4JHP: RPGR RCC1-like domain

The crystal structure of the RPGR RCC1-like domain in complex with PDE6D. Determined by X-ray diffraction at 1.9 Å resolution. Released 17 Apr 2013.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,336
Mol. weight: 60.13 kDa
Released: 17 Apr 2013

Explore 4JHP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JHP contains 9 α-helices and 40 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-14	10
β-strand	15-24	10	1
β-strand	30-34	5	1
β-strand	44-49	6	2
α-helix	51-55	5
β-strand	58-67	10	1
β-strand	71-82	12	2
β-strand	85-97	13	2
β-strand	101-110	10	1
α-helix	120-123	4
β-strand	127-135	9	2
β-strand	138-149	12	2

Chain C: 6 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	3
β-strand	29-30	2	3
β-strand	32	1	4
β-strand	35	1	4
β-strand	37-42	6	5
β-strand	46-51	6	5
β-strand	56-60	5	5
β-strand	69	1	6
β-strand	79-80	2	5
α-helix	82-84	3
β-strand	89-94	6	7
β-strand	98-103	6	7
β-strand	108-112	5	7
β-strand	127-132	6	7
β-strand	142-147	6	8
β-strand	151-156	6	8
β-strand	161-166	6	8
β-strand	179-186	8	8
β-strand	192-197	6	9
β-strand	201-206	6	9
β-strand	211-215	5	9
α-helix	226-231	6
β-strand	236-237	2	9
α-helix	244	1
β-strand	245-250	6	10
β-strand	254-259	6	10
β-strand	263-268	6	10
β-strand	282-288	7	10
α-helix	290-292	3
β-strand	297-302	6	11
β-strand	306-311	6	11
β-strand	316-320	5	11
α-helix	323-325	3
β-strand	337-342	6	11
α-helix	344-346	3
β-strand	349-356	8	3
β-strand	360-367	8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	B	protein	152	Homo sapiens	O43924 (AlphaFold model)
X-linked retinitis pigmentosa GTPase regulator	C	protein	391	Homo sapiens	Q92834 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>4JHP_1 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (chains B)
GSMSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKA
VSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMM
PASVLTGNVIIETKFFDDDLLVSTSRVRLFYV

Sequence of entity 2 (C), FASTA

>4JHP_2 X-linked retinitis pigmentosa GTPase regulator (chains C)
LMPDSGAVFTFGKSKFAENNPGKFWFKNDVPVHLSCGDEHSAVVTGNNKLYMFGSNNWGQ
LGLGSKSAISKPTCVKALKPEKVKLAACGRNHTLVSTEGGNVYATGGNNEGQLGLGDTEE
RNTFHVISFFTSEHKIKQLSAGSNTSAALTEDGRLFMWGDNSEGQIGLKNVSNVCVPQQV
TIGKPVSWISCGYYHSAFVTTDGELYVFGEPENGKLGLPNQLLGNHRTPQLVSEIPEKVI
QVACGGEHTVVLTENAVYTFGLGQFGQLGLGTFLFETSEPKVIENIRDQTISYISCGENH
TALITDIGLMYTFGDGRHGKLGLGLENFTNHFIPTLCSNFLRFIVKLVACGGCHMVVFAA
PHPRRPPAYVEQKLISEEDLNSAVDHHHHHH

Primary citation

The interplay between RPGR, PDE-delta and Arl2/3 regulate the ciliary targeting of farnesylated cargo. Watzlich, D., Vetter, I., Gotthardt, K. et al. EMBO Rep (2013) 14:465-472. DOI 10.1038/embor.2013.37 · PubMed

Other PDB entries of the same protein (UniProt O43924 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5ML3 1.4 Å, The crystal structure of PDE6D in complex to Deltasonamide1
4JV8 1.45 Å, The crystal structure of PDE6D in complex with rac-S1
7Q9Q 1.45 Å, Crystal structure of PDE6D Geranylgeranylated cystein complex
7PAD 1.49 Å, The crystal structure of DW-0254 in complex with PDE6D
5ML2 1.6 Å, The crystal structure of PDE6D in complex with inhibitor-3
9HMC 1.65 Å, Crystal structure of PDE6D in complex with compound 5e
3T5G 1.7 Å, Structure of fully modified farnesylated Rheb in complex with PDE6D
4JVB 1.75 Å, Crystal structure of PDE6D in complex with the inhibitor rac-2
1KSH 1.8 Å, Complex of Arl2 and PDE delta, Crystal Form 2 (native)
9RP6 1.8 Å, Crystal structure of covalent PDE6delta adduct modified by compound 13b
5F2U 1.85 Å, Structure of Fully modified farnesylated INPP5E Peptide in complex with PDE6D
7PAE 1.85 Å, The crystal structure of Deltarasin in complex with PDE6D

Browse structure collections

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