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- PDB-6d68: Ube2G1 in complex with ubiquitin variant Ubv.G1.1 -

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Basic information

Entry
Database: PDB / ID: 6d68
TitleUbe2G1 in complex with ubiquitin variant Ubv.G1.1
Components
  • Ubiquitin-conjugating enzyme E2 G1
  • Ubv.G1.1
KeywordsTRANSFERASE / Ubiquitin / Ubiquitin conjugating enzyme / Ubiquitin variant / Ube2G1
Function / homology
Function and homology information


E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process ...E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / extracellular exosome / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Ubiquitin conserved site ...Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 G1 / UBC protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.36 Å
AuthorsCeccarelli, D.F. / Garg, P. / Sidhu, S. / Sicheri, F.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-136956 Canada
Canadian Institutes of Health Research (CIHR)MOP-126129 Canada
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural and Functional Analysis of Ubiquitin-based Inhibitors That Target the Backsides of E2 Enzymes.
Authors: Garg, P. / Ceccarelli, D.F. / Keszei, A.F.A. / Kurinov, I. / Sicheri, F. / Sidhu, S.S.
History
DepositionApr 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.4Oct 4, 2023Group: 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 G1
B: Ubiquitin-conjugating enzyme E2 G1
C: Ubv.G1.1
D: Ubv.G1.1


Theoretical massNumber of molelcules
Total (without water)59,2214
Polymers59,2214
Non-polymers00
Water1,53185
1
A: Ubiquitin-conjugating enzyme E2 G1
C: Ubv.G1.1


Theoretical massNumber of molelcules
Total (without water)29,6112
Polymers29,6112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-7 kcal/mol
Surface area13630 Å2
MethodPISA
2
B: Ubiquitin-conjugating enzyme E2 G1
D: Ubv.G1.1


Theoretical massNumber of molelcules
Total (without water)29,6112
Polymers29,6112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-7 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.537, 66.537, 225.098
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11D-103-

HOH

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 G1 / E2 ubiquitin-conjugating enzyme G1 / E217K / UBC7 / Ubiquitin carrier protein G1 / Ubiquitin-protein ligase G1


Mass: 19698.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cysteine modified with beta-mercaptoethanol / Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2G1, UBE2G / Plasmid: Pet28-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P62253, E2 ubiquitin-conjugating enzyme
#2: Protein Ubv.G1.1


Mass: 9912.252 Da / Num. of mol.: 2
Mutation: T7P, L8I, T9R, G10V, A46S, Q49L, S65Y, V70L, L73R, R74H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Ube2G1 / Plasmid: ProEx / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96H31
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG1500, Succinic acid, Sodium phosphate monobasic monohydrate, Glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 24767 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 51.53 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Rrim(I) all: 0.114 / Χ2: 1.332 / Net I/σ(I): 8 / Num. measured all: 168582
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.436.20.40324210.9130.1690.4390.32198.9
2.43-2.536.20.33723990.9340.1420.3670.39499.3
2.53-2.656.60.27324350.9520.1120.2960.4299.8
2.65-2.797.10.21324370.9760.0840.230.497100
2.79-2.967.10.17724490.980.070.1910.65899.6
2.96-3.196.60.14924630.9840.0610.1610.89399.9
3.19-3.517.40.12524720.9870.0480.1351.30599.8
3.51-4.027.10.10624680.990.0420.1151.99699.9
4.02-5.067.10.08925420.9910.0350.0962.80899.8
5.06-406.50.08426810.980.0370.0923.57199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXphenix.refine: 1.13_2998refinement
DENZOdata reduction
HKL-20002.3.12data scaling
PHASER2.5.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AWF, 1FXT

