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- PDB-6ian: T. brucei IFT22/74/81 GTP-bound crystal structure -

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Basic information

Entry
Database: PDB / ID: 6ian
TitleT. brucei IFT22/74/81 GTP-bound crystal structure
Components
  • (Intraflagellar transport protein ...) x 2
  • Rab-like 5
KeywordsCYTOSOLIC PROTEIN / Intraflagellar transport protein 22 / IFT74 / IFT81 / cilium formation / Rab-like / GTPase / RabL5
Function / homology
Function and homology information


intraciliary transport particle / intraciliary transport involved in cilium assembly / intraciliary transport particle B / intraciliary retrograde transport / intraciliary transport / motile cilium / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / beta-tubulin binding / proton motive force-driven ATP synthesis / proton transmembrane transporter activity ...intraciliary transport particle / intraciliary transport involved in cilium assembly / intraciliary transport particle B / intraciliary retrograde transport / intraciliary transport / motile cilium / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / beta-tubulin binding / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / cilium assembly / endomembrane system / tubulin binding / ciliary basal body / intracellular protein transport / cilium / GTPase activity / centrosome / GTP binding / cytoplasm
Similarity search - Function
Intraflagellar transport protein 74 / Intraflagellar transport protein 81 / IFT81, calponin homology domain / IFT81, N-terminal domain superfamily / Intraflagellar transport 81 calponin homology domain / Ras of Complex, Roc, domain of DAPkinase / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Rab-like 5 / Intraflagellar transport protein 22 / C2H2-type domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
Trypanosoma brucei equiperdum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsWachter, S. / Basquin, J. / Lorentzen, E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF15OC0014164 Denmark
CitationJournal: Embo J. / Year: 2019
Title: Binding of IFT22 to the intraflagellar transport complex is essential for flagellum assembly.
Authors: Wachter, S. / Jung, J. / Shafiq, S. / Basquin, J. / Fort, C. / Bastin, P. / Lorentzen, E.
History
DepositionNov 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intraflagellar transport protein 74
C: Intraflagellar transport protein 81
B: Intraflagellar transport protein 74
D: Intraflagellar transport protein 81
E: Rab-like 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,5577
Polymers206,0095
Non-polymers5472
Water82946
1
A: Intraflagellar transport protein 74
C: Intraflagellar transport protein 81


Theoretical massNumber of molelcules
Total (without water)90,6362
Polymers90,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16860 Å2
ΔGint-168 kcal/mol
Surface area44090 Å2
MethodPISA
2
B: Intraflagellar transport protein 74
D: Intraflagellar transport protein 81
E: Rab-like 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9205
Polymers115,3733
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18930 Å2
ΔGint-188 kcal/mol
Surface area51720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.860, 228.300, 115.710
Angle α, β, γ (deg.)90.00, 96.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Intraflagellar transport protein ... , 2 types, 4 molecules ABCD

#1: Protein Intraflagellar transport protein 74 /


Mass: 37731.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.7.3370 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57WF2
#2: Protein Intraflagellar transport protein 81 /


Mass: 52904.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb10.70.5020 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38BY1

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Protein , 1 types, 1 molecules E

#3: Protein Rab-like 5


Mass: 24736.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei equiperdum (eukaryote)
Gene: RABL5, DPX39_110145000 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3L6KZ98, UniProt: Q381A3*PLUS

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Non-polymers , 3 types, 48 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 4.32 Å3/Da / Density % sol: 71.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 15% (v/v) glycerol, 7.5% (w/v) PEG4000, 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97899 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 3.2→83 Å / Num. obs: 113747 / % possible obs: 100 % / Redundancy: 19.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.21 / Net I/σ(I): 11.5
Reflection shellResolution: 3.2→3.4 Å / Rmerge(I) obs: 4.11 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 18991 / CC1/2: 0.395 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→80.982 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 33.1
RfactorNum. reflection% reflection
Rfree0.2797 5663 4.98 %
Rwork0.2412 --
obs0.2431 113665 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→80.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11964 0 33 46 12043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712117
X-RAY DIFFRACTIONf_angle_d1.05816469
X-RAY DIFFRACTIONf_dihedral_angle_d5.8087517
X-RAY DIFFRACTIONf_chiral_restr0.0552001
X-RAY DIFFRACTIONf_plane_restr0.0062189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.43691930.44263635X-RAY DIFFRACTION100
3.2364-3.27450.42291870.41343537X-RAY DIFFRACTION100
3.2745-3.31440.45411870.38753603X-RAY DIFFRACTION100
3.3144-3.35630.37531920.35873662X-RAY DIFFRACTION100
3.3563-3.40050.39691920.33973617X-RAY DIFFRACTION100
3.4005-3.44710.38871850.34363540X-RAY DIFFRACTION100
3.4471-3.49630.3571870.34683600X-RAY DIFFRACTION100
3.4963-3.54850.41191850.3273586X-RAY DIFFRACTION100
3.5485-3.6040.31981900.30873600X-RAY DIFFRACTION100
3.604-3.66310.39441880.28653582X-RAY DIFFRACTION100
3.6631-3.72620.30631950.25013686X-RAY DIFFRACTION100
3.7262-3.7940.30131840.24483569X-RAY DIFFRACTION100
3.794-3.8670.24851850.24083541X-RAY DIFFRACTION100
3.867-3.94590.27361920.23163643X-RAY DIFFRACTION100
3.9459-4.03170.35111890.24233610X-RAY DIFFRACTION100
4.0317-4.12550.29431890.2393576X-RAY DIFFRACTION100
4.1255-4.22860.28361900.23273655X-RAY DIFFRACTION100
4.2286-4.3430.23771850.21673522X-RAY DIFFRACTION100
4.343-4.47070.24681890.21193634X-RAY DIFFRACTION100
4.4707-4.6150.25141890.21263605X-RAY DIFFRACTION100
4.615-4.780.30311900.21563615X-RAY DIFFRACTION100
4.78-4.97130.25271890.21773563X-RAY DIFFRACTION100
4.9713-5.19750.26291910.22923645X-RAY DIFFRACTION100
5.1975-5.47150.38881860.27593567X-RAY DIFFRACTION100
5.4715-5.81420.39241910.3093634X-RAY DIFFRACTION100
5.8142-6.2630.30331910.28263596X-RAY DIFFRACTION100
6.263-6.89290.32291850.25433598X-RAY DIFFRACTION100
6.8929-7.88960.20321890.2143596X-RAY DIFFRACTION100
7.8896-9.93730.20081880.17583620X-RAY DIFFRACTION100
9.9373-81.0080.23531900.21673565X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 21.3313 Å / Origin y: 20.1455 Å / Origin z: 30.2711 Å
111213212223313233
T0.8833 Å20.0493 Å20.0625 Å2-0.9245 Å2-0.0138 Å2--0.8073 Å2
L0.2601 °20.0481 °20.0755 °2-0.1872 °2-0.1032 °2--0.4023 °2
S-0.0502 Å °-0.1288 Å °-0.0371 Å °-0.0448 Å °-0.0583 Å °0.0201 Å °-0.013 Å °-0.1651 Å °0.0808 Å °
Refinement TLS groupSelection details: all

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