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- PDB-7zh9: Uba1 in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 7zh9
TitleUba1 in complex with ATP
ComponentsUbiquitin-activating enzyme E1 1
KeywordsLIGASE / Ubiquitin / E1 / Uba1
Function / homology
Function and homology information


E1 ubiquitin-activating enzyme / Neddylation / ubiquitin activating enzyme activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / ATP binding / nucleus / cytoplasm
Similarity search - Function
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, 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
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / : / Ubiquitin-activating enzyme E1 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsMisra, M. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHI 425-6/1 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
DepositionApr 5, 2022Deposition 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,12519
Polymers114,3941
Non-polymers1,73118
Water14,826823
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-57 kcal/mol
Surface area44180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.720, 118.064, 196.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1117-

K

21A-1948-

HOH

31A-1959-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ubiquitin-activating enzyme E1 1


Mass: 114393.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBA1, YKL210W / Production host: Escherichia coli (E. coli) / References: UniProt: P22515, E1 ubiquitin-activating enzyme

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Non-polymers , 8 types, 841 molecules

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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 823 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M HEPES pH 7.5 and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.705→47.238 Å / Num. obs: 91872 / % possible obs: 99.88 % / Redundancy: 6.65 % / CC1/2: 0.9988 / Net I/σ(I): 10.6
Reflection shellResolution: 1.705→1.705 Å / Num. unique obs: 4617 / CC1/2: 0.7039

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660)refinement
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CMM

3cmm


Resolution: 1.72→47.238 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 4617 5.03 %
Rwork0.1648 --
obs0.1669 91872 69.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→47.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7916 0 105 823 8844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018337
X-RAY DIFFRACTIONf_angle_d0.92411315
X-RAY DIFFRACTIONf_dihedral_angle_d15.15079
X-RAY DIFFRACTIONf_chiral_restr0.0561258
X-RAY DIFFRACTIONf_plane_restr0.0061479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.78110.339470.2674795X-RAY DIFFRACTION6
1.7811-1.85240.2275790.25031464X-RAY DIFFRACTION12
1.8524-1.93670.28971640.23793028X-RAY DIFFRACTION24
1.9367-2.03880.27614150.23177499X-RAY DIFFRACTION60
2.0388-2.16650.25445950.204611121X-RAY DIFFRACTION89
2.1665-2.33380.24476530.186112505X-RAY DIFFRACTION100
2.3338-2.56870.22326630.171812581X-RAY DIFFRACTION100
2.5687-2.94030.21536420.167612630X-RAY DIFFRACTION100
2.9403-3.70430.20016740.150312674X-RAY DIFFRACTION100
3.7043-47.2380.17086850.145912958X-RAY DIFFRACTION100
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)
11.43980.30090.25221.1516-0.07621.69680.0192-0.33850.22610.38590.0555-0.0378-0.04360.551-0.02640.32680.0519-0.01580.4706-0.07630.060220.98715.43940.8762
20.54820.0069-0.12640.7724-0.21830.13-0.0893-0.3590.16820.3220.13140.0392-0.19330.43360.03970.3297-0.071-0.0030.3738-0.07730.123619.146914.539231.8917
30.8847-0.03450.2781.20740.36791.1171-0.0297-0.58260.56640.4616-0.17420.2062-0.3508-0.41730.0540.6431-0.08050.01290.5822-0.28660.63039.685151.610124.5792
40.72230.21030.04580.6698-0.24020.6413-0.11970.18530.1639-0.02610.0656-0.0429-0.20130.1943-0.00060.2208-0.1431-0.03770.19090.01210.16621.525624.5369-4.4687
50.12850.2087-0.13750.5947-0.40830.2663-0.0306-0.15740.22820.18890.15280.1725-0.2880.1352-0.06610.3645-0.08660.01970.197-0.0580.238814.326628.475320.9332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 625 through 764 )
2X-RAY DIFFRACTION2chain 'A' and (resid 765 through 885 )
3X-RAY DIFFRACTION3chain 'A' and (resid 886 through 1024 )
4X-RAY DIFFRACTION4chain 'A' and (resid 10 through 545 )
5X-RAY DIFFRACTION5chain 'A' and (resid 546 through 624 )

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