- PDB-5ghd: SOLUTION STRUCTURE OF LYS39 ACETYLATED HUMAN SUMO1 -
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Basic information
Entry
Database: PDB / ID: 5ghd
Title
SOLUTION STRUCTURE OF LYS39 ACETYLATED HUMAN SUMO1
Components
Small ubiquitin-related modifier 1
Keywords
STRUCTURAL GENOMICS / UBIQUITIN-LIKE PROTEIN / ACETYLATED PROTEIN
Function / homology
Function and homology information
protein localization to nuclear pore / 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 / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...protein localization to nuclear pore / 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 / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / septin ring / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / 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 / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / Formation of Incision Complex in GG-NER / protein tag activity / 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 / nuclear body / protein stabilization / 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
Smallubiquitin-relatedmodifier1 / 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
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
2
isotropic
3
2D 1H-15N HSQC
1
2
1
isotropic
3
2D 1H-13C HSQC
1
3
1
isotropic
2
3D HNCO
1
4
1
isotropic
2
3D HNCA
1
5
1
isotropic
2
3DHN(CO)CA
1
6
1
isotropic
2
3D HN(CA)CB
1
7
1
isotropic
2
3DCBCA(CO)NH
1
8
1
isotropic
2
3D (H)CCH-TOCSY
1
9
1
isotropic
2
3D (H)CCH-COSY
1
10
1
isotropic
2
3DHBHA(CO)NH
1
11
1
isotropic
2
2D-(HB)CB(CGCD)HD
1
12
1
isotropic
2
2D-(HB)CB(CGCDCE)HE
1
13
1
isotropic
2
3D 1H-15N TOCSY
1
14
4
anisotropic
4
2D 1H-1H NOESY
1
15
1
isotropic
3
3D 1H-15N NOESY
1
16
1
isotropic
3
3D 1H-13C NOESY
1
17
3
anisotropic
2
2D 1H-15N HSQCIPAP
1
18
1
isotropic
4
2D NOESY F1 FILTERED
1
19
1
isotropic
4
2D NOESY F2 FILTERED
1
20
1
isotropic
4
2D NOESY F1/F2 FILTERED
1
21
1
isotropic
4
2D TOCSY F1/F2 FILTERED
NMR details
Text: NMR DATA WAS ACQUIRED AT 295K USING SHIGEMI NMR TUBES.
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Sample preparation
Details
Type
Solution-ID
Contents
Details
Label
Solvent system
solution
1
1 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% D2O
13C, 15N- K39Ac SUMO1
CN
90% H2O/10% D2O
solution
2
1 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% D2O
15N- K39Ac SUMO1
N
90% H2O/10% D2O
filamentousvirus
3
1 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% D2O