5ctd

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Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest fragment a2a1a1 of type I collagen

Structural highlights

5ctd is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:MSE
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

CO1A1_HUMAN Defects in COL1A1 are the cause of Caffey disease (CAFFD) [MIM:114000; also known as infantile cortical hyperostosis. Caffey disease is characterized by an infantile episode of massive subperiosteal new bone formation that typically involves the diaphyses of the long bones, mandible, and clavicles. The involved bones may also appear inflamed, with painful swelling and systemic fever often accompanying the illness. The bone changes usually begin before 5 months of age and resolve before 2 years of age.[1] [2] [3] Defects in COL1A1 are a cause of Ehlers-Danlos syndrome type 1 (EDS1) [MIM:130000; also known as Ehlers-Danlos syndrome gravis. EDS is a connective tissue disorder characterized by hyperextensible skin, atrophic cutaneous scars due to tissue fragility and joint hyperlaxity. EDS1 is the severe form of classic Ehlers-Danlos syndrome.[4] [5] [6] [7] Defects in COL1A1 are the cause of Ehlers-Danlos syndrome type 7A (EDS7A) [MIM:130060; also known as autosomal dominant Ehlers-Danlos syndrome type VII. EDS is a connective tissue disorder characterized by hyperextensible skin, atrophic cutaneous scars due to tissue fragility and joint hyperlaxity. EDS7A is marked by bilateral congenital hip dislocation, hyperlaxity of the joints, and recurrent partial dislocations.[8] [9] Defects in COL1A1 are a cause of osteogenesis imperfecta type 1 (OI1) [MIM:166200. A dominantly inherited connective tissue disorder characterized by bone fragility and blue sclerae. Osteogenesis imperfecta type 1 is non-deforming with normal height or mild short stature, and no dentinogenesis imperfecta.[10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] Defects in COL1A1 are a cause of osteogenesis imperfecta type 2 (OI2) [MIM:166210; also known as osteogenesis imperfecta congenita. A connective tissue disorder characterized by bone fragility, with many perinatal fractures, severe bowing of long bones, undermineralization, and death in the perinatal period due to respiratory insufficiency. Defects in COL1A1 are a cause of osteogenesis imperfecta type 3 (OI3) [MIM:259420. A connective tissue disorder characterized by progressively deforming bones, very short stature, a triangular face, severe scoliosis, grayish sclera, and dentinogenesis imperfecta. Defects in COL1A1 are a cause of osteogenesis imperfecta type 4 (OI4) [MIM:166220; also known as osteogenesis imperfecta with normal sclerae. A connective tissue disorder characterized by moderately short stature, mild to moderate scoliosis, grayish or white sclera and dentinogenesis imperfecta. Genetic variations in COL1A1 are a cause of susceptibility to osteoporosis (OSTEOP) [MIM:166710; also known as involutional or senile osteoporosis or postmenopausal osteoporosis. Osteoporosis is characterized by reduced bone mass, disruption of bone microarchitecture without alteration in the composition of bone. Osteoporotic bones are more at risk of fracture.[23] [24] [25] [26] Note=A chromosomal aberration involving COL1A1 is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGF.[27] [28] CO9A1_HUMAN Defects in COL9A1 are the cause of multiple epiphyseal dysplasia type 6 (EDM6) [MIM:614135. A generalized skeletal dysplasia associated with significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. Radiological examination of the skeleton shows delayed, irregular mineralization of the epiphyseal ossification centers and of the centers of the carpal and tarsal bones. Multiple epiphyseal dysplasia is broadly categorized into the more severe Fairbank and the milder Ribbing types. The Fairbank type is characterized by shortness of stature, short and stubby fingers, small epiphyses in several joints, including the knee, ankle, hand, and hip. The Ribbing type is confined predominantly to the hip joints and is characterized by hands that are normal and stature that is normal or near-normal.[29] Defects in COL9A1 are the cause of Stickler syndrome type 4 (STL4) [MIM:614134. An autosomal recessive form of Stickler syndrome, an inherited disorder that associates ocular signs with more or less complete forms of Pierre Robin sequence, bone disorders and sensorineural deafness. Ocular disorders may include juvenile cataract, myopia, strabismus, vitreoretinal or chorioretinal degeneration, retinal detachment, and chronic uveitis. Robin sequence includes an opening in the roof of the mouth (a cleft palate), a large tongue (macroglossia), and a small lower jaw (micrognathia). Bones are affected by slight platyspondylisis and large, often defective epiphyses. Juvenile joint laxity is followed by early signs of arthrosis. The degree of hearing loss varies among affected individuals and may become more severe over time. Syndrome expressivity is variable.[30]

Function

CO1A1_HUMAN Type I collagen is a member of group I collagen (fibrillar forming collagen).CO9A1_HUMAN Structural component of hyaline cartilage and vitreous of the eye.

