4blf: Difference between revisions

Latest revision as of 11:01, 9 May 2024

Variable internal flexibility characterizes the helical capsid formed by Agrobacterium VirE2 protein on single-stranded DNA.

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Structural highlights

4blf is a 1 chain structure with sequence from Agrobacterium tumefaciens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 20Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VIRE2_AGRFC Involved in DNA transformation; mediates the nuclear uptake of single-stranded DNA copies of the transferred DNA (T-DNA) element. Binds single-stranded but not double-stranded DNA regardless of nucleotide sequence composition.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Agrobacterium is known for gene transfer to plants. In addition to a linear ssDNA oligonucleotide, Agrobacterium tumefaciens secretes an abundant ssDNA-binding effector, VirE2. In many ways VirE2 adapts the conjugation mechanism to transform the eukaryotic host. The crystal structure of VirE2 shows two compact domains joined by a flexible linker. Bound to ssDNA, VirE2 forms an ordered solenoidal shell, or capsid known as the T-complex. Here, we present a three-dimensional reconstruction of the VirE2-ssDNA complex using cryo-electron microscopy and iterative helical real-space reconstruction. High-resolution refinement was not possible due to inherent heterogeneity in the protein structure. By a combination of computational modeling, chemical modifications, mass spectroscopy, and electron paramagnetic resonance, we found that the N-terminal domain is tightly constrained by both tangential and longitudinal links, while the C terminus is weakly constrained. The quaternary structure is thus rigidly assembled while remaining locally flexible. This flexibility may be important in accommodating substrates without sequence specificity.

Variable Internal Flexibility Characterizes the Helical Capsid Formed by Agrobacterium VirE2 Protein on Single-Stranded DNA.,Bharat TA, Zbaida D, Eisenstein M, Frankenstein Z, Mehlman T, Weiner L, Sorzano CO, Barak Y, Albeck S, Briggs JA, Wolf SG, Elbaum M Structure. 2013 Jun 11. pii: S0969-2126(13)00157-3. doi:, 10.1016/j.str.2013.04.027. PMID:23769668^[4]

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

References

↑ Tzfira T, Vaidya M, Citovsky V. Increasing plant susceptibility to Agrobacterium infection by overexpression of the Arabidopsis nuclear protein VIP1. Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10435-40. Epub 2002 Jul 17. PMID:12124400 doi:10.1073/pnas.162304099
↑ Citovsky V, DE Vos G, Zambryski P. Single-Stranded DNA Binding Protein Encoded by the virE Locus of Agrobacterium tumefaciens. Science. 1988 Apr 22;240(4851):501-4. PMID:17784072 doi:10.1126/science.240.4851.501
↑ Zupan JR, Citovsky V, Zambryski P. Agrobacterium VirE2 protein mediates nuclear uptake of single-stranded DNA in plant cells. Proc Natl Acad Sci U S A. 1996 Mar 19;93(6):2392-7. PMID:8637884
↑ Bharat TA, Zbaida D, Eisenstein M, Frankenstein Z, Mehlman T, Weiner L, Sorzano CO, Barak Y, Albeck S, Briggs JA, Wolf SG, Elbaum M. Variable Internal Flexibility Characterizes the Helical Capsid Formed by Agrobacterium VirE2 Protein on Single-Stranded DNA. Structure. 2013 Jun 11. pii: S0969-2126(13)00157-3. doi:, 10.1016/j.str.2013.04.027. PMID:23769668 doi:10.1016/j.str.2013.04.027

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Tzfira T, Vaidya M, Citovsky V. Increasing plant susceptibility to Agrobacterium infection by overexpression of the Arabidopsis nuclear protein VIP1. Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10435-40. Epub 2002 Jul 17. PMID:12124400 doi:10.1073/pnas.162304099

[2] Citovsky V, DE Vos G, Zambryski P. Single-Stranded DNA Binding Protein Encoded by the virE Locus of Agrobacterium tumefaciens. Science. 1988 Apr 22;240(4851):501-4. PMID:17784072 doi:10.1126/science.240.4851.501