2awf

1fxt


Resolution: 2.36→37.52 Å / SU ML: 0.2988 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.8971 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2536 1280 5.18 %
Rwork0.2126 23433 -
obs0.2147 24713 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.09 Å2
Refinement stepCycle: LAST / Resolution: 2.36→37.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 0 85 3758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223748
X-RAY DIFFRACTIONf_angle_d0.53855085
X-RAY DIFFRACTIONf_chiral_restr0.0404579
X-RAY DIFFRACTIONf_plane_restr0.0036657
X-RAY DIFFRACTIONf_dihedral_angle_d11.68822291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.450.31811070.27332556X-RAY DIFFRACTION98.05
2.45-2.560.30751330.27422550X-RAY DIFFRACTION99.41
2.56-2.70.31681480.27482537X-RAY DIFFRACTION99.74
2.7-2.870.3371450.27622563X-RAY DIFFRACTION99.78
2.87-3.090.33721440.27622575X-RAY DIFFRACTION99.85
3.09-3.40.27741330.25492624X-RAY DIFFRACTION99.82
3.4-3.890.26771460.20262606X-RAY DIFFRACTION99.93
3.89-4.90.19591770.1642620X-RAY DIFFRACTION99.96
4.9-37.520.22621470.18322802X-RAY DIFFRACTION99.26
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)
17.75661685748-2.760769822980.4344889751759.254702494680.3873543778982.41521075994-0.1309539961560.4386394556270.352116927411-0.1590558557820.1534635034841.04128382962-0.272802514967-0.344156870311-0.2495864935640.466226783279-0.01176591434860.02555517902620.3940141338840.04813725643270.49062505121521.521879463598.7356938282479.688365249
25.13633706607-5.074147266593.376088667935.06483496281-3.546473902288.13547884189-0.5431716934390.821665397371-0.4730521379030.6884899826270.194544143951-0.18961394596-0.2199051409240.471776124122-0.1294455458970.420416945562-0.117218163394-0.08285632139460.349389611783-0.06187717263180.55130177374233.022544983587.3388494502478.957496939
35.47348270387-3.08676941428-2.514573228347.200610641843.303311498054.63742779552-0.2040392159260.160307558965-0.56953221241-0.2385179643960.004776539754480.009615206042190.0903989166279-0.1899153428450.336783062310.411820850876-0.1184193465340.02492553461620.2236007218870.001088315004630.3700821229626.351889600286.0370843876475.528602425
45.432394573870.0026965639910.5798685911664.711310647493.761875241456.44280473507-0.1181088551340.316154938339-1.41553655499-0.1793639531950.435656136042-0.7309900321940.7763645450311.01044051738-0.4009095757490.6904519601630.03779138959010.08003531887540.498963450928-0.1862633855880.94435339482438.08719180163.5184471194466.263446567
51.52266194722-2.51242891362.759641443824.43755229237-5.022083604935.73966788606-0.412955313681-0.381811323194-0.7574050068570.2244423669520.677762539978-0.2982831775-0.0207925748065-0.80346448187-0.3366356516650.865835358558-0.196588016311-0.002167497105630.607703050875-0.006239205664690.61418965333330.598547643867.1227330174474.226131514
65.0706476409-0.741191544711-0.1593200152437.59407547796-3.750872772156.25007971728-0.06212387125010.6119960687220.432338989783-0.6762359394080.08114924231020.405049967149-0.507927539362-0.447305638361-0.1297374987320.586260127172-0.0861827379976-0.1037121013720.5326359071160.04361812311520.50598642295825.5725408385104.451885991461.571745509
74.11967617645-1.392521193170.7699551588371.68659620134-1.092338331982.15218861044-0.1519581833360.2077107394390.228273854859-0.1619400655150.0671804877354-0.107250458334-0.122232337106-0.04621091749740.02057470143760.47229680608-0.0605664367439-0.02748700363290.377003295937-0.03118361670020.40307743765137.400092297496.6834094067470.593527977
87.64280080662-3.328660162231.814723108847.06032807403-1.571859165197.663501097350.3439526977871.299255954820.352015349188-0.7293008707970.255802971609-0.214958728403-0.81048353185-0.2685448675820.05330773244760.70839076566-0.0154596495705-0.02784766341610.6302862860460.08476346032560.56196020034935.6373295955108.004633151457.281147459
96.66033555719-1.129293747972.072365177173.76006809718-2.671119786623.70706146166-0.1628994000820.6979101997750.259909088212-0.5273011027680.0843584972132-0.329995471314-0.2750160783790.1720600066920.1347609824750.568779009679-0.125976958620.08652528420720.456444585420.003708028422390.45386287291946.156634599499.857246881462.474404697
105.84996566562-3.410960105930.6349407005645.75332921038-2.386497460544.84158924820.1416627365540.980691661377-0.186766330719-0.921508928947-0.21252289531-0.766960418920.5271540404310.949754069906-0.04345721775320.635183990082-0.0538971258050.158472290050.573623207173-0.04390945051130.58716054156652.297700878691.5447136165463.22524217
