6ibq

From Proteopedia

(Difference between revisions)

Current revision

Structure of a nonameric RNA duplex at room temperature in ChipX microfluidic device

Structural highlights

6ibq is a 2 chain structure with sequence from Rattus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.55Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept.

A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography.,de Wijn R, Hennig O, Roche J, Engilberge S, Rollet K, Fernandez-Millan P, Brillet K, Betat H, Morl M, Roussel A, Girard E, Mueller-Dieckmann C, Fox GC, Olieric V, Gavira JA, Lorber B, Sauter C IUCrJ. 2019 Apr 19;6(Pt 3):454-464. doi: 10.1107/S2052252519003622. eCollection, 2019 May 1. PMID:31098026^[1]

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

References

↑ de Wijn R, Hennig O, Roche J, Engilberge S, Rollet K, Fernandez-Millan P, Brillet K, Betat H, Morl M, Roussel A, Girard E, Mueller-Dieckmann C, Fox GC, Olieric V, Gavira JA, Lorber B, Sauter C. A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography. IUCrJ. 2019 Apr 19;6(Pt 3):454-464. doi: 10.1107/S2052252519003622. eCollection, 2019 May 1. PMID:31098026 doi:http://dx.doi.org/10.1107/S2052252519003622

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6ibq"

@@ Line 3: / Line 3: @@
 <StructureSection load='6ibq' size='340' side='right'caption='[[6ibq]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ibq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IBQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IBQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ibq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus Rattus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IBQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IBQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.55&#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=6ibq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ibq OCA], [http://pdbe.org/6ibq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ibq RCSB], [http://www.ebi.ac.uk/pdbsum/6ibq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ibq ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6ibq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ibq OCA], [https://pdbe.org/6ibq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ibq RCSB], [https://www.ebi.ac.uk/pdbsum/6ibq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ibq ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
-The crystal structure of the RNA duplex [r(CGUGAUCG)dC]2 has been solved at a resolution of 0.97 A. The model has been refined to R-work and R-free of 14.88% and 19.54% for 23,838 independent reflections. The base-pairing scheme forces the 5'-rC to be excluded from the helix and to be disordered. In the crystals, the sequence promotes the formation of two GoU wobble pairs that cluster around a crystallographic threefold axis in two different ways. In the first contact type, the GoU pairs are exclusively surrounded by water molecules, whereas in the other contact type, the three amino groups of the guanine residues of the symmetry-related GoU pairs trap a sulfate ion. This work provides the first example of the interaction of a GoU pair with a sulfate ion in a helical context. Despite the negative charge on the polynucleotide backbone, the guanine amino N2 is able to attract negatively charged groups that could, in the folding of complex RNA molecules, belong to a negative phosphodiester group from a neighboring strand and, in a RNA-protein complex, to a negative carboxyl group of an aspartate or glutamate side chain.
+Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept.
-A sulfate pocket formed by three GoU pairs in the 0.97 A resolution X-ray structure of a nonameric RNA.,Masquida B, Sauter C, Westhof E RNA. 1999 Oct;5(10):1384-95. PMID:10573129<ref>PMID:10573129</ref>
+A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography.,de Wijn R, Hennig O, Roche J, Engilberge S, Rollet K, Fernandez-Millan P, Brillet K, Betat H, Morl M, Roussel A, Girard E, Mueller-Dieckmann C, Fox GC, Olieric V, Gavira JA, Lorber B, Sauter C IUCrJ. 2019 Apr 19;6(Pt 3):454-464. doi: 10.1107/S2052252519003622. eCollection, 2019 May 1. PMID:31098026<ref>PMID:31098026</ref>
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
@@ Line 21: / Line 22: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Lorber, B]]
+[[Category: Rattus]]
-[[Category: Olieric, V]]
+[[Category: Lorber B]]
-[[Category: Sauter, C]]
+[[Category: Olieric V]]
-[[Category: Wijn, R de]]
+[[Category: Sauter C]]
-[[Category: Chipx]]
+[[Category: De Wijn R]]
-[[Category: Gou pair]]
-[[Category: Rna]]
-[[Category: Rna duplex]]

6ibq

From Proteopedia

Current revision

Structure of a nonameric RNA duplex at room temperature in ChipX microfluidic device

Structural highlights

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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