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- PDB-6cwy: Crystal structure of SUMO E1 in complex with an allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 6cwy
TitleCrystal structure of SUMO E1 in complex with an allosteric inhibitor
Components(SUMO-activating enzyme subunit ...) x 2
Keywordstransferase/transferase inhibitor / ROSSMANN-LIKE FOLD / UBIQUITIN-LIKE FOLD / UBIQUITIN ACTIVATING ENZYME / ACTIVITY / ATP BINDING / LIGASE ACTIVITY / ATP/MG BINDING / UBIQUITIN E2 / LIGASE / TRANSFERASE / transferase-transferase inhibitor complex
Function / homologyThiF family / SUMO-activating enzyme subunit 2 C-terminus / THIF-type NAD/FAD binding fold / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / SUMO-activating enzyme subunit Uba2 / SUMO-activating enzyme subunit 2, C-terminal domain / Ubiquitin-activating enzyme E1, Cys active site ...ThiF family / SUMO-activating enzyme subunit 2 C-terminus / THIF-type NAD/FAD binding fold / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / SUMO-activating enzyme subunit Uba2 / SUMO-activating enzyme subunit 2, C-terminal domain / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme active site. / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Ubiquitin/SUMO-activating enzyme E1 / SUMO activating enzyme activity / ubiquitin activating enzyme activity / SUMO activating enzyme complex / protein modification by small protein conjugation / SUMO binding / ubiquitin-like protein conjugating enzyme binding / small protein activating enzyme binding / positive regulation of protein targeting to mitochondrion / ATP-dependent protein binding / Transferases, Acyltransferases, Aminoacyltransferases / protein sumoylation / enzyme activator activity / transferase activity / protein C-terminus binding / protein ubiquitination / transcription factor binding / protein heterodimerization activity / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / SUMO-activating enzyme subunit 1 / SUMO-activating enzyme subunit 2
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.462 Å resolution
AuthorsLv, Z. / Yuan, L. / Atkison, J.H. / Williams, K.M. / Olsen, S.K.
Funding supportUnited States , 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM115568-02United States
CitationJournal: Nat Commun / Year: 2018
Title: Molecular mechanism of a covalent allosteric inhibitor of SUMO E1 activating enzyme.
Authors: Lv, Z. / Yuan, L. / Atkison, J.H. / Williams, K.M. / Vega, R. / Sessions, E.H. / Divlianska, D.B. / Davies, C. / Chen, Y. / Olsen, S.K.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 1, 2018 / Release: Jan 16, 2019

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: SUMO-activating enzyme subunit 1
D: SUMO-activating enzyme subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,06511
Polyers111,9862
Non-polymers1,0809
Water81145
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)5770
ΔGint (kcal/M)-74
Surface area (Å2)34840
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)56.055, 116.046, 174.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 21

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Components

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SUMO-activating enzyme subunit ... , 2 types, 2 molecules CD

#1: Protein/peptide SUMO-activating enzyme subunit 1 / Ubiquitin-like 1-activating enzyme E1A


Mass: 38499.789 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SAE1, AOS1, SUA1, UBLE1A / Plasmid name: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Codon Plus / References: UniProt: Q9UBE0
#2: Protein/peptide SUMO-activating enzyme subunit 2 / Anthracycline-associated resistance ARX / Ubiquitin-like 1-activating enzyme E1B / Ubiquitin-like modifier-activating enzyme 2


Mass: 73485.891 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: UBA2, SAE2, UBLE1B, HRIHFB2115 / Plasmid name: PET-28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 codon plus
References: UniProt: Q9UBT2, Transferases, Acyltransferases, Aminoacyltransferases

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Non-polymers , 6 types, 54 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Formula: C3H8O3 / Glycerol
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Formula: SO4 / Sulfate
#7: Chemical ChemComp-FHJ / dimethyl (1S,2S,3R,4R)-1-[(1S)-2-(4-methylphenyl)-1-(phenylamino)ethyl]-7-oxabicyclo[2.2.1]hept-5-ene-2,3-dicarboxylate


Mass: 421.486 Da / Num. of mol.: 1 / Formula: C25H27NO5
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Formula: H2O / Water

