1ijq

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Crystal Structure of the LDL Receptor YWTD-EGF Domain Pair

Structural highlights

1ijq is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.5Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

LDLR_HUMAN Defects in LDLR are the cause of familial hypercholesterolemia (FH) [MIM:143890; a common autosomal semi-dominant disease that affects about 1 in 500 individuals. The receptor defect impairs the catabolism of LDL, and the resultant elevation in plasma LDL-cholesterol promotes deposition of cholesterol in the skin (xanthelasma), tendons (xanthomas), and coronary arteries (atherosclerosis).[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [:][32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43]

Function

LDLR_HUMAN Binds LDL, the major cholesterol-carrying lipoprotein of plasma, and transports it into cells by endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated pits. In case of HIV-1 infection, functions as a receptor for extracellular Tat in neurons, mediating its internalization in uninfected cells.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The low-density lipoprotein receptor (LDLR) is the primary mechanism for uptake of cholesterol-carrying particles into cells. The region of the LDLR implicated in receptor recycling and lipoprotein release at low pH contains a pair of calcium-binding EGF-like modules, followed by a series of six YWTD repeats and a third EGF-like module. The crystal structure at 1.5 A resolution of a receptor fragment spanning the YWTD repeats and its two flanking EGF modules reveals that the YWTD repeats form a six-bladed beta-propeller that packs tightly against the C-terminal EGF module, whereas the EGF module that precedes the propeller is disordered in the crystal. Numerous point mutations of the LDLR that result in the genetic disease familial hypercholesterolemia (FH) alter side chains that form conserved packing and hydrogen bonding interactions in the interior and between propeller blades. A second subset of FH mutations are located at the interface between the propeller and the C-terminal EGF module, suggesting a structural requirement for maintaining the integrity of the interdomain interface.

Implications for familial hypercholesterolemia from the structure of the LDL receptor YWTD-EGF domain pair.,Jeon H, Meng W, Takagi J, Eck MJ, Springer TA, Blacklow SC Nat Struct Biol. 2001 Jun;8(6):499-504. PMID:11373616[44]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
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See Also

