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- PDB-6zht: Uba1-Ubc13 disulfide mediated complex -

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Basic information

Entry
Database: PDB / ID: 6zht
TitleUba1-Ubc13 disulfide mediated complex
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 / PINK1-PRKN Mediated Mitophagy / Interleukin-1 signaling / Aggrephagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / free ubiquitin chain polymerization / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin conjugating enzyme complex ...protein targeting to vacuolar membrane / PINK1-PRKN Mediated Mitophagy / Interleukin-1 signaling / Aggrephagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / free ubiquitin chain polymerization / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin conjugating enzyme complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / fungal-type vacuole membrane / postreplication repair / 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 / cytosol / cytoplasm
Similarity search - Function
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, 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/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating 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
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: 2.3 Å
AuthorsSchaefer, A. / Misra, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ubiquitin-activating enzyme E1 1
B: Ubiquitin-conjugating enzyme E2 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,51218
Polymers129,2652
Non-polymers1,24716
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-64 kcal/mol
Surface area50250 Å2
Unit cell
Length a, b, c (Å)181.390, 58.270, 137.460
Angle α, β, γ (deg.)90.000, 109.720, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-1113-

CL

21C-1425-

HOH

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Components

#1: Protein Ubiquitin-activating enzyme E1 1


Mass: 111847.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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: 17417.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: UBC13, YDR092W, YD6652.04 / Production host: Escherichia coli (E. coli)
References: UniProt: P52490, E2 ubiquitin-conjugating enzyme
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / Details: ammonium nitrate, CHES, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 60597 / % possible obs: 71.3 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 7.69
Reflection shellResolution: 2.301→2.383 Å / Num. unique obs: 483 / CC1/2: 0.404