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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: 2.53 / Density percent sol: 51.36 %
Crystal growTemp: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1M Bis-Tris HCl pH 6.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Collection date: Nov 4, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 53.48 Å2 / D resolution high: 2.45 Å / D resolution low: 5 Å / Number obs: 41866 / Rmerge I obs: 0.088 / Rpim I all: 0.042 / Rrim I all: 0.098 / Chi squared: 0.619 / NetI over sigmaI: 5.5 / Number measured all: 216502 / Redundancy: 5.2 % / Percent possible obs: 99.8
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber unique obsCC halfRpim I allRrim I allChi squaredRedundancyPercent possible all
0.8802.4502.54041300.6350.4360.9860.3684.80099.900
0.6822.5402.64041240.7630.3240.7570.3985.20099.900
0.4992.6402.76041140.8690.2390.5550.4245.10099.900
0.3322.7602.90041280.9140.1670.3730.4444.70099.700
0.2502.9003.09041440.9670.1130.2750.4735.600100.000
0.1563.0903.32041420.9850.0710.1710.5705.60099.900
0.1013.3203.66041940.9910.0470.1120.7485.40099.900
0.0693.6604.19041760.9940.0340.0770.8764.80099.600
0.0514.1905.28042640.9970.0230.0560.9365.50099.900
0.0375.28050.00044500.9990.0180.0410.8805.10099.500

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KYC
Overall SU ML: 0.33 / Cross valid method: THROUGHOUT / Sigma F: 1.37 / Overall phase error: 22.9 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 206.5 Å2 / B iso mean: 75.9999 Å2 / B iso min: 27.46 Å2
Least-squares processR factor R free: 0.2369 / R factor R work: 0.1974 / R factor obs: 0.1993 / Highest resolution: 2.462 Å / Lowest resolution: 48.284 Å / Number reflection R free: 2000 / Number reflection R work: 39802 / Number reflection obs: 41802 / Percent reflection R free: 4.78 / Percent reflection obs: 99.34
Refine hist #finalHighest resolution: 2.462 Å / Lowest resolution: 48.284 Å / B iso mean ligand: 87.51 / B iso mean solvent: 52.69 / Number residues total: 791
Number of atoms included #finalProtein: 6214 / Nucleic acid: 0 / Ligand: 65 / Solvent: 45 / Total: 6324
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026408
X-RAY DIFFRACTIONf_angle_d0.4748661
X-RAY DIFFRACTIONf_chiral_restr0.039979
X-RAY DIFFRACTIONf_plane_restr0.0041114
X-RAY DIFFRACTIONf_dihedral_angle_d8.8833890
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 14

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
2.46160.29740.26412.52311332632276593.0000
2.52310.28210.26282.591313927802919100.0000
2.59130.30820.26222.667614228332975100.0000
2.66760.30590.24762.753714228032945100.0000
2.75370.30830.24382.852114128162957100.0000
2.85210.27970.23692.966314328442987100.0000
2.96630.28000.24153.101314228362978100.0000
3.10130.27930.24723.264714228232965100.0000
3.26470.23950.21533.469214328462989100.0000
3.46920.24220.19773.737014528803025100.0000
3.73700.24010.17764.112914228292971100.0000
4.11290.20380.15194.707614529073052100.0000
4.70760.21690.17075.929314729193066100.0000
5.92930.18670.176048.29361543054320899.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.7568-0.8335-0.57121.25990.77761.3374-0.0715-0.35520.22710.25010.3226-0.95980.15030.84130.32120.5038-0.0185-0.12700.5384-0.16100.6075182.1291243.0141567.0620
21.7879-0.4183-0.13833.95151.64492.8312-0.0041-0.16140.12870.20820.04740.1119-0.1237-0.00830.08900.3951-0.0071-0.00360.3218-0.07220.3745165.8821247.7996568.4828
31.6301-0.07800.26882.31261.43241.2454-0.19110.1696-0.14710.00110.2192-0.27900.14690.27750.00080.3444-0.0100-0.01040.3582-0.02080.3374175.6790222.5769550.4142
40.0892-0.04390.26530.8946-0.22130.4754-0.28470.59320.3253-0.3036-0.0309-1.0079-0.43290.8576-0.03980.8473-0.19500.10821.36850.05981.0155195.9773243.2937537.8006
50.60020.8671-0.33481.2067-0.46130.1426-1.13651.18880.1309-1.67910.8332-0.4907-0.01750.3930-0.04251.3768-0.3854-0.05421.5992-0.06720.7725185.9068241.1645524.0388
60.54830.09480.06421.05431.09731.4283-0.26330.3386-0.1401-0.31150.13020.0894-0.06380.04340.08490.4548-0.0496-0.01270.3822-0.07690.3645168.5082232.7123547.6881
71.5457-0.06930.33401.13731.56001.9868-0.00900.4170-0.1102-0.0298-0.09260.2707-0.1152-0.01970.02520.2478-0.0080-0.00450.4878-0.08980.3696166.0049209.3217525.8908
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1C24C951chain 'C' and (resid 24 through 95 )
2C96C3452chain 'C' and (resid 96 through 345 )
3D8D1963chain 'D' and (resid 8 through 196 )
4D197D3154chain 'D' and (resid 197 through 315 )
5D316D3655chain 'D' and (resid 316 through 365 )
6D366D4336chain 'D' and (resid 366 through 433 )
7D434D5487chain 'D' and (resid 434 through 548 )

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