2znf: Difference between revisions
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==HIGH-RESOLUTION STRUCTURE OF AN HIV ZINC FINGERLIKE DOMAIN VIA A NEW NMR-BASED DISTANCE GEOMETRY APPROACH== | |||
<StructureSection load='2znf' size='340' side='right'caption='[[2znf]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2znf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZNF FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2znf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znf OCA], [https://pdbe.org/2znf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2znf RCSB], [https://www.ebi.ac.uk/pdbsum/2znf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2znf ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q9J188_9HIV1 Q9J188_9HIV1] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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<ref>PMID:2105740</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2znf" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Gag polyprotein 3D structures|Gag polyprotein 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Human immunodeficiency virus 1]] | [[Category: Human immunodeficiency virus 1]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Hare | [[Category: Hare DR]] | ||
[[Category: Kim | [[Category: Kim B]] | ||
[[Category: South | [[Category: South TL]] | ||
[[Category: Summers | [[Category: Summers MF]] | ||
Latest revision as of 04:18, 28 December 2023
HIGH-RESOLUTION STRUCTURE OF AN HIV ZINC FINGERLIKE DOMAIN VIA A NEW NMR-BASED DISTANCE GEOMETRY APPROACHHIGH-RESOLUTION STRUCTURE OF AN HIV ZINC FINGERLIKE DOMAIN VIA A NEW NMR-BASED DISTANCE GEOMETRY APPROACH
Structural highlights
FunctionPublication Abstract from PubMedA 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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