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Metal binding protein
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PDB id
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2di2
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PDB id:
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Metal binding protein
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Title:
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Nmr structure of the HIV-2 nucleocapsid protein
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Structure:
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Nucleocapsid protein p7. Chain: a. Fragment: residus 1-29. Synonym: HIV-2 nucleocapsid protein. Engineered: yes. Mutation: yes
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Source:
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Synthetic: yes. Other_details: this peptide has been chemically synthesized
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NMR struc:
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13 models
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Authors:
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T.Matsui,Y.Kodera,H.Endoh,E.Miyauchi,H.Komatsu,K.Sato, T.Tanaka,T.Kohno,T.Maeda
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Key ref:
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T.Matsui
et al.
(2007).
RNA recognition mechanism of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein.
J Biochem (tokyo),
141,
269-277.
PubMed id:
DOI:
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Date:
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27-Mar-06
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Release date:
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13-Mar-07
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PROCHECK
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Headers
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References
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P18041
(GAG_HV2G1) -
Gag polyprotein
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Seq:
Struc:
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522 a.a.
29 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Gene Ontology (GO) functional annotation
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Biochemical function
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nucleic acid binding
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2 terms
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DOI no:
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J Biochem (tokyo)
141:269-277
(2007)
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PubMed id:
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RNA recognition mechanism of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein.
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T.Matsui,
Y.Kodera,
H.Endoh,
E.Miyauchi,
H.Komatsu,
K.Sato,
T.Tanaka,
T.Kohno,
T.Maeda.
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ABSTRACT
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NCp8 of HIV-2 contains two CCHC-type zinc fingers connected by a linker, and is
involved in many critical steps of the virus life cycle. It was previously shown
that the first zinc finger flanked by the linker is the minimal active domain
for specific binding to viral RNA. In our previous study, we determined the
three-dimensional structure of NCp8-f1, including the minimal active domain, and
found that a hydrogen bond between Asn(11) N(delta)H and Arg(27) O stabilized
the conformation of the linker in the vicinity of the zinc finger [Kodera et al.
(1998) Biochemistry 37, 17704-17713]. In this study, RNA binding activities of
NCp8-f1 and three types of its mutant peptides were analysed by native PAGE
assay. The activity and three-dimensional structure of NCp8-f1/N11A, in which
alanine is substituted for Asn(11) thereby affecting the conformation of the
linker, was analyzed and compared with those of NCp8-f1. We demonstrated that
the existence of Arg(4) and/or Lys(5) and Arg(26) and/or Arg(27) were necessary
for binding RNA. Furthermore, the linker's flexible orientation, which is
controlled by the hydrogen bond between Asn(11) N(delta)H and Arg(27) O, appears
to be a structural basis for NCp8 existing as a multi-functional protein.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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H.Hashimoto,
K.Hara,
A.Hishiki,
S.Kawaguchi,
N.Shichijo,
K.Nakamura,
S.Unzai,
Y.Tamaru,
T.Shimizu,
and
M.Sato
(2010).
Crystal structure of zinc-finger domain of Nanos and its functional implications.
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EMBO Rep, 11,
848-853.
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
