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- PDB-5ghd: SOLUTION STRUCTURE OF LYS39 ACETYLATED HUMAN SUMO1 -

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Basic information

Entry
Database: PDB / ID: 5ghd
TitleSOLUTION STRUCTURE OF LYS39 ACETYLATED HUMAN SUMO1
ComponentsSmall ubiquitin-related modifier 1
KeywordsSTRUCTURAL GENOMICS / UBIQUITIN-LIKE PROTEIN / ACETYLATED PROTEIN
Function / homology
Function and homology information


negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding ...negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / protein tag activity / Formation of Incision Complex in GG-NER / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / protein stabilization / nuclear body / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / enzyme binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, DGSA- DISTANCE GEOMETRY SIMULATED ANNEALING
AuthorsNaik, M.T. / Naik, N. / Shih, H. / Huang, T.
CitationJournal: To Be Published
Title: Structures of Human Sumo
Authors: Naik, M.T. / Naik, N. / Shih, H. / Huang, T.
History
DepositionJun 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Small ubiquitin-related modifier 1


Theoretical massNumber of molelcules
Total (without water)12,8091
Polymers12,8091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6420 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: 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: 12809.266 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-97
Source method: isolated from a genetically manipulated source
Details: Lys39 acetylated mature SMALL UBIQUITIN-RELATED MODIFIER 1 (SUMO1) Residues 1-14 (MGSSHHHHHHSQDP) represent a non-native purification tag. These residues were neither assigned nor included ...Details: Lys39 acetylated mature SMALL UBIQUITIN-RELATED MODIFIER 1 (SUMO1) Residues 1-14 (MGSSHHHHHHSQDP) represent a non-native purification tag. These residues were neither assigned nor included in structure calculation.
Source: (gene. exp.) Homo sapiens (human)
Description: PLASMID PCDF PYLT-1 WITH SUMO INSERT WITH K39STOP MUTATION (WITH AMBER CODON) AND PACKRS-3 AS DESCRIBED IN NEUMANN ET AL., MOL CELL, 36, 153, 2009
Gene: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43
Details (production host): Plasmid pCDF PylT-1 with SUMO insert with K39STOP mutation (with amber codon) and pAcKRS-3 as described in Neumann et al., Mol Cell, 36, 153, 2009
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63165

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic32D 1H-15N HSQC
121isotropic32D 1H-13C HSQC
131isotropic23D HNCO
141isotropic23D HNCA
151isotropic23D HN(CO)CA
161isotropic23D HN(CA)CB
171isotropic23D CBCA(CO)NH
181isotropic23D (H)CCH-TOCSY
191isotropic23D (H)CCH-COSY
1101isotropic23D HBHA(CO)NH
1111isotropic22D-(HB)CB(CGCD)HD
1121isotropic22D-(HB)CB(CGCDCE)HE
1131isotropic23D 1H-15N TOCSY
1144anisotropic42D 1H-1H NOESY
1151isotropic33D 1H-15N NOESY
1161isotropic33D 1H-13C NOESY
1173anisotropic22D 1H-15N HSQC IPAP
1181isotropic42D NOESY F1 FILTERED
1191isotropic42D NOESY F2 FILTERED
1201isotropic42D NOESY F1/F2 FILTERED
1211isotropic42D TOCSY F1/F2 FILTERED
NMR detailsText: NMR DATA WAS ACQUIRED AT 295K USING SHIGEMI NMR TUBES.

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-100% 13C; U-100% 15N] SUMO1 K39Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O13C, 15N- K39Ac SUMO1CN90% H2O/10% D2O
solution21 mM [U-100% 15N] SUMO1 K39Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O15N- K39Ac SUMO1N90% H2O/10% D2O
filamentous virus31 mM [U-100% 15N] SUMO1 K39Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 10 mg/mL Pf1 phage, 90% H2O/10% D2O15N- K39Ac SUMO1 in phage alignment mediumPhage90% H2O/10% D2O
solution41 mM SUMO1 K39Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2OUnlabeled K39Ac SUMO1Unlabeled90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSUMO1 K39Ac[U-100% 13C; U-100% 15N]1
10 mMpotassium phosphatenatural abundance1
100 mMpotassium chloridenatural abundance1
2 mMDTTnatural abundance1
0.1 mMEDTAnatural abundance1
0.001 %sodium azidenatural abundance1
1 mMSUMO1 K39Ac[U-100% 15N]2
10 mMpotassium phosphatenatural abundance2
100 mMpotassium chloridenatural abundance2
2 mMDTTnatural abundance2
0.1 mMEDTAnatural abundance2
0.001 %sodium azidenatural abundance2
1 mMSUMO1 K39Ac[U-100% 15N]3
10 mMpotassium phosphatenatural abundance3
100 mMpotassium chloridenatural abundance3
2 mMDTTnatural abundance3
0.1 mMEDTAnatural abundance3
0.001 %sodium azidenatural abundance3
10 mg/mLPf1 phagenatural abundance3
1 mMSUMO1 K39Acnatural abundance4
10 mMpotassium phosphatenatural abundance4
100 mMpotassium chloridenatural abundance4
2 mMDTTnatural abundance4
0.1 mMEDTAnatural abundance4
0.001 %sodium azidenatural abundance4
Sample conditionsDetails: NMR data was acquired in shigemi tubes / Ionic strength: 100 mM KCl mM / Label: Default / pH: 6.5 / PH err: 0.05 / Pressure: AMBIENT ATM atm / Temperature: 290 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCEBrukerAVANCE8003
Bruker AVANCE IIIBrukerAVANCE III8504

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.34Schwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TopSpin3.2Bruker Biospinprocessing
Sparky3.113Goddarddata analysis
RefinementMethod: TORSION ANGLE DYNAMICS, DGSA- DISTANCE GEOMETRY SIMULATED ANNEALING
Software ordinal: 1
Details: INITIAL STRUCTURE ENSEMBLE WAS CALCULATED BY SEMI-AUTOMATED NOESY ASSIGNMENT BY CYANA. THE ASSIGNMENTS WERE MANUALLY VERIFIED IN SPARKY AND FINAL STRUCTURE ANNEALING WAS PERFORMED IN CYANA. ...Details: INITIAL STRUCTURE ENSEMBLE WAS CALCULATED BY SEMI-AUTOMATED NOESY ASSIGNMENT BY CYANA. THE ASSIGNMENTS WERE MANUALLY VERIFIED IN SPARKY AND FINAL STRUCTURE ANNEALING WAS PERFORMED IN CYANA.STRUCTURE AND RESTRAINTS FROM CYANA WERE IMPORTED IN XPLOR-NIH FOR EXPLICIT WATER REFINEMENT., INITIAL STRUCTURE ENSEMBLE WAS CALCULATED BY SEMI-AUTOMATED NOESY ASSIGNMENT BY CYANA. THE ASSIGNMENTS WERE MANUALLY VERIFIED IN SPARKY AND FINAL STRUCTURE ANNEALING WAS PERFORMED IN CYANA.STRUCTURE AND RESTRAINTS FROM CYANA WERE IMPORTED IN XPLOR- NIH FOR EXPLICIT WATER REFINEMENT.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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