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- PDB-5l6i: Uba1 in complex with Ub-MLN4924 covalent adduct -

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Basic information

Entry
Database: PDB / ID: 5l6i
TitleUba1 in complex with Ub-MLN4924 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-B39 / 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: 2.76 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
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
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 1.3May 8, 2019Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4Jan 10, 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
E: Ubiquitin-40S ribosomal protein S31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,64641
Polymers254,5265
Non-polymers3,12036
Water8,161453
1
A: Ubiquitin-activating enzyme E1 1
B: Ubiquitin-40S ribosomal protein S31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,63121
Polymers122,9792
Non-polymers1,65219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-82 kcal/mol
Surface area46770 Å2
MethodPISA
2
C: Ubiquitin-activating enzyme E1 1
D: Ubiquitin-40S ribosomal protein S31
E: Ubiquitin-40S ribosomal protein S31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,01520
Polymers131,5473
Non-polymers1,46817
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-98 kcal/mol
Surface area49640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.500, 191.890, 230.197
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
13B
23E
14D
24E

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
11ALAALALEULEUAA11 - 102411 - 1024
21ALAALALEULEUCC11 - 102411 - 1024
12METMETGLYGLYBB1 - 761 - 76
22METMETGLYGLYDD1 - 761 - 76
13METMETARGARGBB1 - 721 - 72
23METMETARGARGEE1 - 721 - 72
14METMETARGARGDD1 - 721 - 72
24METMETARGARGEE1 - 721 - 72

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 5 molecules ACBDE

#1: Protein Ubiquitin-activating enzyme E1 1


Mass: 114409.844 Da / Num. of mol.: 2
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-40S ribosomal protein S31


Mass: 8568.769 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's 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, 489 molecules

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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 16 / 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-B39 / [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate


Mass: 443.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25N5O4S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 3.15 Å3/Da / Density % sol: 60.9 %
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 PILATUS 6M / Detector: PIXEL / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.76→20 Å / Num. obs: 82916 / % possible obs: 99 % / Redundancy: 5.6 % / Rsym value: 0.133 / Net I/σ(I): 11.2
Reflection shellHighest resolution: 2.76 Å / Rsym value: 0.828

