.520
Angle α, β, γ (deg.)90.000, 112.430, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Ubiquitin-activating enzyme E1 1


Mass: 114393.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: UBA1, YKL210W / Production host: Escherichia coli (E. coli) / References: UniProt: P22515, E1 ubiquitin-activating enzyme
#2: Protein Ubiquitin-conjugating enzyme E2 13 / E2 ubiquitin-conjugating enzyme 13 / Ubiquitin carrier protein 13 / Ubiquitin-protein ligase 13


Mass: 17547.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: UBC13, YDR092W, YD6652.04 / Production host: Escherichia coli (E. coli)
References: UniProt: P52490, E2 ubiquitin-conjugating enzyme
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate, HEPES, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.35→25 Å / Num. obs: 67708 / % possible obs: 66.13 % / Redundancy: 5.6 % / Biso Wilson estimate: 26.91 Å2 / CC1/2: 0.987 / Net I/σ(I): 6.97
Reflection shellResolution: 2.35→2.435 Å / Num. unique obs: 398 / CC1/2: 0.424

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CMM

3cmm


Resolution: 2.35→24.92 Å / SU ML: 0.3688 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 32.5974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 2266 4.97 %RANDOM
Rwork0.2157 43323 --
obs0.2188 45589 66.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.78 Å2
Refinement stepCycle: LAST / Resolution: 2.35→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10283 0 46 307 10636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002710599
X-RAY DIFFRACTIONf_angle_d0.632514358
X-RAY DIFFRACTIONf_chiral_restr0.04261590
X-RAY DIFFRACTIONf_plane_restr0.00441875
X-RAY DIFFRACTIONf_dihedral_angle_d22.21293988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.40970.4469149X-RAY DIFFRACTION3.67
2.4-2.460.508170.3812445X-RAY DIFFRACTION10.96
2.46-2.520.4158460.3422879X-RAY DIFFRACTION21.56
2.52-2.590.3558580.31681387X-RAY DIFFRACTION33.86
2.59-2.660.3841820.31721776X-RAY DIFFRACTION43.44
2.66-2.750.40151010.32492080X-RAY DIFFRACTION50.96
2.75-2.850.3971420.29752445X-RAY DIFFRACTION60.81
2.85-2.960.35371440.27472883X-RAY DIFFRACTION70.35
2.96-3.10.33621730.26493259X-RAY DIFFRACTION79.8
3.1-3.260.33961950.25033668X-RAY DIFFRACTION90.26
3.26-3.460.29162100.2174011X-RAY DIFFRACTION97.84
3.46-3.730.28392250.19333989X-RAY DIFFRACTION97.66
3.73-4.10.23032020.17244071X-RAY DIFFRACTION99.19
4.1-4.690.21112230.16214058X-RAY DIFFRACTION98.89
4.69-5.90.22222180.18794060X-RAY DIFFRACTION98.12
5.9-24.920.2332230.214163X-RAY DIFFRACTION98.47
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)
11.685924869820.509396905158-0.3580366769551.61032181493-0.1955732392042.97992337806-0.00579614382883-0.07415817925190.5658765554270.1178119330750.04636341564920.113926494684-0.5220453191-0.144994367111-0.06728097264150.2506717745380.02715671885460.009204901932380.151259850008-0.01034611357630.163280849488-10.6773910715.4304070230353.2876445226
22.200468926330.436543286548-0.4431296771410.560649276221-0.5178410823730.7161427777380.12713029079-0.0853962636684-0.1523216494460.0981163538452-0.0320624777665-0.03913678202160.0290520606149-0.0274970293543-0.03178914597420.150636530748-0.0225656462692-0.06627809213310.2238313612650.00841478657110.15616631145-12.4767257764-14.99449298657.7649188988
34.827880763181.431187065661.534438586834.699725074411.045740390554.413073899020.1592661097240.0318238372342-0.6469822433360.0771002844525-0.0165904417564-0.09593068133370.412335490803-0.161772632883-0.06062137329290.103073885-0.0283466451195-0.01160430891290.2458088408950.0504681992560.132741285962-33.0509077449-32.339701707257.1225475916
41.535346564770.02662752650190.1153356495811.00326312409-0.1389912577081.893762008520.06387373404130.1216054771750.00527548349125-0.1334743975190.0453841552298-0.0407661366264-0.109501962180.0908450396888-0.02693573860810.130650634723-0.030833973217-0.01854824059710.2046464091610.01893900839160.12731270348-0.364760691377-5.2798341501339.6325415374
