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- PDB-4jhp: The crystal structure of the RPGR RCC1-like domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4jhp
TitleThe crystal structure of the RPGR RCC1-like domain in complex with PDE6D
Components
  • Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
  • X-linked retinitis pigmentosa GTPase regulator
KeywordsLIPID BINDING PROTEIN / immunoglobulin-like beta-sandwich / RCC1-like domain / beta propellar / seven bladed-propeller / STRUCTURAL PROTEIN
Function / homology
Function and homology information


protein localization to non-motile cilium / ARL13B-mediated ciliary trafficking of INPP5E / intraciliary transport / GTPase inhibitor activity / photoreceptor connecting cilium / eye photoreceptor cell development / cilium assembly / photoreceptor outer segment / sperm flagellum / visual perception ...protein localization to non-motile cilium / ARL13B-mediated ciliary trafficking of INPP5E / intraciliary transport / GTPase inhibitor activity / photoreceptor connecting cilium / eye photoreceptor cell development / cilium assembly / photoreceptor outer segment / sperm flagellum / visual perception / positive regulation of autophagy / cytoplasmic vesicle membrane / guanyl-nucleotide exchange factor activity / intracellular protein transport / small GTPase binding / RAS processing / ubiquitin protein ligase activity / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / cytoskeleton / protein ubiquitination / cilium / ciliary basal body / intracellular membrane-bounded organelle / centrosome / Golgi apparatus / RNA binding / cytoplasm / cytosol
Similarity search - Function
: / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / GMP phosphodiesterase, delta subunit / Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. ...: / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / GMP phosphodiesterase, delta subunit / Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Coagulation Factor XIII; Chain A, domain 1 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / X-linked retinitis pigmentosa GTPase regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWaetzlich, D. / Vetter, I. / Wittinghofer, A. / Ismail, S.
CitationJournal: Embo Rep. / Year: 2013
Title: The interplay between RPGR, PDE-delta and Arl2/3 regulate the ciliary targeting of farnesylated cargo.
Authors: Watzlich, D. / Vetter, I. / Gotthardt, K. / Miertzschke, M. / Chen, Y.X. / Wittinghofer, A. / Ismail, S.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
C: X-linked retinitis pigmentosa GTPase regulator


Theoretical massNumber of molelcules
Total (without water)60,1262
Polymers60,1262
Non-polymers00
Water7,440413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.830, 58.780, 92.110
Angle α, β, γ (deg.)90.00, 123.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / GMP-PDE delta / Protein p17


Mass: 17585.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Production host: Escherichia coli (E. coli) / References: UniProt: O43924
#2: Protein X-linked retinitis pigmentosa GTPase regulator


Mass: 42540.832 Da / Num. of mol.: 1 / Fragment: RPGR (8-368) the RCC1-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPGR, RP3, XLRP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92834
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M sodium chloride, 0.1M HEPES pH 7.5 and 12% (w/v) PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97939 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2012
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.9→29.39 Å / Num. all: 47164 / Num. obs: 47164 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.43 / % possible all: 99

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Processing

Software
NameVersionClassification
PRODCdata collection
MOLREPphasing
REFMAC5.6.0093refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JHN

4jhn


Resolution: 1.9→29.39 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.012 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22128 2359 5 %RANDOM
Rwork0.19966 ---
obs0.20074 44805 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å21.05 Å2
2--0.69 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 0 413 4328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224020
X-RAY DIFFRACTIONr_angle_refined_deg0.8971.9425437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6175504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87824.62184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30615677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4021517
X-RAY DIFFRACTIONr_chiral_restr0.0620.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213052
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 169 -
Rwork0.253 3168 -
obs--99.02 %

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