References

  1. ↑ Leitersdorf E, Hobbs HH, Fourie AM, Jacobs M, van der Westhuyzen DR, Coetzee GA. Deletion in the first cysteine-rich repeat of low density lipoprotein receptor impairs its transport but not lipoprotein binding in fibroblasts from a subject with familial hypercholesterolemia. Proc Natl Acad Sci U S A. 1988 Nov;85(21):7912-6. PMID:3263645
  2. ↑ Leitersdorf E, Van der Westhuyzen DR, Coetzee GA, Hobbs HH. Two common low density lipoprotein receptor gene mutations cause familial hypercholesterolemia in Afrikaners. J Clin Invest. 1989 Sep;84(3):954-61. PMID:2569482 doi:http://dx.doi.org/10.1172/JCI114258
  3. ↑ Davis CG, Lehrman MA, Russell DW, Anderson RG, Brown MS, Goldstein JL. The J.D. mutation in familial hypercholesterolemia: amino acid substitution in cytoplasmic domain impedes internalization of LDL receptors. Cell. 1986 Apr 11;45(1):15-24. PMID:3955657
  4. ↑ Rubinsztein DC, Jialal I, Leitersdorf E, Coetzee GA, van der Westhuyzen DR. Identification of two new LDL-receptor mutations causing homozygous familial hypercholesterolemia in a South African of Indian origin. Biochim Biophys Acta. 1993 Aug 4;1182(1):75-82. PMID:8347689
  5. ↑ Leitersdorf E, Tobin EJ, Davignon J, Hobbs HH. Common low-density lipoprotein receptor mutations in the French Canadian population. J Clin Invest. 1990 Apr;85(4):1014-23. PMID:2318961 doi:http://dx.doi.org/10.1172/JCI114531
  6. ↑ Miyake Y, Tajima S, Funahashi T, Yamamura T, Yamamoto A. A point mutation of low-density-lipoprotein receptor causing rapid degradation of the receptor. Eur J Biochem. 1992 Nov 15;210(1):1-7. PMID:1446662
  7. ↑ Meiner V, Landsberger D, Berkman N, Reshef A, Segal P, Seftel HC, van der Westhuyzen DR, Jeenah MS, Coetzee GA, Leitersdorf E. A common Lithuanian mutation causing familial hypercholesterolemia in Ashkenazi Jews. Am J Hum Genet. 1991 Aug;49(2):443-9. PMID:1867200
  8. ↑ Leitersdorf E, Reshef A, Meiner V, Dann EJ, Beigel Y, van Roggen FG, van der Westhuyzen DR, Coetzee GA. A missense mutation in the low density lipoprotein receptor gene causes familial hypercholesterolemia in Sephardic Jews. Hum Genet. 1993 Mar;91(2):141-7. PMID:8462973
  9. ↑ Lelli N, Garuti R, Pedrazzi P, Ghisellini M, Simone ML, Tiozzo R, Cattin L, Valenti M, Rolleri M, Bertolini S, et al.. A new missense mutation (Cys297-->Phe) of the low density lipoprotein receptor in Italian patients with familial hypercholesterolemia (FHTrieste). Hum Genet. 1994 May;93(5):538-40. PMID:8168830
  10. ↑ Soutar AK, Knight BL, Patel DD. Identification of a point mutation in growth factor repeat C of the low density lipoprotein-receptor gene in a patient with homozygous familial hypercholesterolemia that affects ligand binding and intracellular movement of receptors. Proc Natl Acad Sci U S A. 1989 Jun;86(11):4166-70. PMID:2726768
  11. ↑ Rubinsztein DC, Coetzee GA, Marais AD, Leitersdorf E, Seftel HC, van der Westhuyzen DR. Identification and properties of the proline664-leucine mutant LDL receptor in South Africans of Indian origin. J Lipid Res. 1992 Nov;33(11):1647-55. PMID:1464748
  12. ↑ Koivisto UM, Viikari JS, Kontula K. Molecular characterization of minor gene rearrangements in Finnish patients with heterozygous familial hypercholesterolemia: identification of two common missense mutations (Gly823-->Asp and Leu380-->His) and eight rare mutations of the LDL receptor gene. Am J Hum Genet. 1995 Oct;57(4):789-97. PMID:7573037
  13. ↑ Maruyama T, Miyake Y, Tajima S, Harada-Shiba M, Yamamura T, Tsushima M, Kishino B, Horiguchi Y, Funahashi T, Matsuzawa Y, et al.. Common mutations in the low-density-lipoprotein-receptor gene causing familial hypercholesterolemia in the Japanese population. Arterioscler Thromb Vasc Biol. 1995 Oct;15(10):1713-8. PMID:7583548
  14. ↑ Tricot-Guerber F, Saint-Jore B, Valenti K, Foulon T, Bost M, Hadjian AJ. Identification of a mutation, N543H, in exon 11 of the low-density lipoprotein receptor gene in a French family with familial hypercholesterolemia. Hum Mutat. 1995;6(1):87-8. PMID:7550239 doi:http://dx.doi.org/10.1002/humu.1380060117
  15. ↑ Ekstrom U, Abrahamson M, Sveger T, Lombardi P, Nilsson-Ehle P. An efficient screening procedure detecting six novel mutations in the LDL receptor gene in Swedish children with hypercholesterolemia. Hum Genet. 1995 Aug;96(2):147-50. PMID:7635461
