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- PDB-2n1w: Solution structure of human SUMO2 -

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Basic information

Entry
Database: PDB / ID: 2n1w
TitleSolution structure of human SUMO2
ComponentsSmall ubiquitin-related modifier 2
KeywordsSTRUCTURAL GENOMICS / Ubiquitin-like protein
Function / homology
Function and homology information


SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation ...SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / SUMOylation of transcription factors / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / PML body / protein tag activity / Formation of Incision Complex in GG-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / ubiquitin protein ligase binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
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
DepositionApr 24, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small ubiquitin-related modifier 2


Theoretical massNumber of molelcules
Total (without water)12,2431
Polymers12,2431
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 2 / SUMO-2 / HSMT3 / SMT3 homolog 2 / SUMO-3 / Sentrin-2 / Ubiquitin-like protein SMT3B / Smt3B


Mass: 12242.603 Da / Num. of mol.: 1 / Fragment: UNP residues 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Plasmid pCDF PylT-1 with SUMO2 insert and pAcKRS-3 as described in Neumann et al., Mol Cell, 36, 153, 2009
Gene: SMT3B, SMT3H2, SUMO2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61956

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of Small Ubiquitin-related MOdifier 2.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY
11013D HBHA(CO)NH
11112D-(HB)CB(CGCD)HD
11212D-(HB)CB(CGCDCE)HE
11313D 1H-15N TOCSY
11442D 1H-1H NOESY
11513D 1H-15N NOESY
11613D 1H-13C NOESY
11732D 1H-15N HSQC IPAP
NMR detailsText: NMR data was acquired at 295K using Shigemi NMR tubes.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 13C; U-100% 15N] SUMO2-1, 10 mM potassium phosphate-2, 100 mM potassium chloride-3, 2 mM DTT-4, 0.1 mM EDTA-5, 0.001 % sodium azide-6, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM [U-100% 15N] SUMO2-7, 10 mM potassium phosphate-8, 100 mM potassium chloride-9, 2 mM DTT-10, 0.1 mM EDTA-11, 0.001 % sodium azide-12, 90% H2O/10% D2O90% H2O/10% D2O
30.5-1 mM [U-100% 15N] SUMO2-13, 10 mM potassium phosphate-14, 100 mM potassium chloride-15, 2 mM DTT-16, 0.1 mM EDTA-17, 0.001 % sodium azide-18, 10 w/v Pf1 phage-19, 90% H2O/10% D2O90% H2O/10% D2O
40.5-1 mM SUMO2-20, 10 mM potassium phosphate-21, 100 mM potassium chloride-22, 2 mM DTT-23, 0.1 mM EDTA-24, 0.001 % sodium azide-25, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSUMO2-1[U-100% 13C; U-100% 15N]0.5-11
10 mMpotassium phosphate-21
100 mMpotassium chloride-31
2 mMDTT-41
0.1 mMEDTA-51
0.001 %sodium azide-61
mMSUMO2-7[U-100% 15N]0.5-12
10 mMpotassium phosphate-82
100 mMpotassium chloride-92
2 mMDTT-102
0.1 mMEDTA-112
0.001 %sodium azide-122
mMSUMO2-13[U-100% 15N]0.5-13
10 mMpotassium phosphate-143
100 mMpotassium chloride-153
2 mMDTT-163
0.1 mMEDTA-173
0.001 %sodium azide-183
10 w/vPf1 phage-193
mMSUMO2-200.5-14
10 mMpotassium phosphate-214
100 mMpotassium chloride-224
2 mMDTT-234
0.1 mMEDTA-244
0.001 %sodium azide-254
Sample conditionspH: 6.5 / Pressure: ambient atm / Temperature: 290 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE8504

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
CYANA3.9Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3.9Guntert, Mumenthaler and Wuthrichgeometry optimization
X-PLOR NIH2.34Schwieters, Kuszewski, Tjandra and Clorerefinement
CYANArefinement
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 constraintsNOE constraints total: 2519 / NOE intraresidue total count: 526 / NOE long range total count: 902 / NOE medium range total count: 453 / NOE sequential total count: 638 / Disulfide bond constraints total count: 0 / Hydrogen bond constraints total count: 56 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 68 / Protein psi angle constraints total count: 68
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum distance constraint violation: 0.77 Å / Maximum torsion angle constraint violation: 5 ° / Representative conformer: 1 / Torsion angle constraint violation method: PSVS 1.5
NMR ensemble rmsDistance rms dev: 0.03 Å

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