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- PDB-6sdw: Solution structure of Staufen1 dsRBD3+4 - hARF1 SBS dsRNA complex. -

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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 phosphatase 1 binding / protein localization to synapse / positive regulation by virus of viral protein levels in host cell / microtubule associated complex / germ cell development / positive regulation of viral genome replication ...lncRNA-mediated post-transcriptional gene silencing / anterograde dendritic transport of messenger ribonucleoprotein complex / modification of postsynaptic structure / intracellular mRNA localization / protein phosphatase 1 binding / protein localization to synapse / 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 / neuronal cell body / mRNA binding / dendrite / glutamatergic synapse / endoplasmic reticulum / RNA binding / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Staufen 1, third double-stranded RNA binding domain / Staufen, C-terminal / : / Staufen C-terminal domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain ...Staufen 1, third double-stranded RNA binding domain / Staufen, C-terminal / : / Staufen C-terminal domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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)

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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
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

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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

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NMR measurement

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

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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

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