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NNJ

4nnj


Resolution: 2.76→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 25.207 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.918 / ESU R Free: 0.299 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21966 4093 5 %RANDOM
Rwork0.17421 ---
obs0.17643 78520 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--2.1 Å2-0 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 2.76→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17657 0 184 453 18294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01918193
X-RAY DIFFRACTIONr_bond_other_d0.0050.0217400
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.97824584
X-RAY DIFFRACTIONr_angle_other_deg1.203340236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42152236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42425.409856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.232153227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3731578
X-RAY DIFFRACTIONr_chiral_restr0.0890.22767
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02120459
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023983
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_it1.1472.828947
X-RAY DIFFRACTIONr_mcbond_other1.1472.828946
X-RAY DIFFRACTIONr_mcangle_it24.22611173
X-RAY DIFFRACTIONr_mcangle_other24.22611174
X-RAY DIFFRACTIONr_scbond_it1.3712.9759246
X-RAY DIFFRACTIONr_scbond_other1.372.9759246
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2894.39113409
X-RAY DIFFRACTIONr_long_range_B_refined3.91521.6619475
X-RAY DIFFRACTIONr_long_range_B_other3.89321.61919408
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)
11A1261080.07
12C1261080.07
21B93520.07
22D93520.07
31B87540.11
32E87540.11
41D86720.12
42E86720.12
LS refinement shellResolution: 2.763→2.833 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 284 -
Rwork0.299 5315 -
obs--94.01 %
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)
11.0790.28460.03951.5682-0.04220.9655-0.01640.02060.0258-0.1209-0.04380.4380.0887-0.26740.06020.09890.0059-0.03760.1788-0.02670.1333-20.77727.9977-41.8283
24.68772.76771.21666.94091.33322.8568-0.05340.1039-0.0035-0.07480.0843-0.3564-0.23720.1817-0.03090.04580.02830.02180.11340.04560.0453.165357.0565-41.8225
30.7458-0.11340.12461.57760.33371.0048-0.00410.0141-0.20910.02060.00380.04870.19080.04340.00020.0523-0.00390.00950.11150.01320.0759-8.158418.4237-31.0587
41.07470.446-1.51253.0513-1.20244.8345-0.0122-0.52310.03740.369-0.1009-0.2767-0.35480.38350.11320.26930.0501-0.00930.3019-0.04210.0961-10.417762.3362-4.5813
50.2-0.10560.27920.91460.37390.7755-0.019-0.0303-0.07890.12140.00450.18390.036-0.04010.01450.09160.00560.04310.10570.02380.0701-5.319433.1862-21.93
62.55730.30221.41721.4718-0.10594.5711-0.0468-0.41230.23460.42450.18880.127-0.4159-0.4094-0.1420.39560.1304-0.00310.17930.02170.190718.011415.20663.4424
73.81450.84950.1237.5112-0.53632.4607-0.02950.27850.0184-0.45060.0708-0.82490.06530.3974-0.04120.12450.00070.01610.20990.030.178715.252931.7746-37.166
87.10542.9391-5.44891.5929-3.210710.9570.08240.00770.2933-0.00710.013-0.0405-0.22730.1971-0.09550.16080.0223-0.02790.0481-0.00540.16183.302930.9354-30.5605
91.80750.06150.33271.0645-0.1341.7133-0.096-0.251-0.04850.20810.14770.2090.1641-0.1746-0.05170.08730.0430.04290.14760.05490.0469-36.147364.5556-39.4898
104.2614-1.5887-3.47954.31671.64634.1413-0.00180.1383-0.2145-0.3454-0.0161-0.38050.19060.37990.01790.10870.0414-0.02430.2408-0.00110.1398-3.189551.8299-59.9526
111.1845-0.50570.38881.6809-0.26941.7921-0.0966-0.01860.15890.08560.1180.0694-0.3298-0.0542-0.02150.07770.04690.02130.14340.06410.0618-36.142779.1335-50.9371
120.1492-0.28550.03173.06390.77590.29360.21320.18640.0501-0.8476-0.0983-0.4609-0.08520.0892-0.11490.42120.1260.10370.38560.07320.0869-28.424863.9473-74.8438
133.6555-1.14011.53342.17580.32931.83870.14450.6294-0.1535-0.4526-0.0099-0.0460.25620.0457-0.13450.4317-0.0191-0.08980.351-0.07260.1472-29.647133.4605-82.5734
140.3329-0.07940.05280.50550.25311.7316-0.02290.12020.00230.06480.0703-0.0312-0.1920.0397-0.04730.03970.00940.00110.18110.03550.0164-27.719872.6098-65.0866
153.78520.3438-0.95892.0592-0.7195.54530.08910.1547-0.1445-0.1055-0.02020.24350.383-0.5441-0.06880.1643-0.0024-0.0320.21990.09380.1098-38.411687.2579-98.1705
165.3405-2.3031-0.43315.8358-0.44833.9710.10030.10180.5801-0.2557-0.0283-0.8913-0.34960.4662-0.0720.1582-0.02680.06920.29250.06020.1896-8.785377.4342-66.614
178.7876-0.83711.03880.4393-0.83821.7390.0270.0177-0.255-0.0558-0.0582-0.05570.04530.09980.03120.12860.01250.05620.13670.04280.1454-20.759470.9645-65.2324
182.06953.1074-0.533711.62350.75245.3254-0.25530.3399-0.2831-0.55720.36060.3631-0.0224-0.1851-0.10540.4715-0.02350.00820.6152-0.02790.51579.906358.8716-81.6376
195.6582-1.5438-1.45966.3871-0.13960.44160.00720.5439-0.1938-0.0274-0.01410.649-0.0821-0.14120.00690.44340.026-0.00330.3998-0.02310.35422.691855.6887-79.743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 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
18X-RAY DIFFRACTION18E1 - 65
19X-RAY DIFFRACTION19E66 - 72

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