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Processing

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

3cmm


Resolution: 2.3→24.71 Å / SU ML: 0.2989 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2632 2177 5.04 %
Rwork0.2062 41021 -
obs0.2091 43198 71.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8977 0 76 335 9388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00329274
X-RAY DIFFRACTIONf_angle_d0.681612547
X-RAY DIFFRACTIONf_chiral_restr0.04271390
X-RAY DIFFRACTIONf_plane_restr0.00461639
X-RAY DIFFRACTIONf_dihedral_angle_d22.85663478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.3992120.2919181X-RAY DIFFRACTION5.16
2.35-2.410.4066300.2947520X-RAY DIFFRACTION14.68
2.41-2.470.3723480.27581035X-RAY DIFFRACTION28.97
2.47-2.530.2986850.27661498X-RAY DIFFRACTION41.54
2.53-2.610.3108770.26671827X-RAY DIFFRACTION51.71
2.61-2.690.31591110.26772175X-RAY DIFFRACTION60.44
2.69-2.790.34371230.26172492X-RAY DIFFRACTION69.55
2.79-2.90.30031460.26692836X-RAY DIFFRACTION79.31
2.9-3.030.31831810.26093183X-RAY DIFFRACTION89.92
3.03-3.190.3021820.2483556X-RAY DIFFRACTION98.65
3.19-3.390.31262020.22463577X-RAY DIFFRACTION99.97
3.39-3.650.27691940.19783594X-RAY DIFFRACTION99.92
3.65-4.020.23281920.17353561X-RAY DIFFRACTION99.92
4.02-4.590.21752010.15193606X-RAY DIFFRACTION99.9
4.59-5.770.22061900.16653654X-RAY DIFFRACTION99.92
5.78-24.710.22172030.19493726X-RAY DIFFRACTION99.85
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)
10.05377981675690.04243555003830.01728140408090.03168487277340.02134032912750.0916814940158-0.0477558936726-0.03214422203290.1086752081440.0458934143262-0.06579432788160.0322770524211-0.2070566033720.0235865196519-0.2130917581550.203699590377-0.0884633182098-0.00332696126336-0.06003874043350.07258487846940.205444884474-1.8024972473733.852221384554.9059279
20.00855334528217-0.01888203480470.004393456725030.057694401459-0.01180141410350.002992231611440.1351011609140.0247840171659-0.107203609152-0.05023898576160.02513927889950.100026846342-0.0333440030890.03436472021370.00173525780710.186324594061-0.0803753269067-0.02639304736670.288783766665-0.01886761611890.242693248492-27.43333040363.2811367432254.1398898557
30.180872553510.2307253444220.1591092573740.3872616565230.1359101885670.145826859738-0.07635386087070.135488597439-0.1961278954030.02093786460260.191219843453-0.2232255258670.0931551495370.02318694108380.2072691494880.0655580146163-0.119654278382-0.01432879632440.07254477885670.1037835354740.195729558921.7155846391817.737059880446.5684030962
40.107786678511-0.0420408148767-0.0631067379810.1029543661190.06973336535330.0643494088703-0.1409581362130.1539998324270.045923175071-0.069666899470.02320466498290.0400404840593-0.123702948568-0.0905471693379-0.06272444945680.381327963436-0.12703456113-0.1302818101550.4018827662550.1720108965830.290340148301-10.615398676633.734519001825.8265601339
50.03946303662780.0381591918381-0.02180466928240.0441692324563-0.01387378237340.0101990546388-0.01445483293940.138004253057-0.013336519883-0.1024597019120.0672069458439-0.068195343137-0.07485053306060.09534581850740.1696857895120.0499370083324-0.1872965760820.112222713580.274554769433-0.02681634109990.0390411413635-29.495725077218.813394063925.8636485869
60.03678539156810.01430074889440.005994761159180.03062438872460.0008377276544250.117827647915-0.1242012810690.0125093924177-0.0412722329769-0.03246588285410.1098339041770.0249830774967-0.189894085934-0.23007008841-0.006327518386410.2187344870650.0304432518723-0.03148348082140.213881669475-0.002210502282210.180181297389-55.699294818823.799857020738.2108893434
70.107784587096-0.02317339821240.01950740475260.0153512519679-0.03254049561870.0384848218086-0.1016714870020.02042029460140.026297311698-0.112065598980.0825065561856-0.0419355587436-0.1823477068910.052773144286-0.01853085443220.15106062766-0.0977679390833-0.02470252535450.155849474757-0.02549376410610.178117551321-30.256501424225.860624986538.8629062669
8-0.006274957703030.008382509637790.007958388866420.00540878655229-0.009792912571250.0202234197762-0.06165307661330.358609228138-0.11610658051-0.2359917408420.0276461123511-0.07193425410410.102153429802-0.0260278596183-0.004017688901790.306972796359-0.2483102646210.1448052588980.561323843472-0.1725066099930.15773747893-11.77233443677.257376191428.31088985213
90.0265927339080.02225307689080.003206113674670.0241636098183-0.001649489909770.00394660875115-0.01485541264180.02275635781350.038152075943-0.05195024177660.0364151045243-0.00626191225867-0.05743586599840.08083648454520.01443716843540.23868483784-0.1968599158290.06935322610820.434168256076-0.1611611538120.225252800221-36.30754172783.0062785533315.2112653263
100.0009837653894686.57318203163E-69.5751543367E-50.001046583739360.001221084289760.00111930891794-0.00300797691712-0.0014166914963-0.0122018139640.0239663793669-0.01344962127920.007407186648850.009888708024730.00150771918459-4.97186645658E-70.409523154325-0.1273426756360.007393055158160.469970589678-0.04003249515990.42502864152-31.76983605971.2371116710226.9087333801
110.001416058000280.001767025593280.001755631587190.00617082539799-0.006067543835380.01240479779950.0132352707657-0.02790712864110.00295940357315-0.04932092173740.00586759377858-0.009235872963080.0690025477151-0.01885875892430.000435317100830.234082933351-0.1487527323710.07598398550860.325756396991-0.07522751249940.258773575563-47.3269771334-1.8576801822326.5885579886
120.002182168185370.001993631735090.000868051914920.001826024283460.001615504298420.00183798712229-0.0117576646364-0.00972202434353-0.0138967268388-0.00576864536879-0.02918355168030.02814241305930.011450073231-0.02417390004249.45186857422E-70.25461886093-0.1822081946550.02003682848380.413902916119-0.08187771157220.376058975902-56.6665878825-3.2210281144215.6178347167
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 166 )CA24 - 1661 - 146
22chain 'A' and (resid 167 through 219 )CA167 - 219147 - 199
33chain 'A' and (resid 220 through 474 )CA220 - 474200 - 457
44chain 'A' and (resid 475 through 545 )CA475 - 545458 - 534
55chain 'A' and (resid 546 through 650 )CA546 - 650535 - 639
66chain 'A' and (resid 651 through 810 )CA651 - 810640 - 781
77chain 'A' and (resid 811 through 885 )CA811 - 885782 - 856
88chain 'A' and (resid 886 through 1024 )CA886 - 1024857 - 995
99chain 'B' and (resid 0 through 86 )BB0 - 861 - 90
1010chain 'B' and (resid 87 through 100 )BB87 - 10091 - 104
1111chain 'B' and (resid 101 through 132 )BB101 - 132105 - 136
1212chain 'B' and (resid 133 through 152 )BB133 - 152137 - 156

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