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4jhp, resolution 1.90Å ()
Gene: PDE6D, PDED (Homo sapiens), RPGR, RP3, XLRP3 (Homo sapiens)
Related: 4jhn

Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


The crystal structure of the RPGR RCC1-like domain in complex with PDE6D

Publication Abstract from PubMed

Defects in primary cilia result in human diseases known as ciliopathies. The retinitis pigmentosa GTPase regulator (RPGR), mutated in the most severe form of the eye disease, is located at the transition zone of the ciliary organelle. The RPGR-interacting partner PDEdelta is involved in trafficking of farnesylated ciliary cargo, but the significance of this interaction is unknown. The crystal structure of the propeller domain of RPGR shows the location of patient mutations and how they perturb the structure. The RPGR.PDEdelta complex structure shows PDEdelta on a highly conserved surface patch of RPGR. Biochemical experiments and structural considerations show that RPGR can bind with high affinity to cargo-loaded PDEdelta and exposes the Arl2/Arl3-binding site on PDEdelta. On the basis of these results, we propose a model where RPGR is acting as a scaffold protein recruiting cargo-loaded PDEdelta and Arl3 to release lipidated cargo into cilia.

The interplay between RPGR, PDEdelta and Arl2/3 regulate the ciliary targeting of farnesylated cargo., Watzlich D, Vetter I, Gotthardt K, Miertzschke M, Chen YX, Wittinghofer A, Ismail S, EMBO Rep. 2013 Apr 5. doi: 10.1038/embor.2013.37. PMID:23559067

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


[RPGR_HUMAN] Primary ciliary dyskinesia;Achromatopsia;Primary ciliary dyskinesia - retinitis pigmentosa;Cone rod dystrophy;Retinitis pigmentosa. Defects in RPGR are the cause of retinitis pigmentosa type 3 (RP3) [MIM:300029]; also known as X-linked retinitis pigmentosa 3 (XLRP-3) or retinitis pigmentosa type 15 (RP15). A X-linked retinal dystrophy belonging to the group of pigmentary retinopathies. RP is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. In RP3, affected males have a severe phenotype, and carrier females show a wide spectrum of clinical features ranging from completely asymptomatic to severe retinitis pigmentosa. Heterozygous women can manifest a form of choroidoretinal degeneration which is distinguished from other types by the absence of visual defects in the presence of a brilliant, scintillating, golden-hued, patchy appearance most striking around the macula, called a tapetal-like retinal reflex.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] Defects in RPGR are the cause of retinitis pigmentosa and sinorespiratory infections with or without deafness (RPDSI) [MIM:300455]. A disease characterized by the association primary ciliary dyskinesia features with retinitis pigmentosa. Some patients also manifest deafness.[15] [16] Defects in RPGR are the cause of cone-rod dystrophy X-linked type 1 (CORDX1) [MIM:304020]; also known as cone dystrophy 1 (CO1). CORDs are inherited retinal dystrophies belonging to the group of pigmentary retinopathies. CORDs are characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa. In CORDX1 the degree of rod-photoreceptor involvement can be variable, with degeneration increasing as the disease progresses. Affected individuals (essentially all of whom are males) present with decreased visual acuity, myopia, photophobia, abnormal color vision, full peripheral visual fields, decreased photopic electroretinographic responses, and granularity of the macular retinal pigment epithelium. Although penetrance appears to be nearly 100%, there is variable expressivity with respect to age at onset and severity of symptoms.[17] Defects in RPGR are a cause of macular degeneration X-linked atrophic (MDXLA) [MIM:300834]. MDXLA is an ocular disorder characterized by macular atrophy causing progressive loss of visual acuity with minimal peripheral visual impairment. Some patients manifest extensive macular degeneration plus peripheral loss of retinal pigment epithelium and choriocapillaries. Full-field electroretinograms (ERGs) show normal cone and rod responses in some affected males despite advanced macular degeneration.[18]


[PDE6D_HUMAN] Acts as a GTP specific dissociation inhibitor (GDI). Increases the affinity of ARL3 for GTP by several orders of magnitude and does so by decreasing the nucleotide dissociation rate. Stabilizes Arl3-GTP by decreasing the nucleotide dissociation (By similarity). [RPGR_HUMAN] Could be a guanine-nucleotide releasing factor. Plays a role in ciliogenesis. Probably regulates cilia formation by regulating actin stress filaments and cell contractility. Plays an important role in photoreceptor integrity. May play a critical role in spermatogenesis and in intraflagellar transport processes (By similarity). May be involved in microtubule organization and regulation of transport in primary cilia.[19]

About this Structure

4jhp is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA.


