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PDBsum entry 1n7d

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Lipid transport PDB id
1n7d
Jmol
Contents
Protein chain
639 a.a. *
Ligands
NAG-NAG-BMA-MAN-
MAN
NAG-NAG-BMA-MAN
KEG ×3
Metals
_CA ×8
* Residue conservation analysis

References listed in PDB file
Key reference
Title Structure of the ldl receptor extracellular domain at endosomal ph.
Authors G.Rudenko, L.Henry, K.Henderson, K.Ichtchenko, M.S.Brown, J.L.Goldstein, J.Deisenhofer.
Ref. Science, 2002, 298, 2353-2358. [DOI no: 10.1126/science.1078124]
PubMed id 12459547
Abstract
The low-density lipoprotein receptor mediates cholesterol homeostasis through endocytosis of lipoproteins. It discharges its ligand in the endosome at pH < 6. In the crystal structure at pH = 5.3, the ligand-binding domain (modules R2 to R7) folds back as an arc over the epidermal growth factor precursor homology domain (the modules A, B, beta propeller, and C). The modules R4 and R5, which are critical for lipoprotein binding, associate with the beta propeller via their calcium-binding loop. We propose a mechanism for lipoprotein release in the endosome whereby the beta propeller functions as an alternate substrate for the ligand-binding domain, binding in a calcium-dependent way and promoting lipoprotein release.
Figure 2.
Fig. 2. Two monomers stabilized by tungsten clusters; the ligand-binding domains have been labeled R2 to R7 and R2* to R7*, respectively. The linkers between R4 and R5 and R4* and R5* meet at a crystallographic twofold axis. At a distance below, a cluster (center) sits on the twofold as well.
Figure 3.
Fig. 3. Interface formed between R4, R5, and propeller. Residues discussed in the text are shown and labeled except for Ser191, which was omitted for clarity. R4, magenta trace; R5, red trace; propeller, cyan trace; and calcium ions, maroon spheres.
The above figures are reprinted by permission from the AAAs: Science (2002, 298, 2353-2358) copyright 2002.
Added reference #1*
Title 'MAD'ly phasing the extracellular domain of the LDL receptor: a medium-sized protein, large tungsten clusters and multiple non-isomorphous crystals.
Authors G.Rudenko, L.Henry, C.Vonrhein, G.Bricogne, J.Deisenhofer.
Ref. Acta Crystallogr D Biol Crystallogr, 2003, 59, 1978-1986. [DOI no: 10.1107/S0907444903021383]
PubMed id 14573953
Full text Abstract
Figure 1.
Figure 1 Modular organization of the extracellular region of LDL-R. The `ligand-binding domain' and the `EGF precursor homology domain' are indicated. The cysteine-rich repeats R1-R7 are separated by short linkers of approximately four residues, with the exception of R4 and R5 which are separated by a 12-residue linker. The EGF-like repeats A, B and C flank the -propeller domain.
Figure 5.
Figure 5 Improvement of the electron-density map before (a) and after (b) sharpening the data, as discussed in the text. Examples are shown for residues Trp144, Glu219 and Asp299 (contoured at 1 ) and the 12-tungstophosphate cluster (contoured at 3.5 ).
The above figures are reproduced from the cited reference with permission from the IUCr
*Note, "added" references are those not in the PDB file but which have either been obtained from the journal or suggested by the author(s).
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