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- PDB-6xoi: Structure of SUMO1-ML00752641 adduct bound to SAE -

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Basic information

Entry
Database: PDB / ID: 6xoi
TitleStructure of SUMO1-ML00752641 adduct bound to SAE
Components
  • (SUMO-activating enzyme subunit ...) x 2
  • Small ubiquitin-related modifier 1
KeywordsLIGASE/LIGASE inhibitor / SAE / SUMO1 / covalent inhibitor / LIGASE / LIGASE-LIGASE inhibitor complex
Function / homology
Function and homology information


SUMO activating enzyme activity / SUMO activating enzyme complex / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / ubiquitin activating enzyme activity / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) ...SUMO activating enzyme activity / SUMO activating enzyme complex / negative regulation of potassium ion transmembrane transporter activity / protein localization to nuclear pore / : / SUMOylation of nuclear envelope proteins / ubiquitin activating enzyme activity / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of delayed rectifier potassium channel activity / PML body organization / negative regulation of DNA binding / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / nuclear stress granule / SUMO binding / positive regulation of protein sumoylation / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / XY body / regulation of calcium ion transmembrane transport / ATP-dependent protein binding / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of protein targeting to mitochondrion / Maturation of nucleoprotein / ubiquitin-like protein conjugating enzyme binding / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / transcription factor binding / ubiquitin-specific protease binding / cellular response to cadmium ion / roof of mouth development / SUMOylation of transcription factors / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / postsynaptic cytosol / nuclear pore / transporter activator activity / negative regulation of DNA-binding transcription factor activity / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / enzyme activator activity / PML body / PKR-mediated signaling / regulation of protein stability / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / transferase activity / nuclear membrane / protein stabilization / nuclear speck / nuclear body / protein heterodimerization activity / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / magnesium ion binding / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / 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 E1, conserved site / Ubiquitin-activating enzyme signature 1. / Small ubiquitin-related modifier 1, Ubl domain / Ubiquitin-activating enzyme E1, Cys active site ...SUMO-activating enzyme subunit 2, C-terminal domain / SUMO-activating enzyme subunit 2 C-terminus / 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 E1, conserved site / Ubiquitin-activating enzyme signature 1. / Small ubiquitin-related modifier 1, Ubl domain / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-VBA / Small ubiquitin-related modifier 1 / SUMO-activating enzyme subunit 1 / SUMO-activating enzyme subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSintchak, M. / Lane, W. / Bump, N.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of TAK-981, a First-in-Class Inhibitor of SUMO-Activating Enzyme for the Treatment of Cancer.
Authors: Langston, S.P. / Grossman, S. / England, D. / Afroze, R. / Bence, N. / Bowman, D. / Bump, N. / Chau, R. / Chuang, B.C. / Claiborne, C. / Cohen, L. / Connolly, K. / Duffey, M. / Durvasula, N. ...Authors: Langston, S.P. / Grossman, S. / England, D. / Afroze, R. / Bence, N. / Bowman, D. / Bump, N. / Chau, R. / Chuang, B.C. / Claiborne, C. / Cohen, L. / Connolly, K. / Duffey, M. / Durvasula, N. / Freeze, S. / Gallery, M. / Galvin, K. / Gaulin, J. / Gershman, R. / Greenspan, P. / Grieves, J. / Guo, J. / Gulavita, N. / Hailu, S. / He, X. / Hoar, K. / Hu, Y. / Hu, Z. / Ito, M. / Kim, M.S. / Lane, S.W. / Lok, D. / Lublinsky, A. / Mallender, W. / McIntyre, C. / Minissale, J. / Mizutani, H. / Mizutani, M. / Molchinova, N. / Ono, K. / Patil, A. / Qian, M. / Riceberg, J. / Shindi, V. / Sintchak, M.D. / Song, K. / Soucy, T. / Wang, Y. / Xu, H. / Yang, X. / Zawadzka, A. / Zhang, J. / Pulukuri, S.M.
History
DepositionJul 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUMO-activating enzyme subunit 1
B: SUMO-activating enzyme subunit 2
C: Small ubiquitin-related modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0396
Polymers121,3893
Non-polymers6503
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-51 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.224, 72.400, 127.407
Angle α, β, γ (deg.)90.000, 93.293, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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