  16. ↑ Leren TP, Solberg K, Rodningen OK, Tonstad S, Ose L. Two novel point mutations in the EGF precursor homology domain of the LDL receptor gene causing familial hypercholesterolemia. Hum Genet. 1995 Aug;96(2):241-2. PMID:7635482
  17. ↑ Giesel J, Holzem G, Oette K. Screening for mutations in exon 4 of the LDL receptor gene in a German population with severe hypercholesterolemia. Hum Genet. 1995 Sep;96(3):301-4. PMID:7649546
  18. ↑ Pereira E, Ferreira R, Hermelin B, Thomas G, Bernard C, Bertrand V, Nassiff H, Mendez del Castillo D, Bereziat G, Benlian P. Recurrent and novel LDL receptor gene mutations causing heterozygous familial hypercholesterolemia in La Habana. Hum Genet. 1995 Sep;96(3):319-22. PMID:7649549
  19. ↑ Gundersen KE, Solberg K, Rodningen OK, Tonstad S, Ose L, Berg K, Leren TP. Two novel missense mutations in the LDL receptor gene causing familial hypercholesterolemia. Clin Genet. 1996 Feb;49(2):85-7. PMID:8740918
  20. ↑ Sundvold H, Solberg K, Tonstad S, Rodningen OK, Ose L, Berg K, Leren TP. A common missense mutation (C210G) in the LDL receptor gene among Norwegian familial hypercholesterolemia subjects. Hum Mutat. 1996;7(1):70-1. PMID:8664907 doi:<70::AID-HUMU12>3.0.CO;2-P 10.1002/(SICI)1098-1004(1996)7:1<70::AID-HUMU12>3.0.CO;2-P
  21. ↑ Webb JC, Sun XM, McCarthy SN, Neuwirth C, Thompson GR, Knight BL, Soutar AK. Characterization of mutations in the low density lipoprotein (LDL)-receptor gene in patients with homozygous familial hypercholesterolemia, and frequency of these mutations in FH patients in the United Kingdom. J Lipid Res. 1996 Feb;37(2):368-81. PMID:9026534
  22. ↑ Peeters AV, Van Gaal LF, du Plessis L, Lombardi MP, Havekes LM, Kotze MJ. Mutational and genetic origin of LDL receptor gene mutations detected in both Belgian and Dutch familial hypercholesterolemics. Hum Genet. 1997 Aug;100(2):266-70. PMID:9254862
  23. ↑ Jensen HK, Jensen TG, Faergeman O, Jensen LG, Andresen BS, Corydon MJ, Andreasen PH, Hansen PS, Heath F, Bolund L, Gregersen N. Two mutations in the same low-density lipoprotein receptor allele act in synergy to reduce receptor function in heterozygous familial hypercholesterolemia. Hum Mutat. 1997;9(5):437-44. PMID:9143924 doi:<437::AID-HUMU10>3.0.CO;2-3 10.1002/(SICI)1098-1004(1997)9:5<437::AID-HUMU10>3.0.CO;2-3
  24. ↑ Day IN, Whittall RA, O'Dell SD, Haddad L, Bolla MK, Gudnason V, Humphries SE. Spectrum of LDL receptor gene mutations in heterozygous familial hypercholesterolemia. Hum Mutat. 1997;10(2):116-27. PMID:9259195 doi:<116::AID-HUMU4>3.0.CO;2-I 10.1002/(SICI)1098-1004(1997)10:2<116::AID-HUMU4>3.0.CO;2-I
  25. ↑ Leren TP, Tonstad S, Gundersen KE, Bakken KS, Rodningen OK, Sundvold H, Ose L, Berg K. Molecular genetics of familial hypercholesterolaemia in Norway. J Intern Med. 1997 Mar;241(3):185-94. PMID:9104431
  26. ↑ Gorski B, Kubalska J, Naruszewicz M, Lubinski J. LDL-R and Apo-B-100 gene mutations in Polish familial hypercholesterolemias. Hum Genet. 1998 May;102(5):562-5. PMID:9654205
  27. ↑ Couture P, Vohl MC, Gagne C, Gaudet D, Torres AL, Lupien PJ, Despres JP, Labrie F, Simard J, Moorjani S. Identification of three mutations in the low-density lipoprotein receptor gene causing familial hypercholesterolemia among French Canadians. Hum Mutat. 1998;Suppl 1:S226-31. PMID:9452094
  28. ↑ Thiart R, Loubser O, de Villiers JN, Marx MP, Zaire R, Raal FJ, Kotze MJ. Two novel and two known low-density lipoprotein receptor gene mutations in German patients with familial hypercholesterolemia. Hum Mutat. 1998;Suppl 1:S232-3. PMID:9452095
  29. ↑ Mak YT, Zhang J, Chan YS, Mak TW, Tomlinson B, Masarei JR, Pang CP. Possible common mutations in the low density lipoprotein receptor gene in Chinese. Hum Mutat. 1998;Suppl 1:S310-3. PMID:9452118
  30. ↑ Cenarro A, Jensen HK, Casao E, Civeira F, Gonzalez-Bonillo J, Rodriguez-Rey JC, Gregersen N, Pocovi M. Identification of recurrent and novel mutations in the LDL receptor gene in Spanish patients with familial hypercholesterolemia. Mutations in brief no. 135. Online. Hum Mutat. 1998;11(5):413. PMID:10206683 doi:<413::AID-HUMU16>3.0.CO;2-I 10.1002/(SICI)1098-1004(1998)11:5<413::AID-HUMU16>3.0.CO;2-I
  31. ↑ Motti C, Bertolini S, Rampa P, Trovatello G, Liberatoscioli L, Calandra S, Federici G, Cortese C. Two novel mutations consisting in minor gene rearrangements in the human low density lipoprotein receptor gene in Italian patients affected by familial hypercholesterolemia. Mutations in brief no. 194. Online. Hum Mutat. 1998;12(3):290. PMID:10660340
