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- PDB-3bh6: Crystal structure of the RP2-Arl3 complex bound to GppNHp -

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Basic information

Entry
Database: PDB / ID: 3bh6
TitleCrystal structure of the RP2-Arl3 complex bound to GppNHp
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 / mitotic cytokinesis / axoneme / cilium assembly / cytoplasmic microtubule / visual perception / centriole / GTPase activator activity / spindle microtubule / kidney development / GDP binding / unfolded protein binding / protein folding / protein transport / cytoplasmic vesicle / midbody / microtubule binding / nuclear body / cilium / ciliary basal body / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / GTP binding / magnesium ion binding / Golgi apparatus / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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 / 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. / ADP-ribosylation factor-like protein 2/3 ...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 / 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. / ADP-ribosylation factor-like protein 2/3 / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / Nucleoside diphosphate kinase-like domain / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Nucleoside diphosphate kinase-like domain superfamily / Pectate Lyase C-like / ARF-like small GTPases; ARF, ADP-ribosylation factor / 3 Solenoid / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 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: 2.6 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 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)58,7434
Polymers58,1972
Non-polymers5472
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-15.9 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.860, 78.490, 98.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18369.828 Da / Num. of mol.: 1 / Fragment: residues 14-177 / Mutation: Q71L
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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M potassium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→19.81 Å / Num. all: 18118 / Num. obs: 18118 / % possible obs: 99.6 % / Observed criterion σ(I): 3.8 / Redundancy: 5.9 % / Biso Wilson estimate: 36.068 Å2 / Rsym value: 0.082 / Net I/σ(I): 16.12
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.75 / Num. unique all: 1919 / Rsym value: 0.435 / % possible all: 99.9

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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: 2.6→19.81 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.879 / SU B: 11.431 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 1.133 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27078 1812 10 %RANDOM
Rwork0.21466 ---
obs0.22029 16304 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: 36.051 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---1.57 Å20 Å2
3---2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 33 48 3825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223849
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9635219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4485473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.7924.945182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.28315664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5031521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022894
X-RAY DIFFRACTIONr_nbd_refined0.2320.21763
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22608
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2143
X-RAY DIFFRACTIONr_metal_ion_refined0.1490.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.27
X-RAY DIFFRACTIONr_mcbond_it0.5531.52413
X-RAY DIFFRACTIONr_mcangle_it1.00823822
X-RAY DIFFRACTIONr_scbond_it1.32431619
X-RAY DIFFRACTIONr_scangle_it2.2114.51397
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 129 -
Rwork0.307 1165 -
obs-1165 100 %

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