[English] 日本語
Yorodumi
- PDB-6sdw: Solution structure of Staufen1 dsRBD3+4 - hARF1 SBS dsRNA complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sdw
TitleSolution structure of Staufen1 dsRBD3+4 - hARF1 SBS dsRNA complex.
Components
  • Double-stranded RNA-binding protein Staufen homolog 1
  • hARF1 SBS dsRNA
KeywordsRNA BINDING PROTEIN / dsRBD-dsRNA binding protein / Staufen1 protein / Staufen mediated mRNA decay / NMR structure of RNA-protein complex / RNA binding domain.
Function / homology
Function and homology information


lncRNA-mediated post-transcriptional gene silencing / anterograde dendritic transport of messenger ribonucleoprotein complex / : / modification of postsynaptic structure / intracellular mRNA localization / protein localization to synapse / protein phosphatase 1 binding / positive regulation by virus of viral protein levels in host cell / microtubule associated complex / germ cell development ...lncRNA-mediated post-transcriptional gene silencing / anterograde dendritic transport of messenger ribonucleoprotein complex / : / modification of postsynaptic structure / intracellular mRNA localization / protein localization to synapse / protein phosphatase 1 binding / positive regulation by virus of viral protein levels in host cell / microtubule associated complex / germ cell development / positive regulation of viral genome replication / rough endoplasmic reticulum / dendrite cytoplasm / positive regulation of long-term synaptic potentiation / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / double-stranded RNA binding / cellular response to oxidative stress / cell body / neuron projection / mRNA binding / neuronal cell body / glutamatergic synapse / dendrite / endoplasmic reticulum / RNA binding / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Staufen 1, third double-stranded RNA binding domain / Staufen, C-terminal / Staufen C-terminal domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
RNA / RNA (> 10) / Double-stranded RNA-binding protein Staufen homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / na
AuthorsYadav, D.K. / Lukavsky, P.J.
Funding support Czech Republic, Germany, Belgium, 4items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic18-08153S Czech Republic
European Molecular Biology Organization3014 Germany
European CommissionPCIG14-GA-2013-630758 Belgium
Ministry of Education (Czech Republic)LQ1601 Czech Republic
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.
Authors: Yadav, D.K. / Zigackova, D. / Zlobina, M. / Klumpler, T. / Beaumont, C. / Kubickova, M. / Vanacova, S. / Lukavsky, P.J.
History
DepositionJul 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Double-stranded RNA-binding protein Staufen homolog 1
B: hARF1 SBS dsRNA


Theoretical massNumber of molelcules
Total (without water)30,6712
Polymers30,6712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4700 Å2
ΔGint-48 kcal/mol
Surface area16590 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy and restraint violation
RepresentativeModel #1medoid

-
Components

#1: Protein Double-stranded RNA-binding protein Staufen homolog 1


Mass: 19771.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAU1, STAU / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O95793
#2: RNA chain hARF1 SBS dsRNA