117.60658975706-2.69500686155-4.460450413497.066862217080.6148699635887.700421054010.0464962037226-1.559694880460.5069665726060.3874054858370.346006365636-0.725871559892-0.3051859153710.937808956413-0.1761320333140.461788872437-0.00959658875038-0.08920978246890.5517149164960.008108032026620.54955827936351.236685909490.6781398901479.251530936
127.679519474330.5925029904512.980701897224.97857375019-1.127567037746.13113359716-0.3438617444861.272531444761.11749738494-0.287382931842-0.2074608705310.783637653172-0.2092943849230.2563931335430.4060880017240.970104404373-0.2523984271970.2751224802630.673753035203-0.07599665165950.63742188956722.109927257668.7564721842449.50022204
134.475220969050.88558270282-0.6169387461653.09560856836-1.110785621294.14002384974-0.123563945710.494588344947-0.185320089714-0.6211661747550.237900898599-0.1172045082670.2737021881080.252872041958-0.1005648349620.650711372834-0.1021359227880.05370193179810.309559725278-0.03209360750270.40985299965116.664042879164.5450447628462.794410565
142.6262899339-1.17885176072-0.3085260711114.51034464893-2.097232161383.24420627288-0.03070774679990.5380452828390.17078250375-0.4662663789220.03834665432540.0594922895713-0.134379605498-0.0778942246892-0.01703542593550.687402641054-0.131712979633-0.02809117709710.4834417049560.02552726607980.4887967637238.2920979785170.0867963531463.1774209
155.74140330350.617335990538-3.32023487647.15286933114-2.789193903532.811672884110.01987365379030.3257195029910.2432569435490.6974517736620.003134124978620.641188398462-1.06778057874-1.001172473510.08047072524830.7819714151240.0443620919420.1267515045970.521656567461-0.02054868434930.63686205730.87723381255968.3586711018478.641784343
169.67715659689-0.430940382357-2.808848415847.77587355891-0.01706977840477.339031419410.00470069702359-1.41748375528-2.113774361140.8820522931380.00873054633680.1217241558831.012059763990.5480596024870.06682302467660.684785626182-0.11430976279-0.06751690614120.5684145111080.1382508948930.54584968072116.919299836360.6557112919480.887375752
174.684808696452.59412343824-6.267015206382.33352671956-3.575862065968.673431164170.21756385845-0.143051928103-0.0123455090244-0.7890422871530.355587779746-0.352674702029-0.7329049454340.800386617551-0.5793426100280.78141217296-0.1331671989480.1729686523940.552533259461-0.2076886462970.63077260113736.01485303771.6904081834464.952336174
183.95666364177-0.7286348566480.2820435530766.485467934175.159809418496.686508920870.2173050094670.276038255907-0.0161964759159-0.129630461865-0.3649461124150.117198364906-0.33814360635-0.6304794576530.2170940831940.470895688316-0.06167678670210.08657714968940.4114080032640.032629879080.48045567529620.26819886389.0508950632482.362736038
194.48466779489-0.509532953251-0.5602358047222.900827757120.1481417578265.79045395206-0.262255842081-0.793045096277-0.211682838760.6063436888260.2651593194710.09853953419060.117440918897-0.1432571492970.05132258533250.408088699412-0.06457592189240.05858120364230.459962783966-0.07772201907960.50087743421729.214507218788.2133702412485.463004744
206.40945489804-5.0649701473-1.62261535924.927491908831.464512202612.454204597610.505875725982-0.6713559477311.159875496220.3219488655740.190210546263-0.839342720912-0.1907208347621.87955773597-0.09684863256210.599726257464-0.169006968828-0.02535433314460.493583638229-0.1118245765070.49668395869930.686818923798.290297486486.792650241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 55 through 64 )
2X-RAY DIFFRACTION2chain 'C' and (resid 65 through 74 )
3X-RAY DIFFRACTION3chain 'D' and (resid -1 through 13 )
4X-RAY DIFFRACTION4chain 'D' and (resid 14 through 67 )
5X-RAY DIFFRACTION5chain 'D' and (resid 68 through 72 )
6X-RAY DIFFRACTION6chain 'A' and (resid 0 through 19 )
7X-RAY DIFFRACTION7chain 'A' and (resid 20 through 60 )
8X-RAY DIFFRACTION8chain 'A' and (resid 61 through 70 )
9X-RAY DIFFRACTION9chain 'A' and (resid 71 through 116 )
10X-RAY DIFFRACTION10chain 'A' and (resid 117 through 151 )
11X-RAY DIFFRACTION11chain 'A' and (resid 152 through 170 )
12X-RAY DIFFRACTION12chain 'B' and (resid 3 through 19 )
13X-RAY DIFFRACTION13chain 'B' and (resid 20 through 79 )
14X-RAY DIFFRACTION14chain 'B' and (resid 80 through 129 )
15X-RAY DIFFRACTION15chain 'B' and (resid 130 through 151 )
16X-RAY DIFFRACTION16chain 'B' and (resid 152 through 170 )
17X-RAY DIFFRACTION17chain 'C' and (resid 0 through 9 )
18X-RAY DIFFRACTION18chain 'C' and (resid 10 through 22 )
19X-RAY DIFFRACTION19chain 'C' and (resid 23 through 49 )
20X-RAY DIFFRACTION20chain 'C' and (resid 50 through 54 )

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