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- PDB-4uzz: Crystal structure of the TtIFT52-46 complex -

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Basic information

Entry
Database: PDB / ID: 4uzz
TitleCrystal structure of the TtIFT52-46 complex
Components
  • INTRAFLAGELLAR TRANSPORT COMPLEX B PROTEIN 46 CARBOXY-TERMINAL PROTEIN
  • INTRAFLAGELLAR TRANSPORTER-LIKE PROTEIN
KeywordsMOTOR PROTEIN / CILIUM / IFT / INTRACELLULAR TRANSPORT / FLAGELLUM
Function / homology
Function and homology information


intraciliary transport / motile cilium / cytoskeleton / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2800 / Intraflagellar transport complex B protein 46 / Intraflagellar transport complex B protein 46 C terminal / Intraflagellar transport protein 52 homolog / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Intraflagellar transporter-like protein / Intraflagellar transport complex B protein 46 carboxy-terminal protein
Similarity search - Component
Biological speciesTETRAHYMENA THERMOPHILA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.318 Å
AuthorsBraeuer, P. / Taschner, M. / Lorentzen, E.
CitationJournal: J.Cell Biol. / Year: 2014
Title: Crystal Structures of Ift70/52 and Ift52/46 Provide Insight Into Intraflagellar Transport B Core Complex Assembly.
Authors: Taschner, M. / Kotsis, F. / Braeuer, P. / Kuehn, E.W. / Lorentzen, E.
History
DepositionSep 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTRAFLAGELLAR TRANSPORT COMPLEX B PROTEIN 46 CARBOXY-TERMINAL PROTEIN
B: INTRAFLAGELLAR TRANSPORTER-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,1732
Polymers21,1732
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-31.4 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.394, 84.394, 95.477
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein INTRAFLAGELLAR TRANSPORT COMPLEX B PROTEIN 46 CARBOXY-TERMINAL PROTEIN / INTRAFLAGELLAR TRANSPORT PROTEIN 46


Mass: 13460.124 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 221-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TETRAHYMENA THERMOPHILA (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q23KH7
#2: Protein INTRAFLAGELLAR TRANSPORTER-LIKE PROTEIN / INTRAFLAGELLAR TRANSPORT PROTEIN 52


Mass: 7712.705 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 371-434
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TETRAHYMENA THERMOPHILA (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I7LT74
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGAAS IS A LEFTOVER SEQUENCE FROM THE N-TERMINAL AFFINITY TAG

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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: 4.6 Å3/Da / Density % sol: 73 % / Description: NONE
Crystal growpH: 8.2 / Details: 50MM TRISD PH 8.2, 0.6M TRI-SODIUM- CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→40 Å / Num. obs: 17160 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 71.12 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.6 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.318→42.197 Å / SU ML: 0.32 / σ(F): 1.33 / Phase error: 38.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 878 5.1 %
Rwork0.2393 --
obs0.2406 17159 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.318→42.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 0 3 1372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091397
X-RAY DIFFRACTIONf_angle_d1.2191898
X-RAY DIFFRACTIONf_dihedral_angle_d17.786511
X-RAY DIFFRACTIONf_chiral_restr0.043216
X-RAY DIFFRACTIONf_plane_restr0.005248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3175-2.46270.39121320.39012453X-RAY DIFFRACTION90
2.4627-2.65280.4071550.35742709X-RAY DIFFRACTION99
2.6528-2.91970.36091560.32042678X-RAY DIFFRACTION99
2.9197-3.34210.34591500.30482751X-RAY DIFFRACTION99
3.3421-4.210.30091330.25212792X-RAY DIFFRACTION100
4.21-42.2040.20851520.19572898X-RAY DIFFRACTION100

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