Mass: 10899.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli DH5[alpha] (bacteria)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D 1H-15N HSQC
131isotropic32D 1H-15N HSQC
142isotropic12D 1H-13C HSQC aliphatic
152isotropic22D 1H-13C HSQC aliphatic
162isotropic13D HNCA
172isotropic13D HNCO
182isotropic13D CBCA(CO)NH
192isotropic13D HN(CA)CB
1102isotropic13D HBHA(CO)NH
1112isotropic13D (H)CC(CO)NH-TOCSY
1122isotropic13D CC(CO)NH-TOCSY
1132isotropic23D 1H-13C NOESY aliphatic
1142isotropic13D 1H-13C NOESY aromatic
1151isotropic33D 1H-15N NOESY
1166isotropic22D 1H-1H, 13C 2F-filtered NOESY
1176isotropic23D 13C 1F-filtered 2F-edited HSQC-NOESY
1185isotropic23D 1H-13C NOESY ribose
1193isotropic22D 1H-1H TOCSY
1203isotropic22D 1H-1H NOESY
1214isotropic22D 1H-13C HSQC
1224isotropic23D (H)CCH-TOCSY
1234isotropic23D 1H-13C NOESY
1244isotropic22D 1H-13C HSQC aliphatic
1256isotropic22D 13C 1F-filtered 2F-filtered NOESY
1265isotropic22D 1H-13C HSQC
1277isotropic22D 1H-1H TOCSY
1287isotropic22D 1H-1H NOESY
1294isotropic23D (H)CCH-COSY aromatic
1308isotropic12D 1H-15N HSQC
1318isotropic22D 1H-15N HSQC
1328isotropic32D 1H-15N HSQC
1339isotropic12D 1H-13C HSQC aliphatic
1349isotropic22D 1H-13C HSQC aliphatic
1359isotropic13D HNCA
1369isotropic13D HNCO
1379isotropic13D CBCA(CO)NH
1389isotropic13D HN(CA)CB
1399isotropic13D HBHA(CO)NH
1409isotropic13D HA(CO)NH
1419isotropic13D (H)CC(CO)NH-TOCSY
1429isotropic13D CC(CO)NH-TOCSY
14310isotropic23D (H)CCH-TOCSY
14410isotropic23D (H)CCH-TOCSY
1459isotropic23D 1H-13C NOESY aliphatic
1469isotropic13D 1H-13C NOESY aromatic
14710isotropic22D 1H-13C HSQC aliphatic
14810isotropic22D 1H-13C HSQC aromatic
1499isotropic12D 1H-13C HSQC aromatic
1508isotropic33D 1H-15N NOESY
15111isotropic22D 1H-1H, 13C 2F-filtered NOESY
15211isotropic22D 1H-1H, 13C 1F-filtered 2F-filtered NOESY
15311isotropic23D 13C 1F-filtered 2F-edited HSQC-NOESY
1542isotropic12D 1H-13C HSQC aromatic
1552isotropic22D 1H-13C HSQC aromatic
1566isotropic22D 1H-13C HSQC aliphatic
1574isotropic22D 1H-13C HSQC aromatic
1585isotropic22D 1H-13C HSQC ribose
1595isotropic22D 1H-13C HSQC aromatic

