3pak

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Rat Surfactant Protein A neck and carbohydrate recognition domain (NCRD) complexed with Mannose

Structural highlights

3pak is a 1 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SFTPA_RAT In presence of calcium ions, it binds to surfactant phospholipids and contributes to lower the surface tension at the air-liquid interface in the alveoli of the mammalian lung and is essential for normal respiration.

Publication Abstract from PubMed

Surfactant protein A (SP-A), a C-type lectin, plays an important role in innate lung host defense against inhaled pathogens. Crystallographic SP-A.ligand complexes have not been reported to date, limiting available molecular information about SP-A interactions with microbial surface components. This study describes crystal structures of calcium-dependent complexes of the C-terminal neck and carbohydrate recognition domain of SP-A with d-mannose, d-alpha-methylmannose, and glycerol, which represent subdomains of glycans on pathogen surfaces. Comparison of these complexes with the unliganded SP-A neck and carbohydrate recognition domain revealed an unexpected ligand-associated conformational change in the loop region surrounding the lectin site, one not previously reported for the lectin homologs SP-D and mannan-binding lectin. The net result of the conformational change is that the SP-A lectin site and the surrounding loop region become more compact. The Glu-202 side chain of unliganded SP-A extends out into the solvent and away from the calcium ion; however, in the complexes, the Glu-202 side chain translocates 12.8 A to bind the calcium. The availability of Glu-202, together with positional changes involving water molecules, creates a more favorable hydrogen bonding environment for carbohydrate ligands. The Lys-203 side chain reorients as well, extending outward into the solvent in the complexes, thereby opening up a small cation-friendly cavity occupied by a sodium ion. Binding of this cation brings the large loop, which forms one wall of the lectin site, and the adjacent small loop closer together. The ability to undergo conformational changes may help SP-A adapt to different ligand classes, including microbial glycolipids and surfactant lipids.

Crystallographic Complexes of Surfactant Protein A and Carbohydrates Reveal Ligand-induced Conformational Change.,Shang F, Rynkiewicz MJ, McCormack FX, Wu H, Cafarella TM, Head JF, Seaton BA J Biol Chem. 2011 Jan 7;286(1):757-65. Epub 2010 Nov 3. PMID:21047777^[1]

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

References

↑ Shang F, Rynkiewicz MJ, McCormack FX, Wu H, Cafarella TM, Head JF, Seaton BA. Crystallographic Complexes of Surfactant Protein A and Carbohydrates Reveal Ligand-induced Conformational Change. J Biol Chem. 2011 Jan 7;286(1):757-65. Epub 2010 Nov 3. PMID:21047777 doi:10.1074/jbc.M110.175265

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3pak"

@@ Line 3: / Line 3: @@
 <StructureSection load='3pak' size='340' side='right'caption='[[3pak]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3pak]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PAK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3pak]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PAK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1r13|1r13]], [[1r14|1r14]], [[3paq|3paq]], [[3par|3par]], [[3pbf|3pbf]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Sftp-1, Sftp1, Sftpa, Sftpa1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=3pak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pak OCA], [https://pdbe.org/3pak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pak RCSB], [https://www.ebi.ac.uk/pdbsum/3pak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pak ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SFTPA_RAT SFTPA_RAT]] In presence of calcium ions, it binds to surfactant phospholipids and contributes to lower the surface tension at the air-liquid interface in the alveoli of the mammalian lung and is essential for normal respiration.
+[https://www.uniprot.org/uniprot/SFTPA_RAT SFTPA_RAT] In presence of calcium ions, it binds to surfactant phospholipids and contributes to lower the surface tension at the air-liquid interface in the alveoli of the mammalian lung and is essential for normal respiration.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Buffalo rat]]
 [[Category: Large Structures]]
-[[Category: Cafarella, T M]]
+[[Category: Rattus norvegicus]]
-[[Category: Head, J]]
+[[Category: Cafarella TM]]
-[[Category: McCormack, F X]]
+[[Category: Head J]]
-[[Category: Rynkiewicz, M J]]
+[[Category: McCormack FX]]
-[[Category: Seaton, B A]]
+[[Category: Rynkiewicz MJ]]
-[[Category: Shang, F]]
+[[Category: Seaton BA]]
-[[Category: Wu, H]]
+[[Category: Shang F]]
-[[Category: Collectin]]
+[[Category: Wu H]]
-[[Category: Mannose]]
-[[Category: Sugar binding protein]]

3pak

From Proteopedia

Current revision

Crystal Structure of Rat Surfactant Protein A neck and carbohydrate recognition domain (NCRD) complexed with Mannose

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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