  • Watzlich D, Vetter I, Gotthardt K, Miertzschke M, Chen YX, Wittinghofer A, Ismail S. The interplay between RPGR, PDEdelta and Arl2/3 regulate the ciliary targeting of farnesylated cargo. EMBO Rep. 2013 Apr 5. doi: 10.1038/embor.2013.37. PMID:23559067 doi:10.1038/embor.2013.37
  1. Linari M, Ueffing M, Manson F, Wright A, Meitinger T, Becker J. The retinitis pigmentosa GTPase regulator, RPGR, interacts with the delta subunit of rod cyclic GMP phosphodiesterase. Proc Natl Acad Sci U S A. 1999 Feb 16;96(4):1315-20. PMID:9990021
  2. Meindl A, Dry K, Herrmann K, Manson F, Ciccodicola A, Edgar A, Carvalho MR, Achatz H, Hellebrand H, Lennon A, Migliaccio C, Porter K, Zrenner E, Bird A, Jay M, Lorenz B, Wittwer B, D'Urso M, Meitinger T, Wright A. A gene (RPGR) with homology to the RCC1 guanine nucleotide exchange factor is mutated in X-linked retinitis pigmentosa (RP3). Nat Genet. 1996 May;13(1):35-42. PMID:8673101 doi:10.1038/ng0596-35
  3. Roepman R, van Duijnhoven G, Rosenberg T, Pinckers AJ, Bleeker-Wagemakers LM, Bergen AA, Post J, Beck A, Reinhardt R, Ropers HH, Cremers FP, Berger W. Positional cloning of the gene for X-linked retinitis pigmentosa 3: homology with the guanine-nucleotide-exchange factor RCC1. Hum Mol Genet. 1996 Jul;5(7):1035-41. PMID:8817343
  4. Vervoort R, Lennon A, Bird AC, Tulloch B, Axton R, Miano MG, Meindl A, Meitinger T, Ciccodicola A, Wright AF. Mutational hot spot within a new RPGR exon in X-linked retinitis pigmentosa. Nat Genet. 2000 Aug;25(4):462-6. PMID:10932196 doi:10.1038/78182
  5. Mears AJ, Hiriyanna S, Vervoort R, Yashar B, Gieser L, Fahrner S, Daiger SP, Heckenlively JR, Sieving PA, Wright AF, Swaroop A. Remapping of the RP15 locus for X-linked cone-rod degeneration to Xp11.4-p21.1, and identification of a de novo insertion in the RPGR exon ORF15. Am J Hum Genet. 2000 Oct;67(4):1000-3. Epub 2000 Sep 1. PMID:10970770 doi:S0002-9297(07)63294-7
  6. Buraczynska M, Wu W, Fujita R, Buraczynska K, Phelps E, Andreasson S, Bennett J, Birch DG, Fishman GA, Hoffman DR, Inana G, Jacobson SG, Musarella MA, Sieving PA, Swaroop A. Spectrum of mutations in the RPGR gene that are identified in 20% of families with X-linked retinitis pigmentosa. Am J Hum Genet. 1997 Dec;61(6):1287-92. PMID:9399904 doi:S0002-9297(07)60229-8
  7. Fishman GA, Grover S, Jacobson SG, Alexander KR, Derlacki DJ, Wu W, Buraczynska M, Swaroop A. X-linked retinitis pigmentosa in two families with a missense mutation in the RPGR gene and putative change of glycine to valine at codon 60. Ophthalmology. 1998 Dec;105(12):2286-96. PMID:9855162 doi:S0161-6420(98)91231-3
  8. Miano MG, Testa F, Strazzullo M, Trujillo M, De Bernardo C, Grammatico B, Simonelli F, Mangino M, Torrente I, Ruberto G, Beneyto M, Antinolo G, Rinaldi E, Danesino C, Ventruto V, D'Urso M, Ayuso C, Baiget M, Ciccodicola A. Mutation analysis of the RPGR gene reveals novel mutations in south European patients with X-linked retinitis pigmentosa. Eur J Hum Genet. 1999 Sep;7(6):687-94. PMID:10482958 doi:10.1038/sj.ejhg.5200352
  9. Zito I, Gorin MB, Plant C, Bird AC, Bhattacharya SS, Hardcastle AJ. Novel mutations of the RPGR gene in RP3 families. Hum Mutat. 2000 Apr;15(4):386. PMID:10737996 doi:<386::AID-HUMU23>3.0.CO;2-4 10.1002/(SICI)1098-1004(200004)15:4<386::AID-HUMU23>3.0.CO;2-4
