[English] 日本語
Yorodumi
- PDB-5xqm: NMR solution structure of SMO1, Sumo homologue in Caenorhabditis ... -

+
Open data


ID or keywords:

Loading...

-
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 DNA damage response and repair proteins / SUMO E3 ligases SUMOylate target proteins / SUMOylation of transcription factors / SUMOylation of ubiquitinylation proteins / SUMOylation of transcription cofactors / SUMOylation of SUMOylation 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 DNA damage response and repair proteins / SUMO E3 ligases SUMOylate target proteins / 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 / Formation of Incision Complex in GG-NER / Regulation of IFNG signaling / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / Postmitotic nuclear pore complex (NPC) reformation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / multicellular organismal locomotion / nematode larval development / protein localization to chromosome / mitotic sister chromatid separation / synaptonemal complex disassembly / embryo development ending in birth or egg hatching / microtubule organizing center / 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 / negative regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytoplasm
Similarity search - Function
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small ubiquitin-related modifier


Theoretical massNumber of molelcules
Total (without water)11,0481
Polymers11,0481
Non-polymers00
Water0
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

-
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

-
Experimental details

-
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

-
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: 6.0 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more