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- PDB-3bh7: Crystal structure of the RP2-Arl3 complex bound to GDP-AlF4 -

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Basic information

Entry
Database: PDB / ID: 3bh7
TitleCrystal structure of the RP2-Arl3 complex bound to GDP-AlF4
Components
  • ADP-ribosylation factor-like protein 3
  • Protein XRP2
KeywordsSIGNALING PROTEIN / Protein-Protein complex / GTPase Activating protein and GTPase / Retinitis pigmentosa / GTP-binding / Lipoprotein / Myristate / Nucleotide-binding / Disease mutation / Membrane / Palmitate / Phosphoprotein / Sensory transduction / Vision / METAL BINDING PROTEIN
Function / homology
Function and homology information


Trafficking of myristoylated proteins to the cilium / Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / periciliary membrane compartment / protein localization to ciliary membrane / intraciliary transport / post-Golgi vesicle-mediated transport / ciliary transition zone / photoreceptor connecting cilium / Golgi to plasma membrane transport ...Trafficking of myristoylated proteins to the cilium / Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / periciliary membrane compartment / protein localization to ciliary membrane / intraciliary transport / post-Golgi vesicle-mediated transport / ciliary transition zone / photoreceptor connecting cilium / Golgi to plasma membrane transport / smoothened signaling pathway / small GTPase-mediated signal transduction / axoneme / cytoplasmic microtubule / mitotic cytokinesis / cilium assembly / visual perception / centriole / GTPase activator activity / ciliary basal body / kidney development / spindle microtubule / cilium / GDP binding / microtubule cytoskeleton / unfolded protein binding / protein transport / protein folding / midbody / cytoplasmic vesicle / microtubule binding / nuclear body / Golgi membrane / GTPase activity / centrosome / GTP binding / Golgi apparatus / magnesium ion binding / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Protein XRP2 / Tubulin binding cofactor C-like domain / Tubulin binding cofactor C / Pectate Lyase C-like - #70 / Adenylate cyclase-associated CAP, C-terminal superfamily / CARP motif / ADP-ribosylation factor-like protein 2/3 / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. ...Protein XRP2 / Tubulin binding cofactor C-like domain / Tubulin binding cofactor C / Pectate Lyase C-like - #70 / Adenylate cyclase-associated CAP, C-terminal superfamily / CARP motif / ADP-ribosylation factor-like protein 2/3 / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / Nucleoside diphosphate kinase-like domain superfamily / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Pectate Lyase C-like / 3 Solenoid / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Protein XRP2 / ADP-ribosylation factor-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVeltel, S. / Gasper, R. / Wittinghofer, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: The retinitis pigmentosa 2 gene product is a GTPase-activating protein for Arf-like 3
Authors: Veltel, S. / Gasper, R. / Eisenacher, E. / Wittinghofer, A.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosylation factor-like protein 3
B: Protein XRP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7825
Polymers58,2122
Non-polymers5703
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-21.1 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.698, 77.943, 97.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ADP-ribosylation factor-like protein 3


Mass: 18384.799 Da / Num. of mol.: 1 / Fragment: residues 14-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ARL3 / Plasmid: pGEX4T5-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q9WUL7
#2: Protein Protein XRP2


Mass: 39827.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RP2 / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: O75695

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Non-polymers , 4 types, 222 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.4M potassium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→19.73 Å / Num. all: 44554 / Num. obs: 44554 / % possible obs: 98.7 % / Observed criterion σ(I): 5.3 / Redundancy: 4.1 % / Biso Wilson estimate: 30.076 Å2 / Rsym value: 0.042 / Net I/σ(I): 20.03
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 6262 / Rsym value: 0.323 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KSG, 2BX6

1ksg

2bx6


Resolution: 1.9→19.73 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.731 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26194 2228 5 %RANDOM
Rwork0.23185 ---
obs0.23336 42324 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.076 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3745 0 34 219 3998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223873
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9635254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2515479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02124.946184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35515671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5691521
X-RAY DIFFRACTIONr_chiral_restr0.0760.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022918
X-RAY DIFFRACTIONr_nbd_refined0.1940.21834
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2241
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.215
X-RAY DIFFRACTIONr_mcbond_it0.5281.52455
X-RAY DIFFRACTIONr_mcangle_it0.87923840
X-RAY DIFFRACTIONr_scbond_it1.10831633
X-RAY DIFFRACTIONr_scangle_it1.7424.51411
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 161 -
Rwork0.27 3066 -
obs-3066 100 %

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