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- PDB-5xqm: NMR solution structure of SMO1, Sumo homologue in Caenorhabditis ... -

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Basic information

Entry
Database: PDB / ID: 5xqm
TitleNMR solution structure of SMO1, Sumo homologue in Caenorhabditis elegans
ComponentsSmall ubiquitin-related modifier
KeywordsSIGNALING PROTEIN / solution structure / Caenorhabditis elegans / Sumo homologue
Function / homology
Function and homology information


positive regulation of nematode male tail tip morphogenesis / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of ubiquitinylation proteins / SUMOylation of transcription cofactors / SUMOylation of SUMOylation proteins / SUMOylation of intracellular receptors / SUMOylation of chromatin organization proteins ...positive regulation of nematode male tail tip morphogenesis / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of ubiquitinylation proteins / SUMOylation of transcription cofactors / SUMOylation of SUMOylation proteins / SUMOylation of intracellular receptors / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Regulation of IFNG signaling / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of nuclear envelope proteins / SUMOylation of DNA damage response and repair proteins / Formation of Incision Complex in GG-NER / multicellular organismal locomotion / nematode larval development / protein localization to chromosome / synaptonemal complex disassembly / mitotic sister chromatid separation / embryo development ending in birth or egg hatching / mitotic metaphase chromosome alignment / muscle cell cellular homeostasis / ubiquitin-like protein ligase binding / protein sumoylation / regulation of protein stability / spindle / protein tag activity / chromosome / regulation of gene expression / negative regulation of DNA-templated transcription / centrosome / negative regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Small ubiquitin-related modifier
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsGowda, C.M. / Surana, P. / Das, R.
CitationJournal: PLoS ONE / Year: 2017
Title: Structural and functional analysis of SMO-1, the SUMO homolog in Caenorhabditis elegans
Authors: Surana, P. / Gowda, C.M. / Tripathi, V. / Broday, L. / Das, R.
History
DepositionJun 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small ubiquitin-related modifier


Theoretical massNumber of molelcules
Total (without water)11,0481
Polymers11,0481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5850 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400target function
RepresentativeModel #1target function

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Components

#1: Protein Small ubiquitin-related modifier / SUMO / Ubiquitin-like protein SMT3


Mass: 11048.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: smo-1, smt3, sumo, K12C11.2 / Production host: Escherichia coli (E. coli) / References: UniProt: P55853

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D HN(CO)CA
171isotropic13D C(CO)NH
181isotropic13D H(CCO)NH
191isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 620 uM [U-13C; U-15N] SMO1, Small Ubiquitin like modifier in C. elegans, 90% H2O/10% D2O
Label: 15N-13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 620 uM
Component: SMO1, Small Ubiquitin like modifier in C. elegans
Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 25mM Phosphate buffer pH6.0, 150mM NaCl / Ionic strength: 150 mM / Label: condition_1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGUNTERT, MUMENTHALER AND WUTHRICHrefinement
CYANAstructure solution
Sparkystructure solution
TopSpinstructure solution
NMRPipestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: WATER REFINEMENT PERFORMED USING PONDEROSA-C/S PACKAGE.
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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