#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 / Production host: Spodoptera frugiperda (fall armyworm) / 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: 71314.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA2, SAE2, UBLE1B, HRIHFB2115 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UBT2, Transferases; Acyltransferases; Aminoacyltransferases

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Protein , 1 types, 1 molecules C

#3: Protein Small ubiquitin-related modifier 1 / SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain ...SUMO-1 / GAP-modifying protein 1 / GMP1 / SMT3 homolog 3 / Sentrin / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein SMT3C / Smt3C / Ubiquitin-like protein UBL1


Mass: 11575.005 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63165

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Non-polymers , 4 types, 289 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-VBA / [(1R,2R,3S,4R)-4-{[5-(1-benzyl-1H-pyrazole-3-carbonyl)pyrimidin-4-yl]amino}-2,3-dihydroxycyclopentyl]methyl sulfamate


Mass: 488.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N6O6S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 50 mM BisTris, pH 6.5, 50 mM Ammonium Sulfate, 30% pentaerythritol ethoxylate (Hampton Index 57)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→19.38 Å / Num. obs: 69609 / % possible obs: 95.62 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.07504 / Net I/σ(I): 12.96
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.7795 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6478 / CC1/2: 0.66

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y8R

1y8r


Resolution: 2→19.38 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.361 / SU ML: 0.146 / Cross valid method: FREE R-VALUE / ESU R: 0.205 / ESU R Free: 0.191
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2873 6927 10.108 %
Rwork0.2388 61602 -
all0.244 --
obs-68529 95.641 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.672 Å2
Baniso -1Baniso -2Baniso -3
1--0.062 Å2-0 Å20.205 Å2
2---0.109 Å20 Å2
3---0.147 Å2
Refinement stepCycle: LAST / Resolution: 2→19.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5839 0 40 286 6165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125985
X-RAY DIFFRACTIONr_angle_refined_deg1.51.6378096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5845742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20522.947285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.991151027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1341531
X-RAY DIFFRACTIONr_chiral_restr0.1120.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024495
X-RAY DIFFRACTIONr_nbd_refined0.2290.22783
X-RAY DIFFRACTIONr_nbtor_refined0.310.24083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2330
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.210
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.28
X-RAY DIFFRACTIONr_mcbond_it3.2653.9813007
X-RAY DIFFRACTIONr_mcangle_it4.5815.9343736
X-RAY DIFFRACTIONr_scbond_it3.9374.2932978
X-RAY DIFFRACTIONr_scangle_it5.4526.314360
X-RAY DIFFRACTIONr_lrange_it7.45254.179030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0510.3534990.3074247X-RAY DIFFRACTION90.937
2.051-2.1070.3355060.2854168X-RAY DIFFRACTION91.9174
2.107-2.1670.3314500.2774171X-RAY DIFFRACTION92.7912
2.167-2.2330.3384370.3113987X-RAY DIFFRACTION92.5523
2.233-2.3060.4294430.4133893X-RAY DIFFRACTION92.9076
2.306-2.3850.3333980.2593934X-RAY DIFFRACTION95.8831
2.385-2.4740.3054410.2493808X-RAY DIFFRACTION97.8356
2.474-2.5730.2913990.2383778X-RAY DIFFRACTION98.4909
2.573-2.6860.3113800.2283578X-RAY DIFFRACTION98.3598
2.686-2.8140.2854190.2253418X-RAY DIFFRACTION98.8154
2.814-2.9630.2963290.2273272X-RAY DIFFRACTION98.4956
2.963-3.1390.2953350.2453089X-RAY DIFFRACTION98.3061
3.139-3.3490.3013460.2392905X-RAY DIFFRACTION98.1582
3.349-3.6090.2753220.2262641X-RAY DIFFRACTION96.3891
3.609-3.9410.2512830.222463X-RAY DIFFRACTION97.0318
3.941-4.3850.2272350.1852230X-RAY DIFFRACTION95.8398
4.385-5.0220.2142450.1782008X-RAY DIFFRACTION97.744
5.022-6.0560.2672110.2211759X-RAY DIFFRACTION99.3444
6.056-8.1930.2851640.2271414X-RAY DIFFRACTION99.4329
8.193-19.380.291850.246839X-RAY DIFFRACTION89.8833

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