  32. ↑ Hirayama T, Yamaki E, Hata A, Tsuji M, Hashimoto K, Yamamoto M, Emi M. Five familial hypercholesterolemic kindreds in Japan with novel mutations of the LDL receptor gene. J Hum Genet. 1998;43(4):250-4. PMID:9852677 doi:10.1007/s100380050083
  33. ↑ Lee WK, Haddad L, Macleod MJ, Dorrance AM, Wilson DJ, Gaffney D, Dominiczak MH, Packard CJ, Day IN, Humphries SE, Dominiczak AF. Identification of a common low density lipoprotein receptor mutation (C163Y) in the west of Scotland. J Med Genet. 1998 Jul;35(7):573-8. PMID:9678702
  34. ↑ Ekstrom U, Abrahamson M, Floren CH, Tollig H, Wettrell G, Nilsson G, Sun XM, Soutar AK, Nilsson-Ehle P. An individual with a healthy phenotype in spite of a pathogenic LDL receptor mutation (C240F). Clin Genet. 1999 May;55(5):332-9. PMID:10422803
  35. ↑ Ebhardt M, Schmidt H, Doerk T, Tietge U, Haas R, Manns MP, Schmidtke J, Stuhrmann M. Mutation analysis in 46 German families with familial hypercholesterolemia: identification of 8 new mutations. Mutations in brief no. 226. Online. Hum Mutat. 1999;13(3):257. PMID:10090484 doi:<257::AID-HUMU15>3.0.CO;2-A 10.1002/(SICI)1098-1004(1999)13:3<257::AID-HUMU15>3.0.CO;2-A
  36. ↑ Hattori H, Nagano M, Iwata F, Homma Y, Egashira T, Okada T. Identification of recurrent and novel mutations in the LDL receptor gene in Japanese familial hypercholesterolemia. Mutation in brief no. 248. Online. Hum Mutat. 1999;14(1):87. PMID:10447263 doi:<87::AID-HUMU14>3.0.CO;2-N 10.1002/(SICI)1098-1004(1999)14:1<87::AID-HUMU14>3.0.CO;2-N
  37. ↑ Bertolini S, Cantafora A, Averna M, Cortese C, Motti C, Martini S, Pes G, Postiglione A, Stefanutti C, Blotta I, Pisciotta L, Rolleri M, Langheim S, Ghisellini M, Rabbone I, Calandra S. Clinical expression of familial hypercholesterolemia in clusters of mutations of the LDL receptor gene that cause a receptor-defective or receptor-negative phenotype. Arterioscler Thromb Vasc Biol. 2000 Sep;20(9):E41-52. PMID:10978268
  38. ↑ Miltiadous G, Elisaf M, Xenophontos S, Manoli P, Cariolou MA. Segregation of a novel LDLR gene mutation (I430T) with familial hypercholesterolaemia in a Greek pedigree. Hum Mutat. 2000 Sep;16(3):277. PMID:10980548 doi:<277::AID-HUMU24>3.0.CO;2-Y 10.1002/1098-1004(200009)16:3<277::AID-HUMU24>3.0.CO;2-Y
  39. ↑ Thiart R, Scholtz CL, Vergotine J, Hoogendijk CF, de Villiers JN, Nissen H, Brusgaard K, Gaffney D, Hoffs MS, Vermaak WJ, Kotze MJ. Predominance of a 6 bp deletion in exon 2 of the LDL receptor gene in Africans with familial hypercholesterolaemia. J Med Genet. 2000 Jul;37(7):514-9. PMID:10882754
  40. ↑ Takahashi M, Ikeda U, Takahashi S, Hattori H, Iwasaki T, Ishihara M, Egashira T, Honma S, Asano Y, Shimada K. A novel mutation in exon 2 of the low-density lipoprotein-receptor gene in a patient with homozygous familial hypercholesterolemia. Clin Genet. 2001 Apr;59(4):290-2. PMID:11298688
  41. ↑ Humphries SE, Whittall RA, Hubbart CS, Maplebeck S, Cooper JA, Soutar AK, Naoumova R, Thompson GR, Seed M, Durrington PN, Miller JP, Betteridge DJ, Neil HA. Genetic causes of familial hypercholesterolaemia in patients in the UK: relation to plasma lipid levels and coronary heart disease risk. J Med Genet. 2006 Dec;43(12):943-9. PMID:17142622 doi:10.1136/jmg.2006.038356
  42. ↑ Abifadel M, Rabes JP, Jambart S, Halaby G, Gannage-Yared MH, Sarkis A, Beaino G, Varret M, Salem N, Corbani S, Aydenian H, Junien C, Munnich A, Boileau C. The molecular basis of familial hypercholesterolemia in Lebanon: spectrum of LDLR mutations and role of PCSK9 as a modifier gene. Hum Mutat. 2009 Jul;30(7):E682-91. doi: 10.1002/humu.21002. PMID:19319977 doi:10.1002/humu.21002
  43. ↑ Walus-Miarka M, Sanak M, Idzior-Walus B, Miarka P, Witek P, Malecki MT, Czarnecka D. A novel mutation (Cys308Phe) of the LDL receptor gene in families from the South-Eastern part of Poland. Mol Biol Rep. 2012 May;39(5):5181-6. doi: 10.1007/s11033-011-1314-0. Epub 2011, Dec 13. PMID:22160468 doi:10.1007/s11033-011-1314-0
  44. ↑ Jeon H, Meng W, Takagi J, Eck MJ, Springer TA, Blacklow SC. Implications for familial hypercholesterolemia from the structure of the LDL receptor YWTD-EGF domain pair. Nat Struct Biol. 2001 Jun;8(6):499-504. PMID:11373616 doi:10.1038/88556

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PDB ID 1ijq

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