1xx5

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Natrin from Naja atra snake venom

Structural highlights

1xx5 is a 3 chain structure with sequence from Naja atra. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CRVP1_NAJAT Inhibits calcium-activated potassium channels (KCa1.1/KCNMA1), voltage-gated potassium channel Kv1.3/KCNA3, and the calcium release channel/ryanodine receptor (RyR). Binds specifically to type 1 RyR (RyR1) from skeletal muscle. Inhibit both the binding of ryanodine to RyR1, and RyR1's calcium-channel activity. Inhibits carbachol-induced muscle contraction and weakly blocks muscle contraction evoked by potassium.^[1] ^[2] ^[3] ^[4]

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

Cysteine-rich secretory proteins (CRISPs) are widespread in snake venoms. Some members of these CRISPs recently have been found to block L-type Ca(2+) channels or cyclic nucleotide-gated ion (CNG) channels. Here, natrin purified from Naja atra venom, a member of the CRISP family, can induce a further contractile response in the endothelium-denuded thoracic aorta of mouse which has been contracted by a high-K(+) solution. Further experiments show it can block the high-conductance calcium-activated potassium (BK(Ca)) channel in a concentration-dependent manner with an IC(50) of 34.4 nM and a Hill coefficient of 1.02, which suggests that only a single natrin molecule is required to bind an ion channel to block BK(Ca) current. The crystal structure of natrin displaying two domains in tandem shows its cysteine-rich domain (CRD) has relatively independent flexibility, especially for the C-terminal long loop (loop I) of CRD to participate in the interface of two domains. On the basis of previous studies of CNG channel and L-Ca(2+) channel blockers, and the sequence and structural comparison of natrin and stecrisp, the deviation of the vital loop I of CRD is suggested to contribute to different effects of some CRISPs in protein-protein interaction.

Blocking effect and crystal structure of natrin toxin, a cysteine-rich secretory protein from Naja atra venom that targets the BKCa channel.,Wang J, Shen B, Guo M, Lou X, Duan Y, Cheng XP, Teng M, Niu L, Liu Q, Huang Q, Hao Q Biochemistry. 2005 Aug 2;44(30):10145-52. PMID:16042391^[5]

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

References

↑ Chang LS, Liou JC, Lin SR, Cheng YC. Purification and characterization of Taiwan cobra venom proteins with weak toxicity. Toxicon. 2005 Jan;45(1):21-5. PMID:15581679 doi:10.1016/j.toxicon.2004.09.002
↑ Wang F, Li H, Liu MN, Song H, Han HM, Wang QL, Yin CC, Zhou YC, Qi Z, Shu YY, Lin ZJ, Jiang T. Structural and functional analysis of natrin, a venom protein that targets various ion channels. Biochem Biophys Res Commun. 2006 Dec 15;351(2):443-8. Epub 2006 Oct 20. PMID:17070778 doi:10.1016/j.bbrc.2006.10.067
↑ Zhou Q, Wang QL, Meng X, Shu Y, Jiang T, Wagenknecht T, Yin CC, Sui SF, Liu Z. Structural and functional characterization of ryanodine receptor-natrin toxin interaction. Biophys J. 2008 Nov 1;95(9):4289-99. doi: 10.1529/biophysj.108.137224. Epub 2008 , Jul 25. PMID:18658224 doi:10.1529/biophysj.108.137224
↑ Wang J, Shen B, Guo M, Lou X, Duan Y, Cheng XP, Teng M, Niu L, Liu Q, Huang Q, Hao Q. Blocking effect and crystal structure of natrin toxin, a cysteine-rich secretory protein from Naja atra venom that targets the BKCa channel. Biochemistry. 2005 Aug 2;44(30):10145-52. PMID:16042391 doi:10.1021/bi050614m
↑ Wang J, Shen B, Guo M, Lou X, Duan Y, Cheng XP, Teng M, Niu L, Liu Q, Huang Q, Hao Q. Blocking effect and crystal structure of natrin toxin, a cysteine-rich secretory protein from Naja atra venom that targets the BKCa channel. Biochemistry. 2005 Aug 2;44(30):10145-52. PMID:16042391 doi:10.1021/bi050614m

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1xx5"

