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- PDB-4zi2: BART-like domain of BARTL1/CCDC104 in complex with Arl3FL bound t... -

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Basic information

Entry
Database: PDB / ID: 4zi2
TitleBART-like domain of BARTL1/CCDC104 in complex with Arl3FL bound to GppNHp in P21 21 21
Components
  • ADP-ribosylation factor-like protein 3
  • Cilia- and flagella-associated protein 36
KeywordsHYDROLASE / Complex / Arf-like GTPase / GTP-binding / BART-like domain / cilia
Function / homology
Function and homology information


Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / protein localization to ciliary membrane / intraciliary transport / post-Golgi vesicle-mediated transport / ciliary transition zone / photoreceptor connecting cilium / Golgi to plasma membrane transport / motile cilium / ciliary base ...Trafficking of myristoylated proteins to the cilium / photoreceptor cell development / protein localization to ciliary membrane / intraciliary transport / post-Golgi vesicle-mediated transport / ciliary transition zone / photoreceptor connecting cilium / Golgi to plasma membrane transport / motile cilium / ciliary base / smoothened signaling pathway / small GTPase-mediated signal transduction / cytoplasmic microtubule / axoneme / mitotic cytokinesis / cilium assembly / ciliary basal body / kidney development / spindle microtubule / cilium / GDP binding / microtubule cytoskeleton / protein transport / midbody / microtubule binding / Golgi membrane / GTPase activity / centrosome / GTP binding / Golgi apparatus / magnesium ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Cilia- and flagella-associated protein 36 / Adp-ribosylation factor-like protein 2-binding protein fold / ADP-ribosylation factor-like 2-binding protein, domain / BART domain / BART domain superfamily / The ARF-like 2 binding protein BART / ADP-ribosylation factor-like protein 2/3 / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type ...Cilia- and flagella-associated protein 36 / Adp-ribosylation factor-like protein 2-binding protein fold / ADP-ribosylation factor-like 2-binding protein, domain / BART domain / BART domain superfamily / The ARF-like 2 binding protein BART / ADP-ribosylation factor-like protein 2/3 / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Cilia- and flagella-associated protein 36 / ADP-ribosylation factor-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLokaj, M. / Koerner, C. / Koesling, S. / Wittinghofer, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council (ERC) Advanced GrantARCID; No. 268782 Germany
CitationJournal: Structure / Year: 2015
Title: The Interaction of CCDC104/BARTL1 with Arl3 and Implications for Ciliary Function.
Authors: Lokaj, M. / Kosling, S.K. / Koerner, C. / Lange, S.M. / van Beersum, S.E. / van Reeuwijk, J. / Roepman, R. / Horn, N. / Ueffing, M. / Boldt, K. / Wittinghofer, A.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 2.0Oct 9, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1Jan 10, 2024Group: 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
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.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

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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: ADP-ribosylation factor-like protein 3
C: Cilia- and flagella-associated protein 36
D: Cilia- and flagella-associated protein 36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3998
Polymers74,3064
Non-polymers1,0934
Water6,900383
1
A: ADP-ribosylation factor-like protein 3
C: Cilia- and flagella-associated protein 36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7004
Polymers37,1532
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-31 kcal/mol
Surface area16550 Å2
MethodPISA
2
B: ADP-ribosylation factor-like protein 3
D: Cilia- and flagella-associated protein 36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7004
Polymers37,1532
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-31 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.700, 98.600, 102.430
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: 21582.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arl3 / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9WUL7
#2: Protein Cilia- and flagella-associated protein 36 / Coiled-coil domain-containing protein 104 / CCDC104/BARTL1


Mass: 15570.520 Da / Num. of mol.: 2 / Fragment: UNP residues 1-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cfap36, Ccdc104 / Plasmid: pGex4T1 Gateway / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q8C6E0
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1 M LiCl, 0.1 M MES pH 6.0, 30% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→29.73 Å / Num. all: 36504 / Num. obs: 36470 / % possible obs: 99.9 % / Redundancy: 6.55 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.87
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.66 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DOE

3doe


Resolution: 2.2→29.727 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1826 5.01 %Random selection
Rwork0.2057 ---
obs0.2087 36470 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4941 0 66 383 5390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085147
X-RAY DIFFRACTIONf_angle_d1.0986980
X-RAY DIFFRACTIONf_dihedral_angle_d17.1281950
X-RAY DIFFRACTIONf_chiral_restr0.042790
X-RAY DIFFRACTIONf_plane_restr0.005891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25950.34391380.23562620X-RAY DIFFRACTION100
2.2595-2.32590.29261390.21432633X-RAY DIFFRACTION100
2.3259-2.4010.24111390.21442637X-RAY DIFFRACTION100
2.401-2.48680.2661380.21242609X-RAY DIFFRACTION100
2.4868-2.58630.29061390.21372653X-RAY DIFFRACTION100
2.5863-2.70390.28721380.22472623X-RAY DIFFRACTION100
2.7039-2.84630.29761400.22212650X-RAY DIFFRACTION100
2.8463-3.02450.26841400.21512653X-RAY DIFFRACTION100
3.0245-3.25780.26941390.21322646X-RAY DIFFRACTION100
3.2578-3.58510.26631410.18742670X-RAY DIFFRACTION100
3.5851-4.10270.22741420.18582701X-RAY DIFFRACTION100
4.1027-5.16460.29541430.18832717X-RAY DIFFRACTION100
5.1646-29.73010.23371500.21992832X-RAY DIFFRACTION100

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