Publication Abstract from PubMed

Collagen plays a fundamental role in all known metazoans. In collagens three polypeptides form a unique triple-helical structure with a one-residue stagger to fit every third glycine residue in the inner core without disturbing the poly-proline type II helical conformation of each chain. There are homo- and hetero-trimeric types of collagen consisting of one, two or three distinct chains. Thus there must be mechanisms that control composition and stagger during collagen folding. Here, we uncover the structural basis for both chain selection and stagger formation of a collagen molecule. Three distinct chains (alpha1, alpha2 and alpha3) of the non-collagenous domain 2 (NC2) of type IX collagen are assembled to guide triple-helical sequences in the leading, middle and trailing positions. This unique domain opens the door for generating any fragment of collagen in its native composition and stagger.

Structural insight for chain selection and stagger control in collagen.,Boudko SP, Bachinger HP Sci Rep. 2016 Nov 29;6:37831. doi: 10.1038/srep37831. PMID:27897211[31]

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

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Citations
2 reviews cite this structure
Collagen Binding Proteins of Gram-Positive Pathogens.
Arora et al. (2021)
1 more
12 other articles
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See Also

References

  1. ↑ Simon MP, Pedeutour F, Sirvent N, Grosgeorge J, Minoletti F, Coindre JM, Terrier-Lacombe MJ, Mandahl N, Craver RD, Blin N, Sozzi G, Turc-Carel C, O'Brien KP, Kedra D, Fransson I, Guilbaud C, Dumanski JP. Deregulation of the platelet-derived growth factor B-chain gene via fusion with collagen gene COL1A1 in dermatofibrosarcoma protuberans and giant-cell fibroblastoma. Nat Genet. 1997 Jan;15(1):95-8. PMID:8988177 doi:10.1038/ng0197-95
  2. ↑ Sandberg AA, Anderson WD, Fredenberg C, Hashimoto H. Dermatofibrosarcoma protuberans of breast. Cancer Genet Cytogenet. 2003 Apr 1;142(1):56-9. PMID:12660034
  3. ↑ Gensure RC, Makitie O, Barclay C, Chan C, Depalma SR, Bastepe M, Abuzahra H, Couper R, Mundlos S, Sillence D, Ala Kokko L, Seidman JG, Cole WG, Juppner H. A novel COL1A1 mutation in infantile cortical hyperostosis (Caffey disease) expands the spectrum of collagen-related disorders. J Clin Invest. 2005 May;115(5):1250-7. PMID:15864348 doi:10.1172/JCI22760
  4. ↑ Simon MP, Pedeutour F, Sirvent N, Grosgeorge J, Minoletti F, Coindre JM, Terrier-Lacombe MJ, Mandahl N, Craver RD, Blin N, Sozzi G, Turc-Carel C, O'Brien KP, Kedra D, Fransson I, Guilbaud C, Dumanski JP. Deregulation of the platelet-derived growth factor B-chain gene via fusion with collagen gene COL1A1 in dermatofibrosarcoma protuberans and giant-cell fibroblastoma. Nat Genet. 1997 Jan;15(1):95-8. PMID:8988177 doi:10.1038/ng0197-95
  5. ↑ Sandberg AA, Anderson WD, Fredenberg C, Hashimoto H. Dermatofibrosarcoma protuberans of breast. Cancer Genet Cytogenet. 2003 Apr 1;142(1):56-9. PMID:12660034
  6. ↑ Nuytinck L, Freund M, Lagae L, Pierard GE, Hermanns-Le T, De Paepe A. Classical Ehlers-Danlos syndrome caused by a mutation in type I collagen. Am J Hum Genet. 2000 Apr;66(4):1398-402. Epub 2000 Mar 17. PMID:10739762 doi:S0002-9297(07)60165-7
  7. ↑ Malfait F, Symoens S, De Backer J, Hermanns-Le T, Sakalihasan N, Lapiere CM, Coucke P, De Paepe A. Three arginine to cysteine substitutions in the pro-alpha (I)-collagen chain cause Ehlers-Danlos syndrome with a propensity to arterial rupture in early adulthood. Hum Mutat. 2007 Apr;28(4):387-95. PMID:17211858 doi:10.1002/humu.20455