50.7550108337920.0702116950703-0.32605721689-0.0214024421962-0.03636684293160.136917846593-0.1836933070180.437550838181-0.429769969126-0.05161891256360.0498818494190.0352397742527-0.022643979257-0.0584811600275-0.05794188910210.22323077863-0.022374989833-0.05381260025780.459992588181-0.03362211671010.0942717390322-26.0398709244-15.676482882429.1311444894
61.543849316490.05790860904610.3337128671082.55129769791-0.2760886232861.39538698009-0.07174162299570.512502367597-0.0423430550124-0.697958535771-0.02715845628210.1304777826560.0197987091027-0.266099993325-0.02847215641970.1166638886740.0720604633964-0.1011629563830.5387443098790.09801878357090.0655564632495-56.775375067-12.177896407632.4610536685
72.16316024856-0.2673805926060.02207785129483.12715916948-0.7146703335283.23478814876-0.0229829684240.3994983015870.301776663361-0.2181417635820.1028757789440.472468179254-0.361378336804-0.469494598350.09700837691680.2383890293250.0585819195614-0.07689955988350.4695442278410.1085790849160.269905980026-58.9534682384-0.74342678597735.6035019837
81.942488118820.176204632107-0.430233743839-0.0521436959836-0.04782913105840.07833729472470.1068277574160.09703876674540.212059852733-0.09632646951970.00706299715282-0.0902761355519-0.202238390457-0.03429797116060.1327923428160.1219418472720.0182858452237-0.09012448962560.3428188065680.05905514572280.130085860112-32.6582834081-6.6831121112939.115225381
91.51012624884-0.08380662186050.8922876755310.7964570701590.8835443575562.68279385237-0.02650910671960.670979065628-0.255643861529-0.296377508030.093087482705-0.02423052226780.1396229341460.0546582612765-0.08534752016840.33046094258-0.148643309341-0.0003221193927730.566398239428-0.05858113224250.12793192488-15.6481777268-21.64761686617.81340356332
104.329136727490.87475068733-2.933901106732.76198579679-1.08084989533.14341749617-0.2638975711880.264915412472-0.229914781556-0.4280869433140.0245859364419-0.2893307013290.4150077693820.7047787337090.1861371630.404744890296-0.08922762575280.1104896668940.737355138835-0.01566361764460.165858454603-25.9033588834-28.440136063611.4397613448
115.319052497870.575922177815-0.9959374520131.388123109810.3626658916962.60175432712-0.1817222575610.8024045340790.101264538211-0.5175668284250.1086811046250.1651994149480.2876770040070.106236582302-0.01010209230050.391415098785-0.03411224897760.02728460701330.578568117698-0.1192247043250.14922152344-38.4240794761-27.83797370468.82449410905
125.842202484060.567837610192-2.372096354921.69440635039-1.607156891753.14775862176-0.333895308810.5198845829490.0328350771936-0.3772080725680.345083003651-0.00330920612287-0.0166000307107-0.06088597927460.07662622340220.305252423855-0.05821879861320.01820008684610.460518407865-0.04113189673330.160797623494-42.5988166381-30.199963805916.6694926593
135.859583196390.391895147017-1.491173712140.735508687286-0.6558264043833.4229851783-0.134340549410.2008760488810.37609160334-0.269649557070.07407777623330.0653268686392-0.446154487421-0.0599411338118-0.2313705536990.286540413872-0.0652495490145-0.03015723218320.402522179988-0.1106324372770.0646551610951-50.7900122937-26.240809081921.1826307134
146.897622339780.986628731602-2.484562570280.441829792748-0.8922535648093.05717278210.303689275254-1.38378605705-0.2107362143480.167306080492-0.143511943664-0.174765202577-0.07416643966230.4095227140060.1789700573330.368509250509-0.06555677676650.01201734946060.693956707022-0.09567096226890.237963792057-35.0013433251-30.067215148326.2085433081
154.859161481581.12710028882-1.491470534241.26931307523-0.9156751957742.56847247753-0.331650485876-0.673625667277-0.24087578113-0.2750726818890.152896711522-0.07897448607980.125348821927-0.001274972159780.01766020318860.164483239653-0.00744946991835-0.009942311411920.329796463483-0.07818873507960.107775604275-49.324614304-34.892782541225.593009595
