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- PDB-7pvn: Crystal Structure of Human UBA6 in Complex with ATP -

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Basic information

Entry
Database: PDB / ID: 7pvn
TitleCrystal Structure of Human UBA6 in Complex with ATP
ComponentsUbiquitin-like modifier-activating enzyme 6
KeywordsHYDROLASE / ATP / E1 Activating Enzyme / FAT10 / Ubiquitin
Function / homology
Function and homology information


FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / ATP binding / metal ion binding ...FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / ATP binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 / 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 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Ubiquitin-like modifier-activating enzyme 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsTruongvan, N. / Li, S. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK2243 Germany
CitationJournal: Nat Commun / Year: 2022
Title: Structures of UBA6 explain its dual specificity for ubiquitin and FAT10.
Authors: Truongvan, N. / Li, S. / Misra, M. / Kuhn, M. / Schindelin, H.
History
DepositionOct 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
A: Ubiquitin-like modifier-activating enzyme 6
B: Ubiquitin-like modifier-activating enzyme 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,78018
Polymers237,8252
Non-polymers1,95516
Water3,531196
1
A: Ubiquitin-like modifier-activating enzyme 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,92810
Polymers118,9121
Non-polymers1,0159
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-like modifier-activating enzyme 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8528
Polymers118,9121
Non-polymers9407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.949, 113.748, 183.537
Angle α, β, γ (deg.)90.000, 96.493, 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
11A-1321-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 37 through 236 or resid 239...A37 - 236
121(chain 'A' and (resid 37 through 236 or resid 239...A239 - 345
131(chain 'A' and (resid 37 through 236 or resid 239...A347 - 680
141(chain 'A' and (resid 37 through 236 or resid 239...A682 - 728
151(chain 'A' and (resid 37 through 236 or resid 239...A734 - 801
161(chain 'A' and (resid 37 through 236 or resid 239...A818 - 1031
171(chain 'A' and (resid 37 through 236 or resid 239...A1035 - 1048
181(chain 'A' and (resid 37 through 236 or resid 239...A1101
191(chain 'A' and (resid 37 through 236 or resid 239...A1201
1101(chain 'A' and (resid 37 through 236 or resid 239...A1301
1111(chain 'A' and (resid 37 through 236 or resid 239...A1401
1121(chain 'A' and (resid 37 through 236 or resid 239...A1901
2131(chain 'B' and (resid 37 through 817 or resid 819...B37 - 236
2141(chain 'B' and (resid 37 through 817 or resid 819...B239 - 345
2151(chain 'B' and (resid 37 through 817 or resid 819...B347 - 680
2161(chain 'B' and (resid 37 through 817 or resid 819...B682 - 728
2171(chain 'B' and (resid 37 through 817 or resid 819...B734 - 801
2181(chain 'B' and (resid 37 through 817 or resid 819...B817
2191(chain 'B' and (resid 37 through 817 or resid 819...B819 - 1031
2201(chain 'B' and (resid 37 through 817 or resid 819...B1035 - 1048
2211(chain 'B' and (resid 37 through 817 or resid 819...B1101
2221(chain 'B' and (resid 37 through 817 or resid 819...B1201
2231(chain 'B' and (resid 37 through 817 or resid 819...B1401
2241(chain 'B' and (resid 37 through 817 or resid 819...B1501
2251(chain 'B' and (resid 37 through 817 or resid 819...B1601

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ubiquitin-like modifier-activating enzyme 6 / Ubiquitin-activating enzyme 6 / Monocyte protein 4 / MOP-4 / Ubiquitin-activating enzyme E1-like ...Ubiquitin-activating enzyme 6 / Monocyte protein 4 / MOP-4 / Ubiquitin-activating enzyme E1-like protein 2 / E1-L2


Mass: 118912.492 Da / Num. of mol.: 2 / Mutation: C625A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA6, MOP4, UBE1L2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AVT1, E1 ubiquitin-activating enzyme

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Non-polymers , 6 types, 212 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.75 Å3/Da / Density % sol: 55.3 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Na-cacodylate, 0.16 M Ca-acetate, 15% PEG 8000 and 16% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.71→50 Å / Num. obs: 49253 / % possible obs: 72.5 % / Redundancy: 6.66 % / Biso Wilson estimate: 53.21 Å2 / CC1/2: 0.9847 / Rmerge(I) obs: 0.294 / Rpim(I) all: 0.123 / Net I/σ(I): 6
Reflection shellResolution: 2.71→3 Å / Redundancy: 5.56 % / Rmerge(I) obs: 2.57 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 986 / CC1/2: 0.1695 / Rpim(I) all: 1.158 / % possible all: 21.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CMM

