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- PDB-1y8q: SUMO E1 ACTIVATING ENZYME SAE1-SAE2-MG-ATP COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1y8q
TitleSUMO E1 ACTIVATING ENZYME SAE1-SAE2-MG-ATP COMPLEX
Components(Ubiquitin-like ...) x 2
KeywordsLIGASE / SUMO / E1 / HETERODIMER / ACTIVATING ENZYME / UBL
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 / 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 / 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
ADENOSINE-5'-TRIPHOSPHATE / SUMO-activating enzyme subunit 1 / SUMO-activating enzyme subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.25 Å
AuthorsLois, L.M. / Lima, C.D.
CitationJournal: Embo J. / Year: 2005
Title: Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1
Authors: Lois, L.M. / Lima, C.D.
History
DepositionDec 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-like 1 activating enzyme E1A
B: Ubiquitin-like 2 activating enzyme E1B
C: Ubiquitin-like 1 activating enzyme E1A
D: Ubiquitin-like 2 activating enzyme E1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,75810
Polymers219,5644
Non-polymers1,1946
Water14,772820
1
A: Ubiquitin-like 1 activating enzyme E1A
B: Ubiquitin-like 2 activating enzyme E1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,3795
Polymers109,7822
Non-polymers5973
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-31 kcal/mol
Surface area35170 Å2
MethodPISA
2
C: Ubiquitin-like 1 activating enzyme E1A
D: Ubiquitin-like 2 activating enzyme E1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,3795
Polymers109,7822
Non-polymers5973
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-31 kcal/mol
Surface area34670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.245, 116.667, 106.078
Angle α, β, γ (deg.)90.00, 112.67, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Ubiquitin-like ... , 2 types, 4 molecules ACBD

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


Mass: 38499.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBLE1A, SAE1 / Plasmid: PET11C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3CP / References: UniProt: Q9UBE0
#2: Protein Ubiquitin-like 2 activating enzyme E1B / SUMO-1 activating enzyme subunit 2 / Anthracycline-associated resistance ARX / HRIHFB2115


Mass: 71282.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBLE1B, SAE2 / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3CP / References: UniProt: Q9UBT2

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Non-polymers , 4 types, 826 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 820 / 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 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium acetate, 10mM ATP, 10-20% PEG4000, 0.1-1.0M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2004
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 111631 / Num. obs: 108617 / % possible obs: 97.3 % / Observed criterion σ(I): -0.5 / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.6 / % possible all: 92.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.25→19.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2911892.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 5252 5 %RANDOM
Rwork0.208 ---
obs0.2081 104390 97 %-
all-108617 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7839 Å2 / ksol: 0.322736 e/Å3
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å27.29 Å2
2---3.95 Å20 Å2
3---1.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-6 Å
Luzzati sigma a0.48 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12931 0 66 820 13817
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 859 5.2 %
Rwork0.35 15783 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE_SAMK2.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ATP_XPLOR_PAR.TXTATP_XPLOR_TOP.TXT

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