164.000874758020.373622463331-1.431523881173.38549477928-2.020293341781.66221359995-0.2038153046111.44327861829-0.21181107338-0.5807692369020.184166382042-0.1335373253340.28062687103-0.410328133081-0.04017593513580.220039883723-0.189703860548-0.0445021374530.858648568221-0.04798745906610.195166182681-60.344509082-36.057482204115.9509622378
177.46986298631-0.3999286392711.26183671415.8317967642-0.1631202333754.768536306520.130988006726-0.202091816524-0.1362714442940.5316649285270.450883584087-0.5465209263230.2114856506270.765947980024-0.2755141921890.1944186942790.1149020319690.02561912265610.550997458396-0.1407357162320.69524151087512.8031622465-41.870797190147.9197701205
185.31136917819-0.08745625149682.714654239432.52109358664-0.03026566844684.56466022991-0.04117207387630.220164825361-0.600477630407-0.1981345482120.0977734888875-0.106078252149-0.0530888600820.216554569744-0.06441539188680.2839637390860.0152861801188-0.01065042717440.18876317698-0.09281907732770.4264244466920.0329660453915-37.390108799838.2128255043
196.465165608510.5657294522881.549672282563.91546660132-0.9426793329857.36246675660.254885660199-0.9351106148240.4418436217170.3027889815670.1626581788680.406336057024-0.762490737418-0.483220069550.4736506115270.2417632584840.0248917719655-0.001799846176120.55951705547-0.1230060117420.521130251891-12.7767496256-32.50742063539.168416817
207.8203661416-0.5405662675084.760820101672.96270526906-0.7523030085216.459865274410.0141765482385-1.32927885619-0.6990466657930.6710182375930.4421620991130.2957952704090.648241438943-1.29862387785-0.3635568972950.64034434146-0.0377977596368-0.04346215852880.5038122160330.1691619313560.65121375279-5.31461807656-42.001873601750.9360791189
214.336399786010.1980606544163.754862553263.750564675690.1061024865153.920973072250.178219736506-0.447864790379-0.2481018083980.232818194125-0.0956005128320.374444902038-0.0319991992613-0.38432929496-0.05249810762990.335968824802-0.0502023910530.04278705089690.241507835192-0.08811753495110.835346517476-11.1543403572-42.107084569941.1791249508
227.29923344290.542334637153.04373062413.17028286168-0.423622385975.59237090097-0.3813928686880.215468055971-0.191079450952-0.3691105850960.08581364308470.361830033269-0.0228659399025-0.346346521563-0.04976053857930.342989382095-0.0220502558036-0.09855530525440.251443448061-0.06639263138310.45837773775-17.3774235436-37.769356324427.8431854372
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 122 )AA10 - 1221 - 113
22chain 'A' and (resid 123 through 200 )AA123 - 200114 - 191
33chain 'A' and (resid 201 through 264 )AA201 - 264192 - 255
44chain 'A' and (resid 265 through 545 )AA265 - 545256 - 538
55chain 'A' and (resid 546 through 624 )AA546 - 624539 - 619
66chain 'A' and (resid 625 through 724 )AA625 - 724620 - 719
77chain 'A' and (resid 725 through 813 )AA725 - 813720 - 787
88chain 'A' and (resid 814 through 885 )AA814 - 885788 - 859
99chain 'A' and (resid 886 through 1024 )AA886 - 1024860 - 998
1010chain 'B' and (resid 0 through 17 )BB0 - 171 - 18
1111chain 'B' and (resid 18 through 40 )BB18 - 4019 - 44
1212chain 'B' and (resid 41 through 67 )BB41 - 6745 - 71
1313chain 'B' and (resid 68 through 86 )BB68 - 8672 - 91
1414chain 'B' and (resid 87 through 100 )BB87 - 10094 - 107
1515chain 'B' and (resid 101 through 132 )BB101 - 132108 - 142
1616chain 'B' and (resid 133 through 151 )BB133 - 151143 - 161
1717chain 'C' and (resid 1 through 17 )CC1 - 171 - 17
1818chain 'C' and (resid 18 through 76 )CC18 - 7618 - 76
1919chain 'C' and (resid 77 through 86 )CC77 - 8677 - 86
2020chain 'C' and (resid 87 through 100 )CC87 - 10087 - 100
2121chain 'C' and (resid 101 through 124 )CC101 - 124101 - 124
2222chain 'C' and (resid 125 through 151 )CC125 - 151125 - 151

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