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- PDB-5l6j: Uba1 in complex with Ub-MLN7243 covalent adduct -

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Basic information

Entry
Database: PDB / ID: 5l6j
TitleUba1 in complex with Ub-MLN7243 covalent adduct
Components
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-activating enzyme E1 1
KeywordsLIGASE / E1 enzyme / ubiquitin activation / Uba1 inhibitor / adenosyl sulfamate
Function / homology
Function and homology information


E1 ubiquitin-activating enzyme / Neddylation / ubiquitin activating enzyme activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome biogenesis / cytoplasmic translation ...E1 ubiquitin-activating enzyme / Neddylation / ubiquitin activating enzyme activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome biogenesis / cytoplasmic translation / ubiquitin-dependent protein catabolic process / protein ubiquitination / structural constituent of ribosome / DNA damage response / ubiquitin protein ligase binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, SCCH 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, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, SCCH 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/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 / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain / Ubiquitin conserved site / Ubiquitin domain / 3-Layer(bba) Sandwich / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Zinc-binding ribosomal protein / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / NAD(P)-binding Rossmann-like Domain / Roll / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-61T / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-activating enzyme E1 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsMisra, M. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFZ82; HS Germany
CitationJournal: Structure / Year: 2017
Title: Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme.
Authors: Misra, M. / Kuhn, M. / Lobel, M. / An, H. / Statsyuk, A.V. / Sotriffer, C. / Schindelin, H.
History
DepositionMay 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
SupersessionJul 19, 2017ID: 3CMM, 4NNJ
Revision 1.1Jul 19, 2017Group: Advisory / Database references / Category: citation / pdbx_database_PDB_obs_spr
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 7, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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-40S ribosomal protein S31
C: Ubiquitin-activating enzyme E1 1
D: Ubiquitin-40S ribosomal protein S31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,86829
Polymers245,9254
Non-polymers2,94325
Water11,962664
1
A: Ubiquitin-activating enzyme E1 1
B: Ubiquitin-40S ribosomal protein S31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,39014
Polymers122,9632
Non-polymers1,42712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-61 kcal/mol
Surface area46350 Å2
MethodPISA
2
C: Ubiquitin-activating enzyme E1 1
D: Ubiquitin-40S ribosomal protein S31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,47815
Polymers122,9632
Non-polymers1,51513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-44 kcal/mol
Surface area46430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.476, 193.920, 230.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEUAA12 - 102412 - 1024
21GLYGLYLEULEUCC12 - 102412 - 1024
12METMETGLYGLYBB1 - 761 - 76
22METMETGLYGLYDD1 - 761 - 76

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Ubiquitin-activating enzyme E1 1


Mass: 114393.844 Da / Num. of mol.: 2
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-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 (strain ATCC 204508 / S288c) (yeast)
Gene: RPS31, RPS37, UBI3, YLR167W, L9470.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P05759

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Non-polymers , 5 types, 689 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-61T / [(1~{R},2~{R},3~{S},4~{R})-2,3-bis(oxidanyl)-4-[[2-[3-(trifluoromethylsulfanyl)phenyl]pyrazolo[1,5-a]pyrimidin-7-yl]amino]cyclopentyl]methyl sulfamate / MLN7243


Mass: 519.518 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20F3N5O5S2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 664 / 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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2M lithium sulfate, 0.1M bis-tris, 15% peg 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.68→20 Å / Num. obs: 91638 / % possible obs: 99 % / Redundancy: 4.5 % / CC1/2: 0.992 / Rsym value: 0.13 / Net I/σ(I): 10.5
Reflection shellHighest resolution: 2.68 Å / Rmerge(I) obs: 0.887

