OCA at 13:28, 1 February 2024

OCA — Thu, 01 Feb 2024 13:28:19 GMT

←Older revision		Revision as of 13:28, 1 February 2024
Line 1:		Line 1:

-	====	+	==Nanobody H11-A10 and F2 bound to RBD==
-	<StructureSection load='7z1b' size='340' side='right'caption='[[7z1b]]' scene=''>	+	<StructureSection load='7z1b' size='340' side='right'caption='[[7z1b]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7z1b]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama] and [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z1B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z1B 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=7z1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z1b OCA], [https://pdbe.org/7z1b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z1b RCSB], [https://www.ebi.ac.uk/pdbsum/7z1b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z1b 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]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=7z1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z1b OCA], [https://pdbe.org/7z1b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z1b RCSB], [https://www.ebi.ac.uk/pdbsum/7z1b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z1b ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SPIKE_SARS2 SPIKE_SARS2] attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.[HAMAP-Rule:MF_04099]<ref>PMID:32075877</ref> <ref>PMID:32142651</ref> <ref>PMID:32155444</ref> mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Camelid single-domain antibodies, also known as nanobodies, can be readily isolated from naive libraries for specific targets but often bind too weakly to their targets to be immediately useful. Laboratory-based genetic engineering methods to enhance their affinity, termed maturation, can deliver useful reagents for different areas of biology and potentially medicine. Using the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and a naive library, we generated closely related nanobodies with micromolar to nanomolar binding affinities. By analyzing the structure-activity relationship using X-ray crystallography, cryoelectron microscopy, and biophysical methods, we observed that higher conformational entropy losses in the formation of the spike protein-nanobody complex are associated with tighter binding. To investigate this, we generated structural ensembles of the different complexes from electron microscopy maps and correlated the conformational fluctuations with binding affinity. This insight guided the engineering of a nanobody with improved affinity for the spike protein.
		+
		+	Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.,Mikolajek H, Weckener M, Brotzakis ZF, Huo J, Dalietou EV, Le Bas A, Sormanni P, Harrison PJ, Ward PN, Truong S, Moynie L, Clare DK, Dumoux M, Dormon J, Norman C, Hussain N, Vogirala V, Owens RJ, Vendruscolo M, Naismith JH Proc Natl Acad Sci U S A. 2022 Aug 2;119(31):e2205412119. doi:, 10.1073/pnas.2205412119. Epub 2022 Jul 15. PMID:35858383<ref>PMID:35858383</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7z1b" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Spike protein 3D structures\|Spike protein 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lama glama]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
		+	[[Category: Mikolajek H]]
		+	[[Category: Naismith JH]]

OCA at 11:22, 23 March 2022

OCA — Wed, 23 Mar 2022 11:22:19 GMT

←Older revision		Revision as of 11:22, 23 March 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7z1b ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7z1b' size='340' side='right'caption='[[7z1b]]' scene=''>
-	~~Authors~~: ~~Mikolajek, H~~.~~, Naismith, J~~.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Nanobody H11~~-~~A10 and F2 bound to RBD~~	+	</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=7z1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z1b OCA], [https://pdbe.org/7z1b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z1b RCSB], [https://www.ebi.ac.uk/pdbsum/7z1b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z1b ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Naismith, J.H~~]]	+	__TOC__
-	[[Category: ~~Mikolajek, H~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA: Protected "7z1b" [edit=sysop:move=sysop]

OCA — Wed, 02 Mar 2022 05:23:44 GMT

Protected "7z1b" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:23, 2 March 2022

OCA: New page: '''Unreleased structure''' The entry 7z1b is ON HOLD Authors: Mikolajek, H., Naismith, J.H. Description: Nanobody H11-A10 and F2 bound to RBD Category: Unreleased Structures [[Cate...

OCA — Wed, 02 Mar 2022 05:23:43 GMT

New page: '''Unreleased structure''' The entry 7z1b is ON HOLD Authors: Mikolajek, H., Naismith, J.H. Description: Nanobody H11-A10 and F2 bound to RBD Category: Unreleased Structures [[Cate...

New page

'''Unreleased structure'''

The entry 7z1b is ON HOLD

Authors: Mikolajek, H., Naismith, J.H.

Description: Nanobody H11-A10 and F2 bound to RBD
[[Category: Unreleased Structures]]
[[Category: Naismith, J.H]]
[[Category: Mikolajek, H]]

7z1b - Revision history

OCA at 13:28, 1 February 2024

OCA at 11:22, 23 March 2022

OCA: Protected "7z1b" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7z1b is ON HOLD Authors: Mikolajek, H., Naismith, J.H. Description: Nanobody H11-A10 and F2 bound to RBD Category: Unreleased Structures [[Cate...