NMR paper NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs

		BioNMR > Educational resources > Journal club
[NMR paper] NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

07-08-2021, 11:44 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs

NMR structure of the Vibrio vulnificus ribosomal protein S1 domains D3 and D4 provides insights into molecular recognition of single-stranded RNAs

The ribosomal S1 protein (rS1) is indispensable for translation initiation in Gram-negative bacteria. rS1 is a multidomain protein that acts as an RNA chaperone and ensures that mRNAs can bind the ribosome in a single-stranded conformation, which could be related to fast recognition. Although many ribosome structures were solved in recent years, a high-resolution structure of a two-domain mRNA-binding competent rS1 construct is not yet available. Here, we present the NMR solution structure of...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Proteomics and (1)H NMR-based metabolomics analysis of pathogenic Vibrio vulnificus aquacultures isolated from sewage drains. Proteomics and (1)H NMR-based metabolomics analysis of pathogenic Vibrio vulnificus aquacultures isolated from sewage drains. Related Articles Proteomics and (1)H NMR-based metabolomics analysis of pathogenic Vibrio vulnificus aquacultures isolated from sewage drains. Environ Sci Pollut Res Int. 2017 Sep 01;: Authors: Zhang C, Wang Z, Zhang D, Zhou J, Lu C, Su X, Ding D Abstract Vibrio bacteria live in both marine and freshwater habitats and are associated with aquatic animals. Vibrio vulnificus is a pathogenic bacterium that...	nmrlearner	Journal club	0	09-04-2017 02:06 AM
Replication Protein A Prohibits Diffusion of the PCNASliding Clamp along Single-Stranded DNA Replication Protein A Prohibits Diffusion of the PCNASliding Clamp along Single-Stranded DNA http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b01213/20170223/images/medium/bi-2016-01213e_0006.gif Biochemistry DOI: 10.1021/acs.biochem.6b01213 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/acrZkrDOr0Q More...	nmrlearner	Journal club	0	03-01-2017 04:13 AM
Electrostatic and Hydrophobic Interactions MediateSingle-Stranded DNA Recognition and Acta2 Repressionby Purine-Rich Element-Binding Protein B Electrostatic and Hydrophobic Interactions MediateSingle-Stranded DNA Recognition and Acta2 Repressionby Purine-Rich Element-Binding Protein B http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b00006/20160503/images/medium/bi-2016-00006y_0009.gif Biochemistry DOI: 10.1021/acs.biochem.6b00006 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/LoA3uztiAco More...	nmrlearner	Journal club	0	05-05-2016 03:15 AM
[NMR paper] Screening protein - single stranded RNA complexes by NMR spectroscopy for structure determination. Screening protein - single stranded RNA complexes by NMR spectroscopy for structure determination. Screening protein - single stranded RNA complexes by NMR spectroscopy for structure determination. Methods. 2013 Oct 1; Authors: Foot JN, Feracci M, Dominguez C Abstract In the past few years, RNA molecules have been revealed to be at the center of numerous biological processes. Long considered as passive molecules transferring genetic information from DNA to proteins, it is now well established that RNA molecules play important regulatory...	nmrlearner	Journal club	0	10-08-2013 02:04 PM
Screening protein – single stranded RNA complexes by NMR spectroscopy for structure determination Screening protein – single stranded RNA complexes by NMR spectroscopy for structure determination Publication date: Available online 1 October 2013 Source:Methods</br> Author(s): Jaelle N. Foot , Mikael Feracci , Cyril Dominguez</br> In the past few years, RNA molecules have been revealed to be at the center of numerous biological processes. Long considered as passive molecules transferring genetic information from DNA to proteins, it is now well established that RNA molecules play important regulatory roles. Associated with that, the number of identified RNA...	nmrlearner	Journal club	0	10-01-2013 11:15 PM
[NMR paper] Comparison of Pf1 and Fd gene 5 proteins and their single-stranded DNA complexes by N Comparison of Pf1 and Fd gene 5 proteins and their single-stranded DNA complexes by NMR spectroscopy and differential scanning calorimetry. Related Articles Comparison of Pf1 and Fd gene 5 proteins and their single-stranded DNA complexes by NMR spectroscopy and differential scanning calorimetry. Biochemistry. 1995 Jan 10;34(1):148-54 Authors: Davis KG, Plyte SE, Robertson SR, Cooper A, Kneale GG The Pf1 gene 5 protein forms a large helical nucleoprotein complex (Mr = 3.1 x 10(7)) with single-stranded viral DNA, from which a 32 amino acid...	nmrlearner	Journal club	0	08-22-2010 03:41 AM
[NMR paper] Secondary structure of the single-stranded DNA binding protein encoded by filamentous Secondary structure of the single-stranded DNA binding protein encoded by filamentous phage Pf3 as determined by NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Secondary structure of the single-stranded DNA binding protein encoded by filamentous phage Pf3 as determined by NMR. Eur J Biochem. 1994 Sep 1;224(2):663-76 Authors: Folmer RH, Folkers PJ, Kaan A, Jonker AJ, Aelen JM, Konings RN, Hilbers CW Nuclear magnetic resonance...	nmrlearner	Journal club	0	08-22-2010 03:29 AM
[NMR paper] Identification of the single-stranded DNA binding surface of the transcriptional coac Identification of the single-stranded DNA binding surface of the transcriptional coactivator PC4 by NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles Identification of the single-stranded DNA binding surface of the transcriptional coactivator PC4 by NMR. J Biol Chem. 1999 Feb 5;274(6):3693-9 Authors: Werten S, Wechselberger R, Boelens R, van der Vliet PC, Kaptein R The C-terminal domain of the eukaryotic transcriptional cofactor PC4...	nmrlearner	Journal club	0	08-21-2010 04:03 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off