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.

6u55

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire E (ZE) Complexed with Sudan ebolavirus Nucleoprotein C-terminal Domain 634-738

Structural highlights

6u55 is a 2 chain structure with sequence from Lama glama and Sudan virus - Boniface, Sudan,1976. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.93Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NCAP_EBOSB Oligomerizes into helical capsid to encapsidate the viral genome, protecting it from nucleases and the cellular innate immune response. VP35 binds to and stabilizes monomeric NP, keeping it soluble. Upon virus replication, NP is recruited to bind cooperatively viral genomic RNA and VP35 is released. The encapsidated genomic RNA is termed the nucleocapsid and serves as template for transcription and replication. The nucleocapsid is helical with a pitch of 10.81 NP per turn and a diameter of about 22nm. Each NP binds to six nucleotides of viral genomic RNA, three being exposed to the solvant and three hidden into the nucleocapsid. Recruits also host PPP2R5C phosphatase to dephosphorylate VP30 and thereby promote viral transcription. Upon virion assembly and budding, NP binds to VP24 and possibly host STAU1.[UniProtKB:P18272]

Publication Abstract from PubMed

We had previously shown that three anti-Marburgvirus nanobodies (VHH or sdAb) targeted a cryptotope within an alpha-helical assembly at the nucleoprotein (NP) C-terminus that was conserved through half a century of viral evolution. Here, we wished to determine whether an anti-Ebola virus sdAb, that was cross-reactive within the Ebolavirus genus, recognized a similar structural feature upstream of the ebolaviral NP C-terminus. Additionally, we sought to determine whether the specificities of a less cross-reactive anti-Zaire ebolavirus sdAb and a totally specific anti-Sudan ebolavirus sdAb were the result of exclusion from this region. Binding and X-ray crystallographic studies revealed that the primary determinant of cross-reactivity did indeed appear to be a preference for the helical feature. Specificity, in the case of the Zaire ebolavirus specific sdAb arose from the footprint shifting away from the helices, to engage more variable residues. While both sdAb employed CDRs they also had atypical side-on approaches with framework 2 (FR2) helping to accommodate parts of the epitope in sizeable paratope gullies. The Sudan ebolavirus specific sdAb was more remarkable and appeared to bind two C-terminal domains simultaneously via non-overlapping epitopes - "paratope duality". One mode involved paratope gullying, while the other involved only CDRs, with CDR3 restructuring to wedge in between opposing walls of an inter-domain crevice. The varied routes used by sdAb to engage antigen discovered here deepen our appreciation of the small scaffold's architectural versatility, and also reveal lucrative opportunities within the ebolavirus NP C-termini that might be leveraged for diagnostics and novel therapeutic targeting.

Paratope duality and gullying are among the atypical recognition mechanisms employed by a trio of nanobodies to differentiate ebolavirus nucleoproteins.,Sherwood LJ, Taylor AB, Hart PJ, Hayhurst A J Mol Biol. 2019 Oct 15. pii: S0022-2836(19)30597-2. doi:, 10.1016/j.jmb.2019.10.005. PMID:31626803^[1]

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

References

↑ Sherwood LJ, Taylor AB, Hart PJ, Hayhurst A. Paratope duality and gullying are among the atypical recognition mechanisms employed by a trio of nanobodies to differentiate ebolavirus nucleoproteins. J Mol Biol. 2019 Oct 15. pii: S0022-2836(19)30597-2. doi:, 10.1016/j.jmb.2019.10.005. PMID:31626803 doi:http://dx.doi.org/10.1016/j.jmb.2019.10.005

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6u55"

@@ Line 3: / Line 3: @@
 <StructureSection load='6u55' size='340' side='right'caption='[[6u55]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6u55]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U55 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6u55]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama] and [https://en.wikipedia.org/wiki/Sudan_virus_-_Boniface,_Sudan,1976 Sudan virus - Boniface, Sudan,1976]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U55 FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6u55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u55 OCA], [http://pdbe.org/6u55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u55 RCSB], [http://www.ebi.ac.uk/pdbsum/6u55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u55 ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93&#8491;</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=6u55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u55 OCA], [https://pdbe.org/6u55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u55 RCSB], [https://www.ebi.ac.uk/pdbsum/6u55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u55 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NCAP_EBOSB NCAP_EBOSB]] Oligomerizes into helical capsid to encapsidate the viral genome, protecting it from nucleases and the cellular innate immune response. VP35 binds to and stabilizes monomeric NP, keeping it soluble. Upon virus replication, NP is recruited to bind cooperatively viral genomic RNA and VP35 is released. The encapsidated genomic RNA is termed the nucleocapsid and serves as template for transcription and replication. The nucleocapsid is helical with a pitch of 10.81 NP per turn and a diameter of about 22nm. Each NP binds to six nucleotides of viral genomic RNA, three being exposed to the solvant and three hidden into the nucleocapsid. Recruits also host PPP2R5C phosphatase to dephosphorylate VP30 and thereby promote viral transcription. Upon virion assembly and budding, NP binds to VP24 and possibly host STAU1.[UniProtKB:P18272]
+[https://www.uniprot.org/uniprot/NCAP_EBOSB NCAP_EBOSB] Oligomerizes into helical capsid to encapsidate the viral genome, protecting it from nucleases and the cellular innate immune response. VP35 binds to and stabilizes monomeric NP, keeping it soluble. Upon virus replication, NP is recruited to bind cooperatively viral genomic RNA and VP35 is released. The encapsidated genomic RNA is termed the nucleocapsid and serves as template for transcription and replication. The nucleocapsid is helical with a pitch of 10.81 NP per turn and a diameter of about 22nm. Each NP binds to six nucleotides of viral genomic RNA, three being exposed to the solvant and three hidden into the nucleocapsid. Recruits also host PPP2R5C phosphatase to dephosphorylate VP30 and thereby promote viral transcription. Upon virion assembly and budding, NP binds to VP24 and possibly host STAU1.[UniProtKB:P18272]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 18: @@
 </div>
 <div class="pdbe-citations 6u55" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Lama glama]]
 [[Category: Large Structures]]
-[[Category: Hart, P J]]
+[[Category: Sudan virus - Boniface, Sudan,1976]]
-[[Category: Hayhurst, A]]
+[[Category: Hart PJ]]
-[[Category: Sherwood, L J]]
+[[Category: Hayhurst A]]
-[[Category: Taylor, A B]]
+[[Category: Sherwood LJ]]
-[[Category: Antibody]]
+[[Category: Taylor AB]]
-[[Category: Ebola]]
-[[Category: Filovirus]]
-[[Category: Immune system]]
-[[Category: Nanobody]]

6u55

From Proteopedia

Current revision

Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire E (ZE) Complexed with Sudan ebolavirus Nucleoprotein C-terminal Domain 634-738

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox