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PDBsum entry 1qqf
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Immune system
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PDB id
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1qqf
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structure at 1.44 a resolution of an n-Terminally truncated form of the rat serum complement c3d fragment.
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Authors
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G.Zanotti,
A.Bassetto,
R.Battistutta,
C.Folli,
P.Arcidiaco,
M.Stoppini,
R.Berni.
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Ref.
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Biochim Biophys Acta, 2000,
1478,
232-238.
[DOI no: ]
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PubMed id
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Abstract
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Complement component C3 plays a key role in the complement-mediated immune
defence, and occupies a central position within the complement cascade system.
One of its degradation products, C3dg, was purified from rat serum and
crystallised in two different crystal forms as N-terminally truncated fragment.
Despite the truncation and the lack of a significant portion of the N-terminus
as compared to C3d, the structure of the fragment is highly similar to that of
recombinant human C3d (Nagar et al., Science 280 (1998) 1277-1281). Structural
details of the reactive site have been obtained, suggesting a possible mode of
thioester bond formation between Cys-1010 and Gln-1013 and thioester bond
cleavage in the transacylation reaction involving His-1126. The truncation at
the N-terminus of C3d leads to the exposure of a surface of the molecule that
favours dimerisation, so that in both crystal forms, the fragment is present as
a dimer, with monomers related by a two-fold axis.
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Secondary reference #1
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Title
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X-Ray crystal structure of c3d: a c3 fragment and ligand for complement receptor 2.
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Authors
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B.Nagar,
R.G.Jones,
R.J.Diefenbach,
D.E.Isenman,
J.M.Rini.
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Ref.
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Science, 1998,
280,
1277-1281.
[DOI no: ]
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PubMed id
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Figure 2.
Fig. 2. Sequence conservation of C3d. (A) Multiple sequence
alignment of selected species of C3d and human C4d (B isotype)
(21). Residues shaded in yellow are at least 90% buried in the^
C3d structure, and those shaded in red are residues composing
the contiguous surface patch labeled in (B). Numbers correspond^
to the degree of conservation in C3d sequences only: 0 (not
conserved) to A (highly conserved), as determined by the program
AMAS (32). In human C4d, approximately 75% of the core residues,
as well as the putative domain interface residues, are highly
conserved^ [a conservation index (cons. index) of 7 or higher
when included^ in the AMAS calculation], which suggests that it
will adopt a^ similar fold and possess the analogous domain
interface. The helical segments in human C3d are indicated by
blue cylinders. [The figure^ was prepared with ALSCRIPT (35).]
(B) Mapping of residue^ conservation as determined in (A) onto
the surface of C3d; white^ (not conserved) to progressively
darker red (highly conserved). [The figure was prepared with
GRASP (36).] The conserved patch includes most of the surface
apolar residues shown in Fig. 1C.
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Figure 3.
Fig. 3. Stereo view of an electrostatic surface rendition of
C3d, showing the acidic pocket on the concave end of the
molecule. Acidic^ and basic residues are colored red and blue,
respectively. Labeled^ are the surface-exposed residues that
form the pocket. The contour level is at ±10 kT.
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The above figures are
reproduced from the cited reference
with permission from the AAAs
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