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- PDB-6cwz: Crystal structure of apo SUMO E1 -

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Basic information

Entry
Database: PDB / ID: 6cwz
TitleCrystal structure of apo SUMO E1
Components
  • SUMO-activating enzyme subunit 1
  • SUMO-activating enzyme subunit 2
KeywordsTRANSFERASE / ROSSMANN-LIKE FOLD / UBIQUITIN-LIKE FOLD / UBIQUITIN ACTIVATING ENZYME / ACTIVITY / ATP BINDING / LIGASE ACTIVITY / ATP/MG BINDING / UBIQUITIN E2 / LIGASE
Function / homology
Function and homology information


SUMO activating enzyme complex / SUMO activating enzyme activity / ubiquitin activating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO binding / small protein activating enzyme binding / positive regulation of protein sumoylation / ATP-dependent protein binding / Transferases; Acyltransferases; Aminoacyltransferases ...SUMO activating enzyme complex / SUMO activating enzyme activity / ubiquitin activating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO binding / small protein activating enzyme binding / positive regulation of protein sumoylation / ATP-dependent protein binding / Transferases; Acyltransferases; Aminoacyltransferases / ubiquitin-like protein conjugating enzyme binding / positive regulation of protein targeting to mitochondrion / protein sumoylation / enzyme activator activity / transferase activity / protein heterodimerization activity / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. ...SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin/SUMO-activating enzyme ubiquitin-like domain / Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / 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 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SUMO-activating enzyme subunit 1 / SUMO-activating enzyme subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLv, Z. / Yuan, L. / Atkison, J.H. / Williams, K.M. / Olsen, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115568-02 United 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.
History
DepositionApr 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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
C: SUMO-activating enzyme subunit 1
D: SUMO-activating enzyme subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0513
Polymers111,9862
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-21 kcal/mol
Surface area35810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.139, 115.378, 172.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 38499.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAE1, AOS1, SUA1, UBLE1A / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: Q9UBE0
#2: Protein SUMO-activating enzyme subunit 2 / Anthracycline-associated resistance ARX / Ubiquitin-like 1-activating enzyme E1B / Ubiquitin-like ...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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA2, SAE2, UBLE1B, HRIHFB2115 / Plasmid: PET-28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 codon plus
References: UniProt: Q9UBT2, Transferases; Acyltransferases; Aminoacyltransferases
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M Bis-Tris HCl pH 6.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.08 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 21123 / % possible obs: 99.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 89.16 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.054 / Rrim(I) all: 0.127 / Χ2: 0.608 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.214.70.98520050.6450.4981.1090.55796.9
3.21-3.345.20.7120440.8140.3430.790.56798.8
3.34-3.495.60.54620990.8570.2530.6040.619100
3.49-3.685.60.35320770.9480.1620.3890.658100
3.68-3.915.70.25920890.9710.1190.2860.711100
3.91-4.215.70.16521030.9850.0770.1820.649100
4.21-4.635.60.10721330.9910.0510.1190.652100
4.63-5.35.60.09221190.9930.0430.1020.683100
5.3-6.675.50.07921650.9940.0380.0880.525100
6.67-505.10.04622890.9970.0220.0510.44199.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KYC

3kyc


Resolution: 3.1→47.992 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.84
RfactorNum. reflection% reflection
Rfree0.2582 1999 9.49 %
Rwork0.225 --
obs0.2282 21054 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 267.59 Å2 / Biso mean: 111.7014 Å2 / Biso min: 49.26 Å2
Refinement stepCycle: final / Resolution: 3.1→47.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6422 0 1 0 6423
Biso mean--77.45 --
Num. residues----818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026544
X-RAY DIFFRACTIONf_angle_d0.4398839
X-RAY DIFFRACTIONf_chiral_restr0.0391002
X-RAY DIFFRACTIONf_plane_restr0.0041148
X-RAY DIFFRACTIONf_dihedral_angle_d13.2623992
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0938-3.17110.38751250.41211210133591
3.1711-3.25690.38781420.36051343148599
3.2569-3.35270.32751390.31991327146699
3.3527-3.46090.33911420.28713551497100
3.4609-3.58450.28321420.255413501492100
3.5845-3.7280.281430.248513691512100
3.728-3.89760.25511410.247813361477100
3.8976-4.1030.26141420.224113591501100
4.103-4.35990.25811440.200313771521100
4.3599-4.69620.20951450.184113751520100
4.6962-5.16830.22591450.19413801525100
5.1683-5.9150.2971450.242413831528100
5.915-7.44780.2641490.232714171566100
7.4478-47.99790.21181550.17711474162998
Refinement TLS params.Method: refined / Origin x: 118.0933 Å / Origin y: 1.076 Å / Origin z: 371.0511 Å
111213212223313233
T0.6736 Å2-0.0348 Å20.011 Å2-0.7138 Å20.0065 Å2--0.6345 Å2
L0.7419 °2-0.3802 °2-0.2763 °2-2.1237 °21.5281 °2--2.7866 °2
S0.084 Å °0.158 Å °0.0663 Å °-0.384 Å °0.0161 Å °-0.2218 Å °-0.5348 Å °0.0538 Å °-0.0693 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allC10 - 345
2X-RAY DIFFRACTION1allD4 - 548
3X-RAY DIFFRACTION1allD999

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