@@ Line 1: / Line 1: @@
-[[Image:1xx5.gif|left|200px]]<br /><applet load="1xx5" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1xx5, resolution 2.40&Aring;" />
-'''Crystal Structure of Natrin from Naja atra snake venom'''<br />
-==Overview==
+==Crystal Structure of Natrin from Naja atra snake venom==
-Cysteine-rich secretory proteins (CRISPs) are widely distributed in mammals and snake venoms. They possess apparent homology but varying functions. The structure of CRISPs has remained elusive. Two novel members of the family, natrin and stecrisp, have been purified from Naja atra and Trimeresurus stejnegeri venoms, respectively. Their crystals diffract X-rays to resolution limits of 2.1 and 1.6 angstroms, respectively, and belong to the orthorhombic system with different space groups, unit-cell parameters and numbers of molecules per asymmetric unit. Their structures will contribute a structural basis for further functional studies of this family.
+<StructureSection load='1xx5' size='340' side='right'caption='[[1xx5]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1xx5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Naja_atra Naja atra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XX5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XX5 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EOH:ETHANOL'>EOH</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=1xx5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xx5 OCA], [https://pdbe.org/1xx5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xx5 RCSB], [https://www.ebi.ac.uk/pdbsum/1xx5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xx5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CRVP1_NAJAT CRVP1_NAJAT] Inhibits calcium-activated potassium channels (KCa1.1/KCNMA1), voltage-gated potassium channel Kv1.3/KCNA3, and the calcium release channel/ryanodine receptor (RyR). Binds specifically to type 1 RyR (RyR1) from skeletal muscle. Inhibit both the binding of ryanodine to RyR1, and RyR1's calcium-channel activity. Inhibits carbachol-induced muscle contraction and weakly blocks muscle contraction evoked by potassium.<ref>PMID:15581679</ref> <ref>PMID:17070778</ref> <ref>PMID:18658224</ref> <ref>PMID:16042391</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xx/1xx5_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xx5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cysteine-rich secretory proteins (CRISPs) are widespread in snake venoms. Some members of these CRISPs recently have been found to block L-type Ca(2+) channels or cyclic nucleotide-gated ion (CNG) channels. Here, natrin purified from Naja atra venom, a member of the CRISP family, can induce a further contractile response in the endothelium-denuded thoracic aorta of mouse which has been contracted by a high-K(+) solution. Further experiments show it can block the high-conductance calcium-activated potassium (BK(Ca)) channel in a concentration-dependent manner with an IC(50) of 34.4 nM and a Hill coefficient of 1.02, which suggests that only a single natrin molecule is required to bind an ion channel to block BK(Ca) current. The crystal structure of natrin displaying two domains in tandem shows its cysteine-rich domain (CRD) has relatively independent flexibility, especially for the C-terminal long loop (loop I) of CRD to participate in the interface of two domains. On the basis of previous studies of CNG channel and L-Ca(2+) channel blockers, and the sequence and structural comparison of natrin and stecrisp, the deviation of the vital loop I of CRD is suggested to contribute to different effects of some CRISPs in protein-protein interaction.
-==About this Structure==
+Blocking effect and crystal structure of natrin toxin, a cysteine-rich secretory protein from Naja atra venom that targets the BKCa channel.,Wang J, Shen B, Guo M, Lou X, Duan Y, Cheng XP, Teng M, Niu L, Liu Q, Huang Q, Hao Q Biochemistry. 2005 Aug 2;44(30):10145-52. PMID:16042391<ref>PMID:16042391</ref>
-XX5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Naja_atra Naja atra] with <scene name='pdbligand=EOH:'>EOH</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XX5 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Purification, partial characterization, crystallization and preliminary X-ray diffraction of two cysteine-rich secretory proteins from Naja atra and Trimeresurus stejnegeri venoms., Tu X, Wang J, Guo M, Zheng D, Teng M, Niu L, Liu Q, Huang Q, Hao Q, Acta Crystallogr D Biol Crystallogr. 2004 Jun;60(Pt 6):1108-11. Epub 2004, May 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15159571 15159571]
+</div>
+<div class="pdbe-citations 1xx5" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Naja atra]]
-[[Category: Single protein]]
+[[Category: Guo M]]
-[[Category: Guo, M.]]
+[[Category: Lou XH]]
-[[Category: Lou, X H.]]
+[[Category: Niu LW]]
-[[Category: Niu, L W.]]
+[[Category: Shen B]]
-[[Category: Shen, B.]]
+[[Category: Teng MK]]
-[[Category: Teng, M K.]]
+[[Category: Wang J]]
-[[Category: Wang, J.]]
-[[Category: EOH]]
-[[Category: crisps]]
-[[Category: naja atra]]
-[[Category: natrin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:59:31 2008''

1xx5

From Proteopedia

Current revision

Crystal Structure of Natrin from Naja atra snake venom

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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