  10. Sharon D, Bruns GA, McGee TL, Sandberg MA, Berson EL, Dryja TP. X-linked retinitis pigmentosa: mutation spectrum of the RPGR and RP2 genes and correlation with visual function. Invest Ophthalmol Vis Sci. 2000 Aug;41(9):2712-21. PMID:10937588
  11. Guevara-Fujita M, Fahrner S, Buraczynska K, Cook J, Wheaton D, Cortes F, Vicencio C, Pena M, Fishman G, Mintz-Hittner H, Birch D, Hoffman D, Mears A, Fujita R, Swaroop A. Five novel RPGR mutations in families with X-linked retinitis pigmentosa. Hum Mutat. 2001 Feb;17(2):151. PMID:11180598 doi:<151::AID-HUMU7>3.0.CO;2-W 10.1002/1098-1004(200102)17:2<151::AID-HUMU7>3.0.CO;2-W
  12. Breuer DK, Yashar BM, Filippova E, Hiriyanna S, Lyons RH, Mears AJ, Asaye B, Acar C, Vervoort R, Wright AF, Musarella MA, Wheeler P, MacDonald I, Iannaccone A, Birch D, Hoffman DR, Fishman GA, Heckenlively JR, Jacobson SG, Sieving PA, Swaroop A. A comprehensive mutation analysis of RP2 and RPGR in a North American cohort of families with X-linked retinitis pigmentosa. Am J Hum Genet. 2002 Jun;70(6):1545-54. Epub 2002 Apr 30. PMID:11992260 doi:10.1086/340848
  13. Sharon D, Sandberg MA, Rabe VW, Stillberger M, Dryja TP, Berson EL. RP2 and RPGR mutations and clinical correlations in patients with X-linked retinitis pigmentosa. Am J Hum Genet. 2003 Nov;73(5):1131-46. Epub 2003 Oct 16. PMID:14564670 doi:S0002-9297(07)61975-2
  14. Bader I, Brandau O, Achatz H, Apfelstedt-Sylla E, Hergersberg M, Lorenz B, Wissinger B, Wittwer B, Rudolph G, Meindl A, Meitinger T. X-linked retinitis pigmentosa: RPGR mutations in most families with definite X linkage and clustering of mutations in a short sequence stretch of exon ORF15. Invest Ophthalmol Vis Sci. 2003 Apr;44(4):1458-63. PMID:12657579
  15. Zito I, Downes SM, Patel RJ, Cheetham ME, Ebenezer ND, Jenkins SA, Bhattacharya SS, Webster AR, Holder GE, Bird AC, Bamiou DE, Hardcastle AJ. RPGR mutation associated with retinitis pigmentosa, impaired hearing, and sinorespiratory infections. J Med Genet. 2003 Aug;40(8):609-15. PMID:12920075
  16. Iannaccone A, Breuer DK, Wang XF, Kuo SF, Normando EM, Filippova E, Baldi A, Hiriyanna S, MacDonald CB, Baldi F, Cosgrove D, Morton CC, Swaroop A, Jablonski MM. Clinical and immunohistochemical evidence for an X linked retinitis pigmentosa syndrome with recurrent infections and hearing loss in association with an RPGR mutation. J Med Genet. 2003 Nov;40(11):e118. PMID:14627685
  17. Demirci FY, Rigatti BW, Wen G, Radak AL, Mah TS, Baic CL, Traboulsi EI, Alitalo T, Ramser J, Gorin MB. X-linked cone-rod dystrophy (locus COD1): identification of mutations in RPGR exon ORF15. Am J Hum Genet. 2002 Apr;70(4):1049-53. Epub 2002 Feb 20. PMID:11857109 doi:S0002-9297(07)60315-2
  18. Ayyagari R, Demirci FY, Liu J, Bingham EL, Stringham H, Kakuk LE, Boehnke M, Gorin MB, Richards JE, Sieving PA. X-linked recessive atrophic macular degeneration from RPGR mutation. Genomics. 2002 Aug;80(2):166-71. PMID:12160730
  19. Gakovic M, Shu X, Kasioulis I, Carpanini S, Moraga I, Wright AF. The role of RPGR in cilia formation and actin stability. Hum Mol Genet. 2011 Dec 15;20(24):4840-50. doi: 10.1093/hmg/ddr423. Epub 2011 Sep, 20. PMID:21933838 doi:10.1093/hmg/ddr423

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