This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2jw8

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Solution structure of stereo-array isotope labelled (SAIL) C-terminal dimerization domain of SARS coronavirus nucleocapsid protein

Structural highlights

2jw8 is a 2 chain structure with sequence from Severe acute respiratory syndrome-related coronavirus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NCAP_SARS Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication (PubMed:17210170). May modulate transforming growth factor-beta signaling by binding host SMAD3 (PubMed:18055455).[HAMAP-Rule:MF_04096]^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP) contains a potential RNA-binding region in its N-terminal portion and also serves as a dimerization domain by forming a homodimer with a molecular mass of 28 kDa. So far, the structure determination of the SARS-CoV NP CTD in solution has been impeded by the poor quality of NMR spectra, especially for aromatic resonances. We have recently developed the stereo-array isotope labeling (SAIL) method to overcome the size problem of NMR structure determination by utilizing a protein exclusively composed of stereo- and regio-specifically isotope-labeled amino acids. Here, we employed the SAIL method to determine the high-quality solution structure of the SARS-CoV NP CTD by NMR. The SAIL protein yielded less crowded and better resolved spectra than uniform (13)C and (15)N labeling, and enabled the homodimeric solution structure of this protein to be determined. The NMR structure is almost identical with the previously solved crystal structure, except for a disordered putative RNA-binding domain at the N-terminus. Studies of the chemical shift perturbations caused by the binding of single-stranded DNA and mutational analyses have identified the disordered region at the N-termini as the prime site for nucleic acid binding. In addition, residues in the beta-sheet region also showed significant perturbations. Mapping of the locations of these residues onto the helical model observed in the crystal revealed that these two regions are parts of the interior lining of the positively charged helical groove, supporting the hypothesis that the helical oligomer may form in solution.

Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method.,Takeda M, Chang CK, Ikeya T, Guntert P, Chang YH, Hsu YL, Huang TH, Kainosho M J Mol Biol. 2008 Jul 18;380(4):608-22. Epub 2007 Dec 5. PMID:18561946^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Stertz S, Reichelt M, Spiegel M, Kuri T, Martínez-Sobrido L, García-Sastre A, Weber F, Kochs G. The intracellular sites of early replication and budding of SARS-coronavirus. Virology. 2007 May 10;361(2):304-15. PMID:17210170 doi:10.1016/j.virol.2006.11.027
↑ Zhao X, Nicholls JM, Chen YG. Severe acute respiratory syndrome-associated coronavirus nucleocapsid protein interacts with Smad3 and modulates transforming growth factor-beta signaling. J Biol Chem. 2008 Feb 8;283(6):3272-3280. PMID:18055455 doi:10.1074/jbc.M708033200
↑ Takeda M, Chang CK, Ikeya T, Guntert P, Chang YH, Hsu YL, Huang TH, Kainosho M. Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method. J Mol Biol. 2008 Jul 18;380(4):608-22. Epub 2007 Dec 5. PMID:18561946 doi:10.1016/j.jmb.2007.11.093

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2jw8"

@@ Line 1: / Line 1: @@
 ==Solution structure of stereo-array isotope labelled (SAIL) C-terminal dimerization domain of SARS coronavirus nucleocapsid protein==
-<StructureSection load='2jw8' size='340' side='right'caption='[[2jw8]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2jw8' size='340' side='right'caption='[[2jw8]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2jw8]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JW8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JW8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2jw8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome-related_coronavirus Severe acute respiratory syndrome-related coronavirus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JW8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JW8 FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jw8 OCA], [https://pdbe.org/2jw8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jw8 RCSB], [https://www.ebi.ac.uk/pdbsum/2jw8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jw8 ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jw8 OCA], [https://pdbe.org/2jw8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jw8 RCSB], [https://www.ebi.ac.uk/pdbsum/2jw8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jw8 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/NCAP_CVHSA NCAP_CVHSA]] Major structural component of virions that associates with genomic RNA to form a long, flexible, helical nucleocapsid (By similarity).
+[https://www.uniprot.org/uniprot/NCAP_SARS NCAP_SARS] Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication (PubMed:17210170). May modulate transforming growth factor-beta signaling by binding host SMAD3 (PubMed:18055455).[HAMAP-Rule:MF_04096]<ref>PMID:17210170</ref> <ref>PMID:18055455</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 36: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Chang, C]]
+[[Category: Severe acute respiratory syndrome-related coronavirus]]
-[[Category: Chang, Y]]
+[[Category: Chang C]]
-[[Category: Guntert, P]]
+[[Category: Chang Y]]
-[[Category: Hsu, Y]]
+[[Category: Guntert P]]
-[[Category: Huang, T]]
+[[Category: Hsu Y]]
-[[Category: Ikeya, T]]
+[[Category: Huang T]]
-[[Category: Kainosho, M]]
+[[Category: Ikeya T]]
-[[Category: Takeda, M]]
+[[Category: Kainosho M]]
-[[Category: Cytoplasm]]
+[[Category: Takeda M]]
-[[Category: Golgi apparatus]]
-[[Category: Nucleocapsid packaging]]
-[[Category: Phosphorylation]]
-[[Category: Rna-binding]]
-[[Category: Sail]]
-[[Category: Sars coronavirus nucleocapsid protein]]
-[[Category: Structural protein]]
-[[Category: Viral nucleoprotein]]
-[[Category: Viral protein]]
-[[Category: Virion]]

2jw8

From Proteopedia

Current revision

Solution structure of stereo-array isotope labelled (SAIL) C-terminal dimerization domain of SARS coronavirus nucleocapsid protein

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox