PDBsum entry 1cb6

Iron transport

PDB id: 1cb6

Contents

Protein chain

691 a.a. *

Metals

_CL ×2

Waters ×357

* Residue conservation analysis

PDB id:

1cb6

Name:

Iron transport

Title:

Structure of human apolactoferrin at 2.0 a resolution.

Structure:

Lactotransferrin. Chain: a. Fragment: unp residues 20-710. Synonym: lactoferrin,growth-inhibiting protein 12,talalactoferrin. Ec: 3.4.21.-

Source:

Homo sapiens. Human. Organism_taxid: 9606. Organ: breast. Secretion: milk

Resolution:

2.00Å R-factor: 0.201 R-free: 0.286

Authors:

G.B.Jameson,B.F.Anderson,G.E.Norris,D.H.Thomas,E.N.Baker

Key ref:

G.B.Jameson et al. (1998). Structure of human apolactoferrin at 2.0 A resolution. Refinement and analysis of ligand-induced conformational change. Acta Crystallogr D Biol Crystallogr, 54, 1319-1335. PubMed id: 10089508 DOI: 10.1107/S0907444998004417

Date:

01-Mar-99 Release date: 12-Mar-99

Protein chain

P02788  (TRFL_HUMAN) -  Lactotransferrin from Homo sapiens

Seq: 710 a.a.

Struc: 691 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.- - ?????

DOI no: 10.1107/S0907444998004417

Acta Crystallogr D Biol Crystallogr 54:1319-1335 (1998)

PubMed id: 10089508

Structure of human apolactoferrin at 2.0 A resolution. Refinement and analysis of ligand-induced conformational change.

G.B.Jameson, B.F.Anderson, G.E.Norris, D.H.Thomas, E.N.Baker.

ABSTRACT

The three-dimensional structure of a form of human apolactoferrin, in which one lobe (the N-lobe) has an open conformation and the other lobe (the C-lobe) is closed, has been refined at 2.0 A resolution. The refinement, by restrained least-squares methods, used synchrotron radiation X-ray diffraction data combined with a lower resolution diffractometer data set. The final refined model (5346 protein atoms from residues 1-691, two Cl- ions and 363 water molecules) gives a crystallographic R factor of 0.201 (Rfree = 0. 286) for all 51305 reflections in the resolution range 10.0-2.0 A. The conformational change in the N-lobe, which opens up the binding cleft, involves a 54 degrees rotation of the N2 domain relative to the N1 domain. This also results in a small reorientation of the two lobes relative to one another with a further approximately 730 A2 of surface area being buried as the N2 domain contacts the C-lobe and the inter-lobe helix. These new contacts also involve the C-terminal helix and provide a mechanism through which the conformational and iron-binding status of the N-lobe can be signalled to the C-lobe. Surface-area calculations indicate a fine balance between open and closed forms of lactoferrin, which both have essentially the same solvent-accessible surface. Chloride ions are bound in the anion-binding sites of both lobes, emphasizing the functional significance of these sites. The closed configuration of the C-lobe, attributed in part to weak stabilization by crystal packing interactions, has important implications for lactoferrin dynamics. It shows that a stable closed structure, essentially identical to that of the iron-bound form, can be formed in the absence of iron binding.

Selected figure(s)

Figure 6.
Figure 6 (a) Conformational changes that result from movement of the N1 and N2 domains, with ApoLf in blue and Fe[2]Lf in orange. (a) Movement of the loop 137-143 to contact residues 334-337 at theN-terminus of the connecting helix in ApoLf. (b) Conformational differences in the 302-303 peptide and the neighbouring region 287-291. Here the N1 domains of ApoLf (blue), human Fe[2]Lf (orange), bovine Fe[2]Lf (magenta) and the ferric N-terminal half-molecules of human transferrin (red) and human lactoferrin (green) are superimposed. (c) Conformational changes in the side chain of Arg89 that maintain the Arg89-Glu211 salt bridge in ApoLf (blue) and Fe[2]Lf (orange). (d) Side-chain interactions linking helix 3, helix 11 and helix 5 in Fe[2]Lf. (e) Helix movements and changes in side-chain hydrogen bonding in the transition between Fe[2]Lf (orange helices, yellow side chains) and ApoLf (blue helices, blue side chains).

Figure 8.
Figure 8 Changes in the solvent-accessible surface (a) for the N1/N2 interface in the lactoferrin N-lobe and (b) for the N-lobe/C-lobe interface. In each case the open ApoLf structure is on the left and the closed Fe[2]Lf structure is on the right. Surface area buried between N1 and N2 domains is much larger in the closed form (a, right panel). On the other hand, the surface area buried between the N- and C-lobes is greater in the open form (b, left panel). In (a) the N2 domain surface is white and the N1 domain surface is magenta; only the portions of the surface that come into contact (within 4.5 Å) are shown. The much larger contact surface for the closed form (a, right) arises because the N2 domain (upper) rotates over the N1 domain (lower) about an axis running left to right across the page. In (b) the N-lobe surface is magenta and the C-lobe surface is white. The greater contact area between the lobes in the open form (left) arises because of the movement of the N2 domain (upper, left) up against the connecting helix (H12) and the C-lobe. The rotation axis is approximately about an axis running top to bottom across the page. Figure prepared with GRASP (Nicholls et al., 1993[Nicholls, A., Bharadwaj, R. & Honig, B. (1993). Biophys. J. 64, 166.]).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1998, 54, 1319-1335) copyright 1998.

Figures were selected by the author.