3cmm


Resolution: 2.71→19.98 Å / SU ML: 0.3737 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.0226 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2617 2486 5.07 %
Rwork0.2326 46512 -
obs0.2341 48998 71.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.09 Å2
Refinement stepCycle: LAST / Resolution: 2.71→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15798 0 116 196 16110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005116259
X-RAY DIFFRACTIONf_angle_d0.872622039
X-RAY DIFFRACTIONf_chiral_restr0.04872483
X-RAY DIFFRACTIONf_plane_restr0.00512832
X-RAY DIFFRACTIONf_dihedral_angle_d17.1169847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.770.3508350.3236495X-RAY DIFFRACTION14.22
2.77-2.820.3377570.3324717X-RAY DIFFRACTION20.42
2.82-2.880.331530.3244931X-RAY DIFFRACTION26.08
2.88-2.950.3886540.32071156X-RAY DIFFRACTION32.22
2.95-3.020.3467810.32391583X-RAY DIFFRACTION43.8
3.02-3.110.30781070.31771867X-RAY DIFFRACTION52.14
3.11-3.20.31951020.30532236X-RAY DIFFRACTION62.26
3.2-3.30.31231420.29532583X-RAY DIFFRACTION72.26
3.3-3.420.29851270.28672978X-RAY DIFFRACTION81.54
3.42-3.550.26021880.26743206X-RAY DIFFRACTION89.27
3.55-3.710.29381550.25683447X-RAY DIFFRACTION96.16
3.71-3.910.29131840.23983612X-RAY DIFFRACTION99.45
3.91-4.150.25462020.21633596X-RAY DIFFRACTION99.87
4.15-4.470.241800.18993614X-RAY DIFFRACTION99.89
4.47-4.910.23991910.1823609X-RAY DIFFRACTION100
4.91-5.610.22131950.20823635X-RAY DIFFRACTION99.9
5.61-7.020.2772300.22943591X-RAY DIFFRACTION99.9
7.02-19.980.22012030.21223656X-RAY DIFFRACTION99.54
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)
10.9837230073190.08930414060420.8794245829761.760549952410.426041860672.122758038360.0713976820553-0.266622696556-0.08505903473710.4327518232680.03647718268990.1819489039630.058324651673-0.221116783087-0.03447227165160.123198171686-0.1184688603420.1425590844610.0654632346444-0.01594604534120.5575044824037.99094776703-48.896025400997.1612130079
20.4344324253750.3768437458860.3279530913022.36308967280.4488922997341.017811161570.02736698347030.219476075023-0.0127178276101-0.02034928445470.104726902416-0.2590104275130.1464953993490.368731490249-0.1979980460420.1839820569470.00536609656774-0.0956520305780.1968090394790.01971681668670.49360317205926.4026479309-60.432074137983.9570835447
30.748250951893-0.1261598283690.3321436026991.26171632513-0.1393798044251.19750275026-0.08099507184150.1397950300710.1772646206570.1301549170160.04414761702480.117112498285-0.521042081173-0.2962496105320.006673874958080.0554337895137-0.239536732434-0.0363375063175-0.2300956007870.03143961880380.54167777286712.1725573047-32.954805524382.3751436136
40.5032153748060.1406012847560.2666939816850.5984041368860.3972047436210.313202648985-0.08247685287880.4979356848670.0598229186433-0.2202372447540.238302769040.256580307187-0.1442190097830.201855030498-0.0404671257660.214409136509-0.0817846542593-0.1137332169510.3688365895020.03449844948410.5345190650928.16136351208-46.722515240360.443604763
51.06796258470.3573234933460.78737361041.0059269420.03170531879691.882897556880.2761141717660.335437437747-0.206908119893-0.6480491286460.2296854469870.2148312839240.373225271174-0.342402311068-0.1732348199970.628916879131-0.0350329116277-0.1659865185860.6604557958520.03253633237790.821077330937-14.109300523-61.953466085147.0706652046
60.7668261091910.4148459910491.121883080131.764603330260.2220696918972.065541491040.248121003208-0.0128304837247-0.357345566739-0.148646842710.06838241328610.2200482803950.400024192681-0.6856658728630.1265653375210.205817476638-0.0849551769936-0.06563423627840.518668449498-0.004626657792150.594996990287-8.85243601674-57.174272644362.0856836259
71.51533840521-0.7642680639610.1828059395432.340825002690.8199241411182.010322054980.1176536355450.7227437524550.400777144157-1.15123579832-0.1031518095790.366682917519-1.264255717810.1297404533590.3507569379750.849573008415-0.212889105176-0.2202422992610.6994258021150.269112579130.62460262835315.135123562-20.796007488646.946355859
