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2znf

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HIGH-RESOLUTION STRUCTURE OF AN HIV ZINC FINGERLIKE DOMAIN VIA A NEW NMR-BASED DISTANCE GEOMETRY APPROACH

Structural highlights

2znf is a 1 chain structure with sequence from Human immunodeficiency virus 1. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9J188_9HIV1

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^[1]

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

References

↑ Summers MF, South TL, Kim B, Hare DR. High-resolution structure of an HIV zinc fingerlike domain via a new NMR-based distance geometry approach. Biochemistry. 1990 Jan 16;29(2):329-40. PMID:2105740

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/2znf"

@@ Line 1: / Line 1: @@
 ==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]], [[NMR_Ensembles_of_Models | 16 NMR models]]' scene=''>
+<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 [http://en.wikipedia.org/wiki/9hiv1 9hiv1]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZNF FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</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='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=2znf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2znf OCA], [http://pdbe.org/2znf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2znf RCSB], [http://www.ebi.ac.uk/pdbsum/2znf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2znf ProSAT]</span></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 ==
-[[http://www.uniprot.org/uniprot/GAG_HV1LW GAG_HV1LW]] Matrix protein p17 targets Gag and Gag-Pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex. Implicated in the release from host cell mediated by Vpu.  Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex.  Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers.  p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1 (By similarity).
+[https://www.uniprot.org/uniprot/Q9J188_9HIV1 Q9J188_9HIV1]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 21: @@
 ==See Also==
-*[[Gag polyprotein|Gag polyprotein]]
+*[[Gag polyprotein 3D structures|Gag polyprotein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Hare, D R]]
+[[Category: Human immunodeficiency virus 1]]
-[[Category: Kim, B]]
+[[Category: Large Structures]]
-[[Category: South, T L]]
+[[Category: Hare DR]]
-[[Category: Summers, M F]]
+[[Category: Kim B]]
-[[Category: Aids-related virus gag polyprotein]]
+[[Category: South TL]]
-[[Category: Viral protein]]
+[[Category: Summers MF]]

2znf

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Current revision

HIGH-RESOLUTION STRUCTURE OF AN HIV ZINC FINGERLIKE DOMAIN VIA A NEW NMR-BASED DISTANCE GEOMETRY APPROACH

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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