  8. ↑ Simon MP, Pedeutour F, Sirvent N, Grosgeorge J, Minoletti F, Coindre JM, Terrier-Lacombe MJ, Mandahl N, Craver RD, Blin N, Sozzi G, Turc-Carel C, O'Brien KP, Kedra D, Fransson I, Guilbaud C, Dumanski JP. Deregulation of the platelet-derived growth factor B-chain gene via fusion with collagen gene COL1A1 in dermatofibrosarcoma protuberans and giant-cell fibroblastoma. Nat Genet. 1997 Jan;15(1):95-8. PMID:8988177 doi:10.1038/ng0197-95
  9. ↑ Sandberg AA, Anderson WD, Fredenberg C, Hashimoto H. Dermatofibrosarcoma protuberans of breast. Cancer Genet Cytogenet. 2003 Apr 1;142(1):56-9. PMID:12660034
  10. ↑ Simon MP, Pedeutour F, Sirvent N, Grosgeorge J, Minoletti F, Coindre JM, Terrier-Lacombe MJ, Mandahl N, Craver RD, Blin N, Sozzi G, Turc-Carel C, O'Brien KP, Kedra D, Fransson I, Guilbaud C, Dumanski JP. Deregulation of the platelet-derived growth factor B-chain gene via fusion with collagen gene COL1A1 in dermatofibrosarcoma protuberans and giant-cell fibroblastoma. Nat Genet. 1997 Jan;15(1):95-8. PMID:8988177 doi:10.1038/ng0197-95
  11. ↑ Sandberg AA, Anderson WD, Fredenberg C, Hashimoto H. Dermatofibrosarcoma protuberans of breast. Cancer Genet Cytogenet. 2003 Apr 1;142(1):56-9. PMID:12660034
  12. ↑ Labhard ME, Wirtz MK, Pope FM, Nicholls AC, Hollister DW. A cysteine for glycine substitution at position 1017 in an alpha 1(I) chain of type I collagen in a patient with mild dominantly inherited osteogenesis imperfecta. Mol Biol Med. 1988 Dec;5(3):197-207. PMID:3244312
  13. ↑ Starman BJ, Eyre D, Charbonneau H, Harrylock M, Weis MA, Weiss L, Graham JM Jr, Byers PH. Osteogenesis imperfecta. The position of substitution for glycine by cysteine in the triple helical domain of the pro alpha 1(I) chains of type I collagen determines the clinical phenotype. J Clin Invest. 1989 Oct;84(4):1206-14. PMID:2794057 doi:http://dx.doi.org/10.1172/JCI114286
  14. ↑ Deak SB, Scholz PM, Amenta PS, Constantinou CD, Levi-Minzi SA, Gonzalez-Lavin L, Mackenzie JW. The substitution of arginine for glycine 85 of the alpha 1(I) procollagen chain results in mild osteogenesis imperfecta. The mutation provides direct evidence for three discrete domains of cooperative melting of intact type I collagen. J Biol Chem. 1991 Nov 15;266(32):21827-32. PMID:1718984
  15. ↑ Mottes M, Sangalli A, Valli M, Gomez Lira M, Tenni R, Buttitta P, Pignatti PF, Cetta G. Mild dominant osteogenesis imperfecta with intrafamilial variability: the cause is a serine for glycine alpha 1(I) 901 substitution in a type-I collagen gene. Hum Genet. 1992 Jul;89(5):480-4. PMID:1634225
  16. ↑ Shapiro JR, Stover ML, Burn VE, McKinstry MB, Burshell AL, Chipman SD, Rowe DW. An osteopenic nonfracture syndrome with features of mild osteogenesis imperfecta associated with the substitution of a cysteine for glycine at triple helix position 43 in the pro alpha 1(I) chain of type I collagen. J Clin Invest. 1992 Feb;89(2):567-73. PMID:1737847 doi:http://dx.doi.org/10.1172/JCI115622
  17. ↑ Valli M, Zolezzi F, Mottes M, Antoniazzi F, Stanzial F, Tenni R, Pignatti P, Cetta G. Gly85 to Val substitution in pro alpha 1(I) chain causes mild osteogenesis imperfecta and introduces a susceptibility to protease digestion. Eur J Biochem. 1993 Oct 1;217(1):77-82. PMID:8223589
  18. ↑ Lee KS, Song HR, Cho TJ, Kim HJ, Lee TM, Jin HS, Park HY, Kang S, Jung SC, Koo SK. Mutational spectrum of type I collagen genes in Korean patients with osteogenesis imperfecta. Hum Mutat. 2006 Jun;27(6):599. PMID:16705691 doi:10.1002/humu.9423
  19. ↑ Pollitt R, McMahon R, Nunn J, Bamford R, Afifi A, Bishop N, Dalton A. Mutation analysis of COL1A1 and COL1A2 in patients diagnosed with osteogenesis imperfecta type I-IV. Hum Mutat. 2006 Jul;27(7):716. PMID:16786509 doi:10.1002/humu.9430
