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- PDB-4uzy: Crystal structure of the Chlamydomonas IFT70 and IFT52 complex -

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Basic information

Entry
Database: PDB / ID: 4uzy
TitleCrystal structure of the Chlamydomonas IFT70 and IFT52 complex
Components
  • FLAGELLAR ASSOCIATED PROTEIN
  • INTRAFLAGELLAR TRANSPORT PROTEIN IFT52
KeywordsMOTOR PROTEIN / CILIUM / INTRAFLAGELLAR TRANSPORT / IFT / INTRACELLUALR TRANSPORT / FLAGELLUM
Function / homology
Function and homology information


intraciliary transport particle B binding / intraciliary transport particle B / intraciliary transport / axonemal microtubule / motile cilium / cilium assembly / centriole / cilium
Similarity search - Function
Tetratricopeptide repeat protein 30 / : / Intraflagellar transport protein 52, C-terminal domain / ABC-type uncharacterised transport system / ABC-type uncharacterized transport system / Intraflagellar transport protein 52 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat / Class I glutamine amidotransferase-like / TPR repeat profile. ...Tetratricopeptide repeat protein 30 / : / Intraflagellar transport protein 52, C-terminal domain / ABC-type uncharacterised transport system / ABC-type uncharacterized transport system / Intraflagellar transport protein 52 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat / Class I glutamine amidotransferase-like / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
CITRATE ANION / MALONATE ION / Uncharacterized protein / Osm-6-like protein
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.477 Å
AuthorsTaschner, 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: FLAGELLAR ASSOCIATED PROTEIN
B: INTRAFLAGELLAR TRANSPORT PROTEIN IFT52
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5544
Polymers80,2632
Non-polymers2912
Water1,928107
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-48.5 kcal/mol
Surface area33510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.177, 143.177, 88.693
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein FLAGELLAR ASSOCIATED PROTEIN / INTRAFLAGELLAR TRANSPORT PROTEIN 70


Mass: 74534.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8ITN7
#2: Protein INTRAFLAGELLAR TRANSPORT PROTEIN IFT52 / INTRAFLAGELLAR TRANSPORT PROTEIN 52


Mass: 5728.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 330-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q946G4
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 7 / Details: 20% TACSIMATE PH 7.0

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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: 2.5→70 Å / Num. obs: 71955 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 69.47 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.7
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.3 / % possible all: 97.2

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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: 2.477→71.588 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 3598 5 %
Rwork0.1855 --
obs0.1878 36787 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.477→71.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 20 107 5459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015487
X-RAY DIFFRACTIONf_angle_d1.3247441
X-RAY DIFFRACTIONf_dihedral_angle_d16.3932044
X-RAY DIFFRACTIONf_chiral_restr0.048816
X-RAY DIFFRACTIONf_plane_restr0.007972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4767-2.50930.40991200.36642271X-RAY DIFFRACTION87
2.5093-2.54370.3891400.32182641X-RAY DIFFRACTION100
2.5437-2.58010.36721390.31672604X-RAY DIFFRACTION100
2.5801-2.61860.33381410.31222662X-RAY DIFFRACTION100
2.6186-2.65950.38831370.32382655X-RAY DIFFRACTION100
2.6595-2.70310.45651420.33172662X-RAY DIFFRACTION100
2.7031-2.74970.38741380.32152614X-RAY DIFFRACTION100
2.7497-2.79970.35231360.28612638X-RAY DIFFRACTION100
2.7997-2.85360.32221430.24842688X-RAY DIFFRACTION100
2.8536-2.91180.24591360.23852604X-RAY DIFFRACTION100
2.9118-2.97510.30781400.23952623X-RAY DIFFRACTION100
2.9751-3.04430.28741410.23162658X-RAY DIFFRACTION100
3.0443-3.12050.2821410.22122687X-RAY DIFFRACTION100
3.1205-3.20480.25881350.22842606X-RAY DIFFRACTION100
3.2048-3.29910.30981420.2312680X-RAY DIFFRACTION100
3.2991-3.40560.27771390.21762620X-RAY DIFFRACTION100
3.4056-3.52730.24491380.19132615X-RAY DIFFRACTION100
3.5273-3.66860.22841440.19462695X-RAY DIFFRACTION100
3.6686-3.83550.19551370.18492605X-RAY DIFFRACTION100
3.8355-4.03770.22811390.16852640X-RAY DIFFRACTION100
4.0377-4.29070.21771380.15212655X-RAY DIFFRACTION100
4.2907-4.62190.23021400.1472651X-RAY DIFFRACTION100
4.6219-5.08690.19531380.14242651X-RAY DIFFRACTION100
5.0869-5.82270.23151330.16222646X-RAY DIFFRACTION100
5.8227-7.33480.19911390.17282651X-RAY DIFFRACTION100
7.3348-71.61840.13581420.13572635X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 44.5489 Å / Origin y: 33.8185 Å / Origin z: 23.2377 Å
111213212223313233
T0.6423 Å20.0797 Å20.0561 Å2-0.4727 Å20.0219 Å2--0.5497 Å2
L0.5087 °2-0.3218 °2-0.6715 °2-0.4067 °20.963 °2--1.6145 °2
S-0.067 Å °-0.07 Å °-0.1402 Å °0.0417 Å °0.0105 Å °-0.004 Å °0.3002 Å °0.0926 Å °0.0392 Å °
Refinement TLS groupSelection details: ALL

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