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- PDB-5n4a: Crystal structure of Chlamydomonas IFT80 -

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Basic information

Entry
Database: PDB / ID: 5n4a
TitleCrystal structure of Chlamydomonas IFT80
ComponentsIntraflagellar transport protein 80
KeywordsTRANSPORT PROTEIN / cilium / intraflagellar transport / IFT80
Function / homology
Function and homology information


intraciliary transport particle B / motile cilium / cilium assembly / cilium
Similarity search - Function
Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
OXALATE ION / Intraflagellar transport protein 80
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å
AuthorsTaschner, M. / Mourao, A.
CitationJournal: Elife / Year: 2018
Title: Crystal structure of intraflagellar transport protein 80 reveals a homo-dimer required for ciliogenesis.
Authors: Taschner, M. / Lorentzen, A. / Mourao, A. / Collins, T. / Freke, G.M. / Moulding, D. / Basquin, J. / Jenkins, D. / Lorentzen, E.
History
DepositionFeb 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intraflagellar transport protein 80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,89715
Polymers86,6121
Non-polymers1,28514
Water13,223734
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-1 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.778, 195.403, 117.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Intraflagellar transport protein 80 /


Mass: 86611.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A5Z0S9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 734 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM MES pH 6.0 and 100 mM Na-oxalate, 18C cryo-protected by the addition of 30% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→47 Å / Num. obs: 173465 / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.3
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1 / Num. unique obs: 27521 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIXdev_1647refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→46.925 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 23.14
RfactorNum. reflection% reflection
Rfree0.2071 8705 5.02 %
Rwork0.1737 --
obs0.1754 173479 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.79→46.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4921 0 84 734 5739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075416
X-RAY DIFFRACTIONf_angle_d1.0567384
X-RAY DIFFRACTIONf_dihedral_angle_d12.7131975
X-RAY DIFFRACTIONf_chiral_restr0.047821
X-RAY DIFFRACTIONf_plane_restr0.004954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7868-1.80710.3632560.36584841X-RAY DIFFRACTION87
1.8071-1.82840.39512920.34765530X-RAY DIFFRACTION100
1.8284-1.85070.34472910.31895484X-RAY DIFFRACTION100
1.8507-1.87410.30822920.30495530X-RAY DIFFRACTION100
1.8741-1.89880.32662880.29875496X-RAY DIFFRACTION100
1.8988-1.92480.36242900.31885534X-RAY DIFFRACTION100
1.9248-1.95230.32282930.30225502X-RAY DIFFRACTION99
1.9523-1.98140.27722910.26685445X-RAY DIFFRACTION100
1.9814-2.01240.29942880.24945551X-RAY DIFFRACTION100
2.0124-2.04540.24162920.24035494X-RAY DIFFRACTION100
2.0454-2.08060.23522930.22325578X-RAY DIFFRACTION100
2.0806-2.11850.23692880.21175504X-RAY DIFFRACTION100
2.1185-2.15920.25522920.20455487X-RAY DIFFRACTION100
2.1592-2.20330.24832940.21045533X-RAY DIFFRACTION100
2.2033-2.25120.29512920.2095525X-RAY DIFFRACTION100
2.2512-2.30360.19922950.19375516X-RAY DIFFRACTION100
2.3036-2.36120.23212980.19035547X-RAY DIFFRACTION100
2.3612-2.4250.24232890.19685497X-RAY DIFFRACTION100
2.425-2.49640.21912880.17695504X-RAY DIFFRACTION100
2.4964-2.57690.22452860.17025529X-RAY DIFFRACTION100
2.5769-2.6690.20062880.16525526X-RAY DIFFRACTION100
2.669-2.77590.19862920.16975530X-RAY DIFFRACTION100
2.7759-2.90220.23262870.16725449X-RAY DIFFRACTION100
2.9022-3.05520.17132960.1525535X-RAY DIFFRACTION100
3.0552-3.24660.1782890.1495528X-RAY DIFFRACTION100
3.2466-3.49720.17652900.1415520X-RAY DIFFRACTION100
3.4972-3.84890.1782930.13545534X-RAY DIFFRACTION100
3.8489-4.40550.17412910.12875511X-RAY DIFFRACTION100
4.4055-5.54910.13982910.12225504X-RAY DIFFRACTION100
5.5491-46.94150.19533000.16915510X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 75.0856 Å / Origin y: 65.6063 Å / Origin z: 67.6085 Å
111213212223313233
T0.175 Å20.008 Å2-0.0284 Å2-0.1702 Å2-0.0031 Å2--0.1952 Å2
L0.4247 °20.0238 °20.0908 °2-0.9322 °2-0.105 °2--1.0581 °2
S0.0041 Å °-0.0004 Å °0.0044 Å °-0.1638 Å °-0.0251 Å °-0.017 Å °-0.0742 Å °-0.041 Å °0.0125 Å °
Refinement TLS groupSelection details: all

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