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- PDB-6gum: Structure of the A.thaliana E1 UFD domain in complex with E2 -

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Basic information

Entry
Database: PDB / ID: 6gum
TitleStructure of the A.thaliana E1 UFD domain in complex with E2
Components
  • SAE2
  • SUMO-conjugating enzyme SCE1
KeywordsTRANSFERASE / SUMOylation complex
Function / homology
Function and homology information


SUMO activating enzyme complex / SUMO activating enzyme activity / protein modification by small protein conjugation / SUMO conjugating enzyme activity / embryo development ending in seed dormancy / SUMO binding / plasmodesma / response to abscisic acid / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity ...SUMO activating enzyme complex / SUMO activating enzyme activity / protein modification by small protein conjugation / SUMO conjugating enzyme activity / embryo development ending in seed dormancy / SUMO binding / plasmodesma / response to abscisic acid / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / protein sumoylation / kinase binding / transferase activity / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family ...Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
SUMO-activating enzyme subunit / SUMO-conjugating enzyme SCE1 / SUMO-activating enzyme subunit 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsLiu, B. / Lois, L.M. / Reverter, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spain
CitationJournal: Biochem.J. / Year: 2019
Title: Structural insights into SUMO E1-E2 interactions in Arabidopsis uncovers a distinctive platform for securing SUMO conjugation specificity across evolution.
Authors: Liu, B. / Lois, L.M. / Reverter, D.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUMO-conjugating enzyme SCE1
B: SAE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6143
Polymers43,5222
Non-polymers921
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-3 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.158, 58.817, 70.230
Angle α, β, γ (deg.)90.00, 92.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SUMO-conjugating enzyme SCE1 / Protein EMBRYO DEFECTIVE 1637 / Protein hus5 homolog / SUMO-conjugating enzyme 1 / AtSCE1


Mass: 20180.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SCE1, AHUS5, EMB1637, At3g57870, T10K17.80 / Production host: Escherichia coli (E. coli)
References: UniProt: Q42551, Transferases; Acyltransferases; Aminoacyltransferases
#2: Protein SAE2


Mass: 23340.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At2g16970 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178VMI9, UniProt: Q9SJT1*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 15% PEG6000, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.792→58.81 Å / Num. obs: 26999 / % possible obs: 97.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.061 / Rrim(I) all: 0.108 / Net I/σ(I): 8.5
Reflection shellResolution: 1.792→1.798 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A3S

1a3s


Resolution: 1.792→45.08 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.79
RfactorNum. reflection% reflection
Rfree0.2203 1339 4.97 %
Rwork0.1782 --
obs0.1803 26964 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.792→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 6 64 2189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172199
X-RAY DIFFRACTIONf_angle_d1.6232984
X-RAY DIFFRACTIONf_dihedral_angle_d14.198835
X-RAY DIFFRACTIONf_chiral_restr0.099320
X-RAY DIFFRACTIONf_plane_restr0.009389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7921-1.85620.37031440.31462472X-RAY DIFFRACTION96
1.8562-1.93050.29771330.27192513X-RAY DIFFRACTION97
1.9305-2.01840.25381500.22292553X-RAY DIFFRACTION96
2.0184-2.12480.23361300.17792559X-RAY DIFFRACTION97
2.1248-2.25790.21591400.17682557X-RAY DIFFRACTION98
2.2579-2.43220.26771230.18032564X-RAY DIFFRACTION97
2.4322-2.6770.21841280.17192591X-RAY DIFFRACTION98
2.677-3.06420.20891420.17242565X-RAY DIFFRACTION98
3.0642-3.86030.19961180.16252610X-RAY DIFFRACTION98
3.8603-45.09450.19631310.16562641X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 12.2417 Å / Origin y: 3.1294 Å / Origin z: 95.0098 Å
111213212223313233
T0.1719 Å2-0.0015 Å2-0.022 Å2-0.1872 Å2-0.0264 Å2--0.1825 Å2
L0.5751 °2-0.1896 °2-0.4942 °2-0.664 °2-0.1751 °2--0.825 °2
S-0.0018 Å °0.0304 Å °0.0168 Å °-0.0274 Å °0.0578 Å °0.0432 Å °-0.0086 Å °-0.0067 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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