[3] Zupan JR, Citovsky V, Zambryski P. Agrobacterium VirE2 protein mediates nuclear uptake of single-stranded DNA in plant cells. Proc Natl Acad Sci U S A. 1996 Mar 19;93(6):2392-7. PMID:8637884

[4] Bharat TA, Zbaida D, Eisenstein M, Frankenstein Z, Mehlman T, Weiner L, Sorzano CO, Barak Y, Albeck S, Briggs JA, Wolf SG, Elbaum M. Variable Internal Flexibility Characterizes the Helical Capsid Formed by Agrobacterium VirE2 Protein on Single-Stranded DNA. Structure. 2013 Jun 11. pii: S0969-2126(13)00157-3. doi:, 10.1016/j.str.2013.04.027. PMID:23769668 doi:10.1016/j.str.2013.04.027

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@@ Line 3: / Line 3: @@
 <SX load='4blf' size='340' side='right' viewer='molstar' caption='[[4blf]], [[Resolution|resolution]] 20.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4blf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BLF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4blf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BLF FirstGlance]. <br>
-</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=4blf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4blf OCA], [https://pdbe.org/4blf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4blf RCSB], [https://www.ebi.ac.uk/pdbsum/4blf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4blf ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 20&#8491;</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=4blf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4blf OCA], [https://pdbe.org/4blf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4blf RCSB], [https://www.ebi.ac.uk/pdbsum/4blf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4blf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/VIRE2_AGRT5 VIRE2_AGRT5]] Involved in DNA transformation; mediates the nuclear uptake of single-stranded DNA copies of the transferred DNA (T-DNA) element. Binds single-stranded but not double-stranded DNA regardless of nucleotide sequence composition.<ref>PMID:17784072</ref> <ref>PMID:8637884</ref> <ref>PMID:12124400</ref>
+[https://www.uniprot.org/uniprot/VIRE2_AGRFC VIRE2_AGRFC] Involved in DNA transformation; mediates the nuclear uptake of single-stranded DNA copies of the transferred DNA (T-DNA) element. Binds single-stranded but not double-stranded DNA regardless of nucleotide sequence composition.<ref>PMID:12124400</ref> <ref>PMID:17784072</ref> <ref>PMID:8637884</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 25: @@
 __TOC__
 </SX>
+[[Category: Agrobacterium tumefaciens]]
 [[Category: Large Structures]]
-[[Category: Albeck, S]]
+[[Category: Albeck S]]
-[[Category: Barak, Y]]
+[[Category: Barak Y]]
-[[Category: Bharat, T A.M]]
+[[Category: Bharat TAM]]
-[[Category: Briggs, J A.G]]
+[[Category: Briggs JAG]]
-[[Category: Eisenstein, M]]
+[[Category: Eisenstein M]]
-[[Category: Elbaum, M]]
+[[Category: Elbaum M]]
-[[Category: Frankenstein, Z]]
+[[Category: Frankenstein Z]]
-[[Category: Mehlman, T]]
+[[Category: Mehlman T]]
-[[Category: Sorzano, C O.S]]
+[[Category: Sorzano COS]]
-[[Category: Weiner, L]]
+[[Category: Weiner L]]
-[[Category: Wolf, S G]]
+[[Category: Wolf SG]]
-[[Category: Zbaida, D]]
+[[Category: Zbaida D]]
-[[Category: Agrobacterium]]
-[[Category: Dna binding protein]]
-[[Category: Helical reconstruction]]
-[[Category: Tcomplex]]

4blf: Difference between revisions

Latest revision as of 11:01, 9 May 2024

Variable internal flexibility characterizes the helical capsid formed by Agrobacterium VirE2 protein on single-stranded DNA.

Structural highlights

Function

Publication Abstract from PubMed

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References

Contents

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