2znf
From Proteopedia
(New page: 200px<br /> <applet load="2znf" size="450" color="white" frame="true" align="right" spinBox="true" caption="2znf" /> '''HIGH-RESOLUTION STRUCTURE OF AN HIV ZINC FI...) |
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| - | [[Image:2znf.gif|left|200px]]<br /> | + | [[Image:2znf.gif|left|200px]]<br /><applet load="2znf" size="350" color="white" frame="true" align="right" spinBox="true" |
| - | <applet load="2znf" size=" | + | |
caption="2znf" /> | caption="2znf" /> | ||
'''HIGH-RESOLUTION STRUCTURE OF AN HIV ZINC FINGERLIKE DOMAIN VIA A NEW NMR-BASED DISTANCE GEOMETRY APPROACH'''<br /> | '''HIGH-RESOLUTION STRUCTURE OF AN HIV ZINC FINGERLIKE DOMAIN VIA A NEW NMR-BASED DISTANCE GEOMETRY APPROACH'''<br /> | ||
==Overview== | ==Overview== | ||
| - | A new method is described for determining molecular structures from NMR | + | A new method is described for determining molecular structures from NMR data. The approach utilizes 2D NOESY back-calculations to generate simulated spectra for structures obtained from distance geometry (DG) computations. Comparison of experimental and back-calculated spectra, including analysis of cross-peak buildup and auto-peak decay with increasing mixing time, provides a quantitative measure of the consistence between the experimental data and generated structures and allows for use of tighter interproton distance constraints. For the first time, the "goodness" of the generated structures is evaluated on the basis of their consistence with the actual experimental data rather than on the basis of consistence with other generated structures. This method is applied to the structure determination of an 18-residue peptide with an amino acid sequence comprising the first zinc fingerlike domain from the gag protein p55 of HIV. This is the first structure determination to atomic resolution for a retroviral zinc fingerlike complex. The peptide [Zn(p55F1)] exhibits a novel folding pattern that includes type I and type II NH-S tight turns and is stabilized both by coordination of the three Cys and one His residues to zinc and by extensive internal hydrogen bonding. The backbone folding is significantly different from that of a "classical" DNA-binding zinc finger. Residues C(1)-F(2)-N(3)-C(4)-G(5)-K(6) fold in a manner virtually identical with the folding observed by X-ray crystallography for related residues in the iron domain of rubredoxin; superposition of all main-chain and Cys side-chain atoms of residues C(1)-K(6) of Zn(p55F1) onto residues C(6)-Y(11) and C(39)-V(44) of rubredoxin gives RMSDs of 0.46 and 0.35 A, respectively. The side chains of conservatively substituted Phe and Ile residues implicated in genomic RNA recognition form a hydrophobic patch on the peptide surface. |
==About this Structure== | ==About this Structure== | ||
| - | 2ZNF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 2ZNF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNF OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Human immunodeficiency virus 1]] | [[Category: Human immunodeficiency virus 1]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Hare, D | + | [[Category: Hare, D R.]] |
[[Category: Kim, B.]] | [[Category: Kim, B.]] | ||
| - | [[Category: South, T | + | [[Category: South, T L.]] |
| - | [[Category: Summers, M | + | [[Category: Summers, M F.]] |
[[Category: ZN]] | [[Category: ZN]] | ||
[[Category: aids-related virus gag polyprotein]] | [[Category: aids-related virus gag polyprotein]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:01:49 2008'' |
Revision as of 17:01, 21 February 2008
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HIGH-RESOLUTION STRUCTURE OF AN HIV ZINC FINGERLIKE DOMAIN VIA A NEW NMR-BASED DISTANCE GEOMETRY APPROACH
Overview
A new method is described for determining molecular structures from NMR data. The approach utilizes 2D NOESY back-calculations to generate simulated spectra for structures obtained from distance geometry (DG) computations. Comparison of experimental and back-calculated spectra, including analysis of cross-peak buildup and auto-peak decay with increasing mixing time, provides a quantitative measure of the consistence between the experimental data and generated structures and allows for use of tighter interproton distance constraints. For the first time, the "goodness" of the generated structures is evaluated on the basis of their consistence with the actual experimental data rather than on the basis of consistence with other generated structures. This method is applied to the structure determination of an 18-residue peptide with an amino acid sequence comprising the first zinc fingerlike domain from the gag protein p55 of HIV. This is the first structure determination to atomic resolution for a retroviral zinc fingerlike complex. The peptide [Zn(p55F1)] exhibits a novel folding pattern that includes type I and type II NH-S tight turns and is stabilized both by coordination of the three Cys and one His residues to zinc and by extensive internal hydrogen bonding. The backbone folding is significantly different from that of a "classical" DNA-binding zinc finger. Residues C(1)-F(2)-N(3)-C(4)-G(5)-K(6) fold in a manner virtually identical with the folding observed by X-ray crystallography for related residues in the iron domain of rubredoxin; superposition of all main-chain and Cys side-chain atoms of residues C(1)-K(6) of Zn(p55F1) onto residues C(6)-Y(11) and C(39)-V(44) of rubredoxin gives RMSDs of 0.46 and 0.35 A, respectively. The side chains of conservatively substituted Phe and Ile residues implicated in genomic RNA recognition form a hydrophobic patch on the peptide surface.
About this Structure
2ZNF is a Single protein structure of sequence from Human immunodeficiency virus 1 with as ligand. Full crystallographic information is available from OCA.
Reference
High-resolution structure of an HIV zinc fingerlike domain via a new NMR-based distance geometry approach., Summers MF, South TL, Kim B, Hare DR, Biochemistry. 1990 Jan 16;29(2):329-40. PMID:2105740
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