PDBsum entry 1c3d

Complement

PDB id: 1c3d

Contents

Protein chain

294 a.a. *

Ligands

GOL ×5

Waters ×102

* Residue conservation analysis

PDB id:

1c3d

Name:

Complement

Title:

X-ray crystal structure of c3d: a c3 fragment and ligand for complement receptor 2

Structure:

C3d. Chain: a. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell_line: bl21. Cellular_location: serum. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.188 R-free: 0.230

Authors:

B.Nagar,R.G.Jones,R.J.Diefenbach,D.E.Isenman,J.M.Rini

Key ref:

B.Nagar et al. (1998). X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2. Science, 280, 1277-1281. PubMed id: 9596584 DOI: 10.1126/science.280.5367.1277

Date:

19-May-98 Release date: 07-Oct-98

Protein chain

P01024  (CO3_HUMAN) -  Complement C3 from Homo sapiens

Seq: 1663 a.a.

Struc: 294 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1126/science.280.5367.1277

Science 280:1277-1281 (1998)

PubMed id: 9596584

X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2.

B.Nagar, R.G.Jones, R.J.Diefenbach, D.E.Isenman, J.M.Rini.

ABSTRACT

Activation and covalent attachment of complement component C3 to pathogens is the key step in complement-mediated host defense. Additionally, the antigen-bound C3d fragment interacts with complement receptor 2 (CR2; also known as CD21) on B cells and thereby contributes to the initiation of an acquired humoral response. The x-ray crystal structure of human C3d solved at 2.0 angstroms resolution reveals an alpha-alpha barrel with the residues responsible for thioester formation and covalent attachment at one end and an acidic pocket at the other. The structure supports a model whereby the transition of native C3 to its functionally active state involves the disruption of a complementary domain interface and provides insight into the basis for the interaction between C3d and CR2.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from the AAAs: Science (1998, 280, 1277-1281) copyright 1998.

Figures were selected by an automated process.