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.

2p47

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:54, 2 March 2022

Complex of a camelid single-domain vhh antibody fragment with RNASE A at 2.5A resolution: SE5B-TRI crystal form with five se-met sites (L4M, M34, M51, F68M, M83) in vhh scaffold.

Structural highlights

2p47 is a 2 chain structure with sequence from Arabian camel and Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Activity:	Pancreatic ribonuclease, with EC number 3.1.27.5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.^[1]

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

A crystallization chaperone is an auxiliary protein that binds to a target of interest, enhances and modulates crystal packing, and provides high-quality phasing information. We critically evaluated the effectiveness of a camelid single-domain antibody (V(H)H) as a crystallization chaperone. By using a yeast surface display system for V(H)H, we successfully introduced additional Met residues in the core of the V(H)H scaffold. We identified a set of SeMet-labeled V(H)H variants that collectively produced six new crystal forms as the complex with the model antigen, RNase A. The crystals exhibited monoclinic, orthorhombic, triclinic, and tetragonal symmetry and have one or two complexes in the asymmetric unit, some of which diffracted to an atomic resolution. The phasing power of the Met-enriched V(H)H chaperone allowed for auto-building the entire complex using single-anomalous dispersion technique (SAD) without the need for introducing SeMet into the target protein. We show that phases produced by combining SAD and V(H)H model-based phases are accurate enough to easily solve structures of the size reported here, eliminating the need to collect multiple wavelength multiple-anomalous dispersion (MAD) data. Together with the presence of high-throughput selection systems (e.g., phage display libraries) for V(H)H, the enhanced V(H)H domain described here will be an excellent scaffold for producing effective crystallization chaperones.

Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold.,Tereshko V, Uysal S, Koide A, Margalef K, Koide S, Kossiakoff AA Protein Sci. 2008 Jul;17(7):1175-87. Epub 2008 Apr 29. PMID:18445622^[2]

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

References

↑ delCardayre SB, Ribo M, Yokel EM, Quirk DJ, Rutter WJ, Raines RT. Engineering ribonuclease A: production, purification and characterization of wild-type enzyme and mutants at Gln11. Protein Eng. 1995 Mar;8(3):261-73. PMID:7479688
↑ Tereshko V, Uysal S, Koide A, Margalef K, Koide S, Kossiakoff AA. Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold. Protein Sci. 2008 Jul;17(7):1175-87. Epub 2008 Apr 29. PMID:18445622 doi:10.1110/ps.034892.108

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/2p47"

@@ Line 3: / Line 3: @@
 <StructureSection load='2p47' size='340' side='right'caption='[[2p47]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2p47]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P47 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2P47 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2p47]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabian_camel Arabian camel] and [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P47 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P47 FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2p47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p47 OCA], [http://pdbe.org/2p47 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p47 RCSB], [http://www.ebi.ac.uk/pdbsum/2p47 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2p47 ProSAT]</span></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=2p47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p47 OCA], [https://pdbe.org/2p47 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p47 RCSB], [https://www.ebi.ac.uk/pdbsum/2p47 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p47 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN]] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
+[[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN]] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 *[[Antibody 3D structures|Antibody 3D structures]]
 *[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-*[[Temp|Temp]]
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
 == References ==
 <references/>

2p47

From Proteopedia

Revision as of 07:54, 2 March 2022

Complex of a camelid single-domain vhh antibody fragment with RNASE A at 2.5A resolution: SE5B-TRI crystal form with five se-met sites (L4M, M34, M51, F68M, M83) in vhh scaffold.

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