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1310 uM [U-15N] Staufen1 dsRBD4, 310 uM Unlabelled hARF1, 90-95% H2O/5-10% D2OIn protein-dsRNA complex, protein was 15N_labelled and dsRNA was unlabelled.15N_dsRBD4 and unlabelled dsRNA90-95% H2O/5-10% D2O
solution2405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1, 90-95% H2O/5-10% D2OIn protein-dsRNA complex, protein was 15N_13C_labelled and dsRNA was unlabelled .15N_13C_dsRBD4 and unlabelled dsRNA90-95% H2O/5-10% D2O
solution3310 uM Unlabelled hARF1, 90-95% H2O/5-10% D2OSample used to measure spectrum for dsRNA assignment.Unlabelled dsRNA90-95% H2O/5-10% D2O
solution4478 uM [U-13C] hARF1, 100% D2OSample used to measure spectrum for dsRNA assignment.13C_dsRNA100% D2O
solution5354 uM [U-15N] Staufen1 dsRBD4, 354 uM [U-13C] hARF1, 100% D2OSample were used for inter molecular NOEs assignments15N_dsRBD4 and 13C_dsRNA100% D2O
solution6451 uM [U-13C; U-15N] Staufen1 dsRDB4, 451 uM Unlabelled hARF1, 100% D2OIn protein-dsRNA complex, protein was 15N_13C_labelled + dsRNA was unlabelled (sample were used for inter molecular NOEs assignments)15N_13C_dsRBD4 + unlabelled dsRNA100% D2O
solution7310 uM Unlabelled hARF1, 100% D2OSample used to measure spectrum for dsRNA assignment.Unlabelled_dsRNA100% D2O
solution8417 uM [U-15N] Staufen1 dsRBD3, 417 uM Unlabelled hARF1, 90-95% H2O/5-10% D2OIn protein-dsRNA complex, protein was 15N_labelled and dsRNA was unlabelled.15N_dsRBD3 and unlabelled dsRNA90-95% H2O/5-10% D2O
solution9458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1, 90-95% H2O/5-10% D2OIn protein-dsRNA complex, protein was 15N_13C_labelled and dsRNA was unlabelled .15N_13C_dsRBD3 and unlabelled dsRNA90-95% H2O/5-10% D2O
solution10458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1, 100% D2OIn protein-dsRNA complex, protein was 15N_13C_labelled + dsRNA was unlabelled.15N_13C_dsRBD3 + unlabelled dsRNA100% D2O
solution11157 uM [U-13C; U-15N] Staufen1 dsRBD3, 157 uM Unlabelled Staufen1 dsRBD4, 157 uM Unlabelled hARF1, 100% D2OIn protein-dsRNA complex, 15N_13C labelled dsRBD3 were ligated with unlabelled dsRBD4. protein-dsRNA complex was prepared by mixing ligated dsRBD3+4 with unlabelled dsRNA (sample were used for inter molecular NOEs assignments)ligated 15N_13C_dsRBD3_with unlabelled dsRBD4 and unlabelled dsRNA100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
310 uMStaufen1 dsRBD4[U-15N]1
310 uMhARF1Unlabelled1
405 uMStaufen1 dsRBD4[U-13C; U-15N]2
405 uMhARF1Unlabelled2
310 uMhARF1Unlabelled3
478 uMhARF1[U-13C]4
354 uMStaufen1 dsRBD4[U-15N]5
354 uMhARF1[U-13C]5
451 uMStaufen1 dsRDB4[U-13C; U-15N]6
451 uMhARF1Unlabelled6
310 uMhARF1Unlabelled7
417 uMStaufen1 dsRBD3[U-15N]8
417 uMhARF1Unlabelled8
458 uMStaufen1 dsRBD3[U-13C; U-15N]9
458 uMhARF1Unlabelled9
458 uMStaufen1 dsRBD3[U-13C; U-15N]10
458 uMhARF1Unlabelled10
157 uMStaufen1 dsRBD3[U-13C; U-15N]11
157 uMStaufen1 dsRBD4Unlabelled11
157 uMhARF1Unlabelled11
Sample conditionsDetails: NMR spectrum for dsRBD4-dsRNA, dsRBD3-dsRNA complex, dsRBD3_labelled_dsRBD4_unlabelled-dsRNA complex, and free dsRNA were measured in condition mentioned below. Buffer composition was: 50mM ...Details: NMR spectrum for dsRBD4-dsRNA, dsRBD3-dsRNA complex, dsRBD3_labelled_dsRBD4_unlabelled-dsRNA complex, and free dsRNA were measured in condition mentioned below. Buffer composition was: 50mM K-phosphate pH 6.5 + 250uM EDTA
Ionic strength: 50 mM / Label: Condition_1 / pH: 6.5 / Pressure: ambient atm / Temperature: 308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III8502
Bruker AVANCE IIIBrukerAVANCE III9503

-
Processing

NMR software
NameVersionDeveloperClassification
AmberAMBER14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAcyana-3.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
CARAcara_1.8.4Keller, Damberger and Wuthrichchemical shift assignment
CARAcara_1.8.4Keller, Damberger and Wuthrichpeak picking
SparkySPARKY3Goddard and Knellerchemical shift assignment
ATNOS-CANDIDUNIO 2.0.3Herrmann and Guntertstructure calculation
SparkySPARKY3Goddard and Knellerpeak picking
TopSpinTOPSPIN3.2Bruker Biospincollection
TopSpinTOPSPIN3.2Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonrefinement
Refinement
MethodSoftware ordinal
simulated annealing1
na11
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy and restraint violation
Conformers calculated total number: 50 / 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://pdbjlvh1.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