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- PDB-3t5i: Structure of Fully modified farnesylated Rheb Peptide in complex ... -

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Basic information

Entry
Database: PDB / ID: 3t5i
TitleStructure of Fully modified farnesylated Rheb Peptide in complex with PDE6D
Components
  • C-terminal Farnesylated Rheb peptide CSQQGKSS(CMT)
  • Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsLIPID BINDING PROTEIN / Immunoglobulin-like beta sandwitch fold / Rheb / Farnesyl / prenyl / SIGNALING PROTEIN
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / visual perception / cytoplasmic vesicle membrane / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cilium / intracellular membrane-bounded organelle ...ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / visual perception / cytoplasmic vesicle membrane / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cilium / intracellular membrane-bounded organelle / cytoplasm / cytosol
Similarity search - Function
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 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
FARNESYL / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIsmail, S.A. / Chen, Y.-X. / Wittinghofer, A.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Arl2-GTP and Arl3-GTP regulate a GDI-like transport system for farnesylated cargo.
Authors: Ismail, S.A. / Chen, Y.X. / Rusinova, A. / Chandra, A. / Bierbaum, M. / Gremer, L. / Triola, G. / Waldmann, H. / Bastiaens, P.I. / Wittinghofer, A.
History
DepositionJul 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
A: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
C: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
D: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Q: C-terminal Farnesylated Rheb peptide CSQQGKSS(CMT)
R: C-terminal Farnesylated Rheb peptide CSQQGKSS(CMT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,05010
Polymers72,2256
Non-polymers8254
Water5,008278
1
A: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
R: C-terminal Farnesylated Rheb peptide CSQQGKSS(CMT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7343
Polymers18,5272
Non-polymers2061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7912
Polymers17,5851
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7912
Polymers17,5851
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Q: C-terminal Farnesylated Rheb peptide CSQQGKSS(CMT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7343
Polymers18,5272
Non-polymers2061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.750, 70.050, 71.230
Angle α, β, γ (deg.)90.00, 81.55, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4 / Fragment: Full length PDE delta
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/peptide C-terminal Farnesylated Rheb peptide CSQQGKSS(CMT)


Mass: 942.051 Da / Num. of mol.: 2 / Fragment: C-terminal Farnesylated Rheb peptide / Source method: obtained synthetically
Details: Peptide synthesis , the sequence is the Cterminal sequence of Rheb
#3: Chemical
ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H26
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 MES 6.5 and 30 % PEG 5000 MME , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2010
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 37401 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.1→2.2 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
ProDCdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T5G

3t5g


Resolution: 2.1→29.91 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.965 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24309 1870 5 %RANDOM
Rwork0.18867 ---
all0.19137 35530 --
obs0.19137 35530 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.721 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20.08 Å2
2---0.38 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4799 0 60 278 5137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225031
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9596782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3775607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80423.613238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3915909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0891540
X-RAY DIFFRACTIONr_chiral_restr0.0880.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213788
X-RAY DIFFRACTIONr_mcbond_it0.731.52993
X-RAY DIFFRACTIONr_mcangle_it1.41524832
X-RAY DIFFRACTIONr_scbond_it2.19632038
X-RAY DIFFRACTIONr_scangle_it3.7214.51939
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 137 -
Rwork0.216 2614 -
obs--100 %

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