  20. ↑ Wang Z, Xu DL, Chen Z, Hu JY, Yang Z, Wang LT. [A new mutation in COL1A1 gene in a family with osteogenesis imperfecta]. Zhonghua Yi Xue Za Zhi. 2006 Jan 17;86(3):170-3. PMID:16638323
  21. ↑ Kataoka K, Ogura E, Hasegawa K, Inoue M, Seino Y, Morishima T, Tanaka H. Mutations in type I collagen genes in Japanese osteogenesis imperfecta patients. Pediatr Int. 2007 Oct;49(5):564-9. PMID:17875077 doi:10.1111/j.1442-200X.2007.02422.x
  22. ↑ Witecka J, Augusciak-Duma AM, Kruczek A, Szydlo A, Lesiak M, Krzak M, Pietrzyk JJ, Mannikko M, Sieron AL. Two novel COL1A1 mutations in patients with osteogenesis imperfecta (OI) affect the stability of the collagen type I triple-helix. J Appl Genet. 2008;49(3):283-95. doi: 10.1007/BF03195625. PMID:18670065 doi:10.1007/BF03195625
  23. ↑ Simon MP, Pedeutour F, Sirvent N, Grosgeorge J, Minoletti F, Coindre JM, Terrier-Lacombe MJ, Mandahl N, Craver RD, Blin N, Sozzi G, Turc-Carel C, O'Brien KP, Kedra D, Fransson I, Guilbaud C, Dumanski JP. Deregulation of the platelet-derived growth factor B-chain gene via fusion with collagen gene COL1A1 in dermatofibrosarcoma protuberans and giant-cell fibroblastoma. Nat Genet. 1997 Jan;15(1):95-8. PMID:8988177 doi:10.1038/ng0197-95
  24. ↑ Sandberg AA, Anderson WD, Fredenberg C, Hashimoto H. Dermatofibrosarcoma protuberans of breast. Cancer Genet Cytogenet. 2003 Apr 1;142(1):56-9. PMID:12660034
  25. ↑ Grant SF, Reid DM, Blake G, Herd R, Fogelman I, Ralston SH. Reduced bone density and osteoporosis associated with a polymorphic Sp1 binding site in the collagen type I alpha 1 gene. Nat Genet. 1996 Oct;14(2):203-5. PMID:8841196 doi:10.1038/ng1096-203
  26. ↑ Uitterlinden AG, Burger H, Huang Q, Yue F, McGuigan FE, Grant SF, Hofman A, van Leeuwen JP, Pols HA, Ralston SH. Relation of alleles of the collagen type Ialpha1 gene to bone density and the risk of osteoporotic fractures in postmenopausal women. N Engl J Med. 1998 Apr 9;338(15):1016-21. PMID:9535665
  27. ↑ Simon MP, Pedeutour F, Sirvent N, Grosgeorge J, Minoletti F, Coindre JM, Terrier-Lacombe MJ, Mandahl N, Craver RD, Blin N, Sozzi G, Turc-Carel C, O'Brien KP, Kedra D, Fransson I, Guilbaud C, Dumanski JP. Deregulation of the platelet-derived growth factor B-chain gene via fusion with collagen gene COL1A1 in dermatofibrosarcoma protuberans and giant-cell fibroblastoma. Nat Genet. 1997 Jan;15(1):95-8. PMID:8988177 doi:10.1038/ng0197-95
  28. ↑ Sandberg AA, Anderson WD, Fredenberg C, Hashimoto H. Dermatofibrosarcoma protuberans of breast. Cancer Genet Cytogenet. 2003 Apr 1;142(1):56-9. PMID:12660034
  29. ↑ Czarny-Ratajczak M, Lohiniva J, Rogala P, Kozlowski K, Perala M, Carter L, Spector TD, Kolodziej L, Seppanen U, Glazar R, Krolewski J, Latos-Bielenska A, Ala-Kokko L. A mutation in COL9A1 causes multiple epiphyseal dysplasia: further evidence for locus heterogeneity. Am J Hum Genet. 2001 Nov;69(5):969-80. Epub 2001 Sep 14. PMID:11565064 doi:10.1086/324023
  30. ↑ Van Camp G, Snoeckx RL, Hilgert N, van den Ende J, Fukuoka H, Wagatsuma M, Suzuki H, Smets RM, Vanhoenacker F, Declau F, Van de Heyning P, Usami S. A new autosomal recessive form of Stickler syndrome is caused by a mutation in the COL9A1 gene. Am J Hum Genet. 2006 Sep;79(3):449-57. Epub 2006 Jun 26. PMID:16909383 doi:10.1086/506478
  31. ↑ Boudko SP, Bachinger HP. Structural insight for chain selection and stagger control in collagen. Sci Rep. 2016 Nov 29;6:37831. doi: 10.1038/srep37831. PMID:27897211 doi:http://dx.doi.org/10.1038/srep37831

Contents


PDB ID 5ctd

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