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6qgy

From Proteopedia

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Current revision

Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12

Structural highlights

6qgy is a 4 chain structure with sequence from Escherichia coli O157:H7 and Lama glama. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.509Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BAMA_ECOLI Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. Constitutes, with BamD, the core component of the assembly machinery.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The insertase BamA is an essential protein of the bacterial outer membrane. Its 16-stranded transmembrane beta-barrel contains a lateral gate as a key functional element. This gate is formed by the C-terminal half of the last beta-strand. The BamA barrel was previously found to sample different conformations in aqueous solution, as well as different gate-open, gate-closed, and collapsed conformations in X-ray crystallography and cryo-electron microscopy structures. Here, we report the successful identification of conformation-selective nanobodies that stabilize BamA in specific conformations. While the initial candidate generation and selection protocol was based on established alpaca immunization and phage display selection procedures, the final selection of nanobodies was enhanced by a solution NMR-based screening step to shortlist the targets for crystallization. In this way, three crystal structures of BamA-nanobody complexes were efficiently obtained, showing two types of nanobodies that indeed stabilized BamA in two different conformations, i.e., with open and closed lateral gate, respectively. Then, by correlating the structural data with high resolution NMR spectra, we could for the first time assign the BamA conformational solution ensemble to defined structural states. The new nanobodies will be valuable tools towards understanding the client insertion mechanism of BamA and towards developing improved antibiotics.

Identification of conformation-selective nanobodies against the membrane protein insertase BamA by an integrated structural biology approach.,Kaur H, Hartmann JB, Jakob RP, Zahn M, Zimmermann I, Maier T, Seeger MA, Hiller S J Biomol NMR. 2019 May 9. pii: 10.1007/s10858-019-00250-8. doi:, 10.1007/s10858-019-00250-8. PMID:31073665^[6]

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

References

↑ Doerrler WT, Raetz CR. Loss of outer membrane proteins without inhibition of lipid export in an Escherichia coli YaeT mutant. J Biol Chem. 2005 Jul 29;280(30):27679-87. Epub 2005 Jun 10. PMID:15951436 doi:http://dx.doi.org/M504796200
↑ Werner J, Misra R. YaeT (Omp85) affects the assembly of lipid-dependent and lipid-independent outer membrane proteins of Escherichia coli. Mol Microbiol. 2005 Sep;57(5):1450-9. PMID:16102012 doi:http://dx.doi.org/MMI4775
↑ Malinverni JC, Werner J, Kim S, Sklar JG, Kahne D, Misra R, Silhavy TJ. YfiO stabilizes the YaeT complex and is essential for outer membrane protein assembly in Escherichia coli. Mol Microbiol. 2006 Jul;61(1):151-64. PMID:16824102 doi:http://dx.doi.org/10.1111/j.1365-2958.2006.05211.x
↑ Hagan CL, Kim S, Kahne D. Reconstitution of outer membrane protein assembly from purified components. Science. 2010 May 14;328(5980):890-2. doi: 10.1126/science.1188919. Epub 2010 Apr, 8. PMID:20378773 doi:10.1126/science.1188919
↑ Hagan CL, Kahne D. The reconstituted Escherichia coli Bam complex catalyzes multiple rounds of beta-barrel assembly. Biochemistry. 2011 Sep 6;50(35):7444-6. doi: 10.1021/bi2010784. Epub 2011 Aug 11. PMID:21823654 doi:10.1021/bi2010784
↑ Kaur H, Hartmann JB, Jakob RP, Zahn M, Zimmermann I, Maier T, Seeger MA, Hiller S. Identification of conformation-selective nanobodies against the membrane protein insertase BamA by an integrated structural biology approach. J Biomol NMR. 2019 May 9. pii: 10.1007/s10858-019-00250-8. doi:, 10.1007/s10858-019-00250-8. PMID:31073665 doi:http://dx.doi.org/10.1007/s10858-019-00250-8

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/6qgy"

@@ Line 3: / Line 3: @@
 <StructureSection load='6qgy' size='340' side='right'caption='[[6qgy]], [[Resolution|resolution]] 2.51&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6qgy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QGY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QGY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6qgy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QGY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QGY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</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]] 2.509&#8491;</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=6qgy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qgy OCA], [http://pdbe.org/6qgy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qgy RCSB], [http://www.ebi.ac.uk/pdbsum/6qgy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qgy ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</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=6qgy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qgy OCA], [https://pdbe.org/6qgy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qgy RCSB], [https://www.ebi.ac.uk/pdbsum/6qgy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qgy ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BAMA_ECO57 BAMA_ECO57]] Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. Constitutes, with BamD, the core component of the assembly machinery.[HAMAP-Rule:MF_01430]
+[https://www.uniprot.org/uniprot/BAMA_ECOLI BAMA_ECOLI] Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. Constitutes, with BamD, the core component of the assembly machinery.<ref>PMID:15951436</ref> <ref>PMID:16102012</ref> <ref>PMID:16824102</ref> <ref>PMID:20378773</ref> <ref>PMID:21823654</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 6qgy" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[Bam complex 3D structures|Bam complex 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Escherichia coli O157:H7]]
+[[Category: Lama glama]]
 [[Category: Large Structures]]
-[[Category: Hartmann, J B]]
+[[Category: Hartmann J-B]]
-[[Category: Hiller, S]]
+[[Category: Hiller S]]
-[[Category: Jakob, R P]]
+[[Category: Jakob RP]]
-[[Category: Kaur, H]]
+[[Category: Kaur H]]
-[[Category: Maier, T]]
+[[Category: Maier T]]
-[[Category: Seeger, M]]
+[[Category: Seeger M]]
-[[Category: Zahn, M]]
+[[Category: Zahn M]]
-[[Category: Zimmermann, I]]
+[[Category: Zimmermann I]]
-[[Category: Beta-barrel]]
-[[Category: Membrane protein]]
-[[Category: Outer membrane]]
-[[Category: Protein folding]]
-[[Category: Protein insertion]]
-[[Category: Protein maturation]]

6qgy

From Proteopedia

Current revision

Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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