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NNJ

4nnj


Resolution: 2.68→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 22.694 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.51 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22398 4499 4.9 %RANDOM
Rwork0.17117 ---
obs0.17375 86846 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.723 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2--2.93 Å2-0 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.68→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17066 0 183 664 17913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01917597
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216787
X-RAY DIFFRACTIONr_angle_refined_deg1.9731.97823791
X-RAY DIFFRACTIONr_angle_other_deg1.068338817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47452160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5825.368829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.736153111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1041576
X-RAY DIFFRACTIONr_chiral_restr0.1050.22671
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02119784
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023858
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4912.6378645
X-RAY DIFFRACTIONr_mcbond_other1.492.6378643
X-RAY DIFFRACTIONr_mcangle_it2.5113.95210799
X-RAY DIFFRACTIONr_mcangle_other2.5083.95210797
X-RAY DIFFRACTIONr_scbond_it1.8842.8558952
X-RAY DIFFRACTIONr_scbond_other1.8842.8558952
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1524.18912990
X-RAY DIFFRACTIONr_long_range_B_refined5.50349.80173099
X-RAY DIFFRACTIONr_long_range_B_other5.48649.73172838
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A654860.08
12C654860.08
21B44620.1
22D44620.1
LS refinement shellResolution: 2.678→2.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 297 -
Rwork0.305 6128 -
obs--97.64 %
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)
11.40470.37820.15471.5156-0.00550.8582-0.0311-0.0024-0.0069-0.1199-0.02930.38750.0454-0.21760.06050.18710.0151-0.02990.0774-0.02720.1137-20.600228.0462-42.2672
23.93412.80251.30446.36471.77382.5306-0.08410.18120.0868-0.07720.0805-0.177-0.18730.30240.00360.10530.03620.02230.09540.03340.02613.041957.3441-41.955
30.7731-0.19960.11351.56990.54131.00710.0131-0.0577-0.22360.10440.01080.05590.17130.0237-0.02390.14360.00380.00530.04680.02640.0674-8.142518.5592-31.4818
41.34860.7273-1.463.3546-1.36884.8559-0.0906-0.5801-0.00310.3351-0.0781-0.2893-0.27870.42470.16870.29190.07860.00390.2771-0.03330.0695-10.651462.2718-4.7208
50.4202-0.40.14031.1410.63320.9832-0.0104-0.0581-0.11950.0859-0.00210.1390.0184-0.01640.01260.166-0.00220.02630.04090.02840.044-5.316533.2143-22.2172
62.06920.88421.78241.6115-0.50994.93530.0614-0.3430.22890.47480.24840.1639-0.2925-0.5349-0.30990.4940.1799-0.00380.25460.0160.209617.977115.21323.1126
74.95640.28680.85657.3661-0.03952.54180.09430.3247-0.0104-0.311-0.0847-0.8888-0.01860.4851-0.00950.1770.02360.01880.17690.03390.187215.279132.0422-37.4975
84.4812.6232-2.96251.8334-2.95026.9421-0.16030.04810.0023-0.1154-0.0633-0.06110.23550.34990.22350.24880.0699-0.01010.04710.02340.08283.397631.1429-30.9898
92.2635-0.1024-0.09441.05050.09412.0551-0.0435-0.1845-0.08670.19130.10960.19680.1458-0.0904-0.06610.13330.02680.02640.03210.02980.0427-36.345664.7649-39.6834
104.3466-1.5254-3.01213.74651.31533.8810.14090.1396-0.0458-0.46360.0364-0.45990.03150.6115-0.17730.19230.03910.01750.3109-0.04510.1363-3.061152.4306-60.0796
111.2859-0.45260.35391.56820.0141.689-0.05080.04230.1683-0.05130.05750.0306-0.3307-0.045-0.00670.14690.03270.03010.04770.03720.048-36.446479.3882-50.9789
120.0727-0.2110.06643.43480.35860.17780.11480.14210.0273-0.8074-0.0808-0.30610.01020.1882-0.0340.36610.1080.04980.3410.04790.0694-28.521364.5077-74.973
133.6224-0.8561.81731.93490.15412.40140.08950.6863-0.0638-0.4676-0.0052-0.09170.33710.2167-0.08440.46420.0609-0.07280.282-0.07630.0992-29.014134.2638-83.1508
140.56390.15010.25060.1365-0.01191.46380.07240.17350.016-0.0075-0.0057-0.0732-0.21850.0663-0.06670.1470.01640.05230.11740.05030.0768-27.981173.0935-65.2415
153.2291-0.044-0.02891.5797-0.52064.6640.06210.112-0.2418-0.1582-0.02360.21120.2388-0.6114-0.03850.34260.04270.03650.24640.07670.1438-38.532188.0576-98.3073
165.7675-2.1455-0.62346.29970.32465.1050.10760.3210.5722-0.1301-0.0277-0.8592-0.39750.405-0.07990.254-0.03060.08680.27970.07980.2343-9.057877.9763-66.7705
176.83931.55431.42952.3323-0.25320.80720.0935-0.0299-0.6159-0.67930.0578-0.6974-0.0430.0327-0.15130.4773-0.06650.32090.085-0.0360.3137-20.927971.3965-65.3625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 197
2X-RAY DIFFRACTION2A198 - 264
3X-RAY DIFFRACTION3A265 - 624
4X-RAY DIFFRACTION4A625 - 810
5X-RAY DIFFRACTION5A811 - 925
6X-RAY DIFFRACTION6A926 - 1024
7X-RAY DIFFRACTION7B1 - 65
8X-RAY DIFFRACTION8B66 - 76
9X-RAY DIFFRACTION9C11 - 166
10X-RAY DIFFRACTION10C167 - 264
11X-RAY DIFFRACTION11C265 - 545
12X-RAY DIFFRACTION12C546 - 624
13X-RAY DIFFRACTION13C625 - 844
14X-RAY DIFFRACTION14C845 - 925
15X-RAY DIFFRACTION15C926 - 1024
16X-RAY DIFFRACTION16D1 - 65
17X-RAY DIFFRACTION17D66 - 76

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