PDBsum entry 1ntj

Immune system

PDB id: 1ntj

Contents

Protein chain

320 a.a.* *

* Residue conservation analysis

* C-alpha coords only

PDB id:

1ntj

Name:

Immune system

Title:

Model of rat crry determined by solution scattering, curve fitting and homology modelling

Structure:

Complement receptor related protein. Chain: a. Fragment: scr-1 to scr-5. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: pichia pastoris. Expression_system_taxid: 4922

Authors:

M.Aslam,J.M.Guthridge,B.K.Hack,R.J.Quigg,V.M.Holers,S.J.Perkins

Key ref:

M.Aslam et al. (2003). The extended multidomain solution structures of the complement protein Crry and its chimeric conjugate Crry-Ig by scattering, analytical ultracentrifugation and constrained modelling: implications for function and therapy. J Mol Biol, 329, 525-550. PubMed id: 12767833 DOI: 10.1016/S0022-2836(03)00492-3

Date:

30-Jan-03 Release date: 03-Feb-04

Protein chain

Q63135  (CR1L_RAT) -  Complement component receptor 1-like protein from Rattus norvegicus

Seq: 559 a.a.

Struc: 320 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/S0022-2836(03)00492-3

J Mol Biol 329:525-550 (2003)

PubMed id: 12767833

The extended multidomain solution structures of the complement protein Crry and its chimeric conjugate Crry-Ig by scattering, analytical ultracentrifugation and constrained modelling: implications for function and therapy.

M.Aslam, J.M.Guthridge, B.K.Hack, R.J.Quigg, V.M.Holers, S.J.Perkins.

ABSTRACT

Complement receptor-related gene/protein y (Crry) is a cell membrane-bound regulator of complement activation found in mouse and rat. Crry contains only short complement/consensus repeat (SCR) domains. X-ray and neutron scattering was performed on recombinant rat Crry containing the first five SCR domains (rCrry) and mouse Crry with five SCR domains conjugated to the Fc fragment of mouse IgG1 (mCrry-Ig) in order to determine their solution structures at medium resolution. The radius of gyration R(G) of rCrry was determined to be 4.9-5.0 nm, and the R(G) of the cross-section was 1.2-1.5 nm as determined by X-ray and neutron scattering. The R(G) of mCrry-Ig was 6.6-6.7 nm, and the R(G) of the cross-section were 2.3-2.4 nm and 1.3 nm. The maximum dimension of rCrry was 18 nm and that for mCrry-Ig was 26 nm. The neutron data indicated that rCrry and mCrry-Ig have molecular mass values of 45,000 Da and 140,000 Da, respectively, in agreement with their sequences, and sedimentation equilibrium data supported these determinations. Time-derivative velocity experiments gave sedimentation coefficients of 2.4S for rCrry and 5.4S for mCrry-Ig. A medium-resolution model of rCrry was determined using homology models that were constructed for the first five SCR domains of Crry from known crystal and NMR structures, and linked by randomly generated linker peptide conformations. These trial-and-error calculations revealed a small family of extended rCrry structures that best accounted for the scattering and ultracentrifugation data. These were shorter than the most extended rCrry models as the result of minor bends in the inter-SCR orientations. The mCrry-Ig solution data were modelled starting from a fixed structure for rCrry and the crystal structure of mouse IgG1, and was based on conformational searches of the hinge peptide joining the mCrry and Fc fragments. The best-fit models showed that the two mCrry antennae in mCrry-Ig were extended from the Fc fragment. No preferred orientation of the antennae was identified, and this indicated that the accessibility of the antennae for the molecular targets C4b and C3b was not affected by the covalent link to Fc. A structural comparison between Crry and complement receptor type 1 indicated that the domain arrangement of Crry SCR 1-3 is as extended as that of the CR1 SCR 15-17 NMR structure.

Selected figure(s)

Figure 1.
Figure 1. SCR domain arrangement in rCrry and mCrry-Ig. The location of the presumed N-linked glycosylation sites are denoted by q symbols, and the number of linker residues between adjacent domains is denoted by the numbers next to the linker in question.

Figure 8.
Figure 8. Ribbon views of 20 linker structures seen in crystal and NMR structures of pairs of SCR domains. The most common linker conformations are shown in yellow. Four linker conformations that deviate from the most common ones are denoted by green ribbons and labelled a to d. Four linkers that show less conformational deviations are labelled w to z. The eight residue and three residue linkers are shown in purple and red, respectively. The left-hand view corresponds to the SCR-1 structure of b2GPI, in which the linkers are shown superimposed at the C terminus at Cys58. The right-hand view corresponds to the SCR-2 structure of b2GPI, in which the linkers are superimposed at the N terminus at Cys4.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 329, 525-550) copyright 2003.

Figures were selected by an automated process.