PDBsum entry 2q7z

Immune system

PDB id

2q7z

Contents

			Protein chain

					1931 a.a.*

* C-alpha coords only

References listed in PDB file

Key reference

Title

The partly folded back solution structure arrangement of the 30 scr domains in human complement receptor type 1 (cr1) permits access to its c3b and c4b ligands.

Authors

P.B.Furtado, C.Y.Huang, D.Ihyembe, R.A.Hammond, H.C.Marsh, S.J.Perkins.

Ref.

J Mol Biol, 2008, 375, 102-118. [DOI no: 10.1016/j.jmb.2007.09.085]

PubMed id

18028942

Abstract

Human complement receptor type 1 (CR1, CD35) is a type I membrane-bound glycoprotein that belongs to the regulators of complement activity (RCA) family. The extra-cellular component of CR1 is comprised of 30 short complement regulator (SCR) domains, whereas complement receptor type 2 (CR2) has 15 SCR domains and factor H (FH) has 20 SCR domains. The domain arrangement of a soluble form of CR1 (sCR1) was studied by X-ray scattering and analytical ultracentrifugation. The radius of gyration R(G) of sCR1 of 13.4(+/-1.1) nm is not much greater than those for CR2 and FH, and its R(G)/R(0) anisotropy ratio is 3.76, compared to ratios of 3.67 for FH and 4.1 for CR2. Unlike CR2, but similar to FH, two cross-sectional R(G) ranges were identified that gave R(XS) values of 4.7(+/-0.2) nm and 1.2(+/-0.7) nm, respectively, showing that the SCR domains adopt a range of conformations including folded-back ones. The distance distribution function P(r) showed that the most commonly occurring distance in sCR1 is at 11.5 nm. Its maximum length of 55 nm is less than double those for CR2 or FH, even though sCR1 has twice the number of SCR domains compared to CR2 Sedimentation equilibrium experiments gave a mean molecular weight of 235 kDa for sCR1. This is consistent with the value of 245 kDa calculated from its composition including 14 N-linked oligosaccharide sites, and confirmed that sCR1 is a monomer in solution. Sedimentation velocity experiments gave a sedimentation coefficient of 5.8 S. From this, the frictional ratio (f/f(0)) of sCR1 was calculated to be 2.29, which is greater than those of 1.96 for CR2 and 1.77 for FH. The constrained scattering modelling of the sCR1 solution structure starting from homologous SCR domain structures generated 5000 trial conformationally randomised models, 43 of which gave good scattering fits to show that sCR1 has a partly folded-back structure. We conclude that the inter-SCR linkers show structural features in common with those in FH, but differ from those in CR2, and the SCR arrangement in CR1 will permit C3b or C4b to access all three ligand sites.



	Figure 1. Figure 1. Organisation of the 30 SCR domains in sCR1. (a) Schematic diagram showing the main features in the 30 SCR domains. The long homologous repeats LHR-A to LHR-D are indicated in bracketed ranges. sCR1 contains 25 putative N-linked oligosaccharide sites (• and ○), of which the 14 sites used for the modelling of sCR1 are shown by ○. The six sites underneath the cartoon schematically correspond to those adjacent to β-strand β7. The three binding sites for C3b and C4b at the start of LHR-A, LHR-B and LHR-C are also indicated. (b) Sequence alignment of the 30 SCR domains in sCR1. Dashes are used to preserve the alignment. The SCR sequence numbering of the mature polypeptide (in brackets) is from residue 1 at the start of the signal peptide (not shown). The four conserved Cys residues (denoted C1–C4) and the conserved Trp residue are highlighted in red. The inter-SCR linker sequences start after the last Cys residue (C4) and end at the first Cys residue (C1) in each SCR and are shown in green. The Thr1876Ile substitution in SCR-29 is shown in blue (Materials and Methods). The six most frequently conserved β-strands observed in the SCR models are represented by grey shaded residues in the alignment according to the DSSP analyses, and are labelled β2 and β4 to β8 to follow previous conventions (see the text). The locations of the 25 putative N-linked oligosaccharide sites are shown in green and yellow when these were used in the sCR1 models, and in red and yellow when these were not used.		Figure 6. Figure 6. Sedimentation velocity analyses of sCR1 using the SEDFIT c(s) method. Boundary fits of the sedimentation scans are shown for (a) interference and (b) absorbance data at 0.21 mg/ml at a rotor speed of 25,000 r.p.m. Only every fifth scan of the 200 interference and absorbance scans are shown for clarity. The position of the major sedimentation species in the c(s) distribution plots for (c) interference and (d) for absorbance data is arrowed.

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