81.28674407606-0.1276691719190.4275669961911.26294840642-0.3298110554241.15095925642-0.0214239494246-0.1711293918920.0197066878439-0.302712300316-0.01715485576010.852099271855-0.439571490654-0.6516968049080.02218199677710.7712420896830.279296380435-0.1788820576880.508330629577-0.04520764436750.93947976854517.266768327-69.36496180547.52706877344
90.156271238692-0.3446793364480.1296191008561.090517843430.7003032139712.27246414955-0.3231969112810.1558861851990.120625054854-0.5687207303120.238270431732-0.0648713014512-0.5781851678090.7131233068420.1795605772941.035597614860.1098145084-0.2487123633920.3837652362260.009978912431490.7018954007537.4873103531-52.16375796585.06993455508
100.740154188396-0.6256837952280.09200257036270.8224358268710.6938524156551.928315779420.09181334666530.0181053368831-0.130582854048-0.6680545235710.0368131158143-0.0361452747195-0.2906644377660.4339089488590.166567940861.153040311660.124311589782-0.1632060782740.454621825610.01460761314270.52851950853939.9130395409-62.1396827526-5.32174860052
111.09585675624-0.2515442317230.4008007257771.32084813976-0.4014069563532.117819574160.00074234202706-0.111052517765-0.174178788074-0.1734755553710.1196391167880.4785754761010.0280320670084-0.0526479814921-0.08134282132470.7083296367770.133457756194-0.1334019747260.2956273086250.01696630318860.57123608605233.056624684-84.117592902411.7899120718
120.0588006600916-0.04811386183820.2601640207030.3072922066470.3767722045522.25624669934-0.0623192504118-0.125254433184-0.03783636695-0.08460230914430.0990663294830.158211681854-0.643996915360.2063244565640.02183686585380.7109751052960.0915137635038-0.01773856868590.4717478291860.04241751037980.58109819742947.2587914499-69.252154728141.989444653
130.9502071755410.2414292137940.06114158911911.62492379005-0.4956602694642.1655984296-0.555424820541-0.4151484100310.202000221848-0.2350779100820.232120467399-0.274038053463-1.223969565210.1239327121480.2204415097271.320006998580.18946590089-0.05457837121190.532387206077-0.0742638387340.63706927970943.1244240383-46.678140741146.8139731375
140.384885740517-0.08424223864160.7655643642691.344684467150.1548753174271.59540570964-0.140411551605-0.2171311050770.4552651911260.270659615434-0.173446383679-0.00776534481545-1.11926195455-0.1624051635450.2561260819361.385057078970.205570201318-0.1363055948891.10481559191-0.06987240464450.84622280736939.6594226232-52.582579211361.2291920354
151.09214257378-0.4284648223970.5947418611081.414498772140.0558294484371.85429787067-0.299128383813-0.150820227480.03773898221-0.142921934906-0.02431565013920.055807719804-0.483824926529-0.1432308633610.1392131136391.037370146780.08500453166-0.100712197430.4910233787190.01289056278670.47885935993135.9718673396-58.989887265640.6038921584
161.2092549658-0.2003992485940.9106993982231.22984857852-0.1339386477281.621578094250.239425396913-0.208951359908-0.4165449451740.131240191728-0.02151538567880.02737376418190.1453497124090.582653046515-0.208756050520.6213513025430.12512273-0.1000845801280.7626468336990.04621259405340.44902682899760.5588177702-92.199264551224.2468333344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 153 )
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 364 )
3X-RAY DIFFRACTION3chain 'A' and (resid 365 through 583 )
4X-RAY DIFFRACTION4chain 'A' and (resid 584 through 649 )
5X-RAY DIFFRACTION5chain 'A' and (resid 650 through 751 )
6X-RAY DIFFRACTION6chain 'A' and (resid 752 through 927 )
7X-RAY DIFFRACTION7chain 'A' and (resid 928 through 1051 )
8X-RAY DIFFRACTION8chain 'B' and (resid 37 through 153 )
9X-RAY DIFFRACTION9chain 'B' and (resid 154 through 259 )
10X-RAY DIFFRACTION10chain 'B' and (resid 260 through 364 )
11X-RAY DIFFRACTION11chain 'B' and (resid 365 through 583 )
12X-RAY DIFFRACTION12chain 'B' and (resid 584 through 695 )
13X-RAY DIFFRACTION13chain 'B' and (resid 696 through 769 )
14X-RAY DIFFRACTION14chain 'B' and (resid 771 through 833 )
15X-RAY DIFFRACTION15chain 'B' and (resid 834 through 894 )
16X-RAY DIFFRACTION16chain 'B' and (resid 895 through 1048 )

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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