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- PDB-4lvp: Crystal structure of IFT81 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4lvp
TitleCrystal structure of IFT81 N-terminal domain
ComponentsIntraflagellar transport protein 81
KeywordsTRANSPORT PROTEIN / CH domain / Tubulin/Microtubules
Function / homology
Function and homology information


intraciliary transport involved in cilium assembly / intraciliary transport particle B / motile cilium / cilium assembly / tubulin binding / apical part of cell
Similarity search - Function
Intraflagellar transport protein 81, N-terminal domain / Intraflagellar transport protein 81 / IFT81, calponin homology domain / IFT81, N-terminal domain superfamily / Intraflagellar transport 81 calponin homology domain / Actin-binding Protein, T-fimbrin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Tantalum / Intraflagellar transport protein 81
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.323 Å
AuthorsBhogaraju, S.
CitationJournal: Science / Year: 2013
Title: Molecular Basis of Tubulin Transport Within the Cilium by IFT74 and IFT81.
Authors: Bhogaraju, S. / Cajanek, L. / Fort, C. / Blisnick, T. / Weber, K. / Taschner, M. / Mizuno, N. / Lamla, S. / Bastin, P. / Nigg, E.A. / Lorentzen, E.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Intraflagellar transport protein 81
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1995
Polymers14,4751
Non-polymers7244
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Intraflagellar transport protein 81
hetero molecules

A: Intraflagellar transport protein 81
hetero molecules

A: Intraflagellar transport protein 81
hetero molecules

A: Intraflagellar transport protein 81
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,79420
Polymers57,8994
Non-polymers2,89516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area8030 Å2
ΔGint-39 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.066, 76.066, 94.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-201-

TA0

21A-203-

TA0

31A-304-

HOH

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Components

#1: Protein Intraflagellar transport protein 81 / IFT81


Mass: 14474.735 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-126)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: IFT81, CHLREDRAFT_138649 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q68RJ5
#2: Chemical
ChemComp-TA0 / Tantalum


Mass: 180.948 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ta
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.8 M ammonium sulfate, 0.1 M Tris, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.2545 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2545 Å / Relative weight: 1
ReflectionResolution: 2.323→38.277 Å / Num. all: 13116 / Num. obs: 13104 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.323→2.47 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXAutosolmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
PHENIXAutosolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.323→38.277 Å / SU ML: 0.73 / σ(F): 2.09 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 660 5.03 %RANDOM
Rwork0.2141 ---
all0.221 13116 --
obs0.2153 13104 99.76 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.109 Å2 / ksol: 0.307 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-0 Å2
2--0.26 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.323→38.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 4 21 1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091003
X-RAY DIFFRACTIONf_angle_d1.2951362
X-RAY DIFFRACTIONf_dihedral_angle_d17.119373
X-RAY DIFFRACTIONf_chiral_restr0.084157
X-RAY DIFFRACTIONf_plane_restr0.005172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.323-2.50210.32471310.29512443X-RAY DIFFRACTION99
2.5021-2.75390.31681360.29192511X-RAY DIFFRACTION100
2.7539-3.15220.31411330.26422486X-RAY DIFFRACTION100
3.1522-3.97080.25231290.2192509X-RAY DIFFRACTION100
3.9708-38.28240.17641310.1692507X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.10590.24330.14780.70330.38680.2136-0.43480.62980.0727-0.2968-0.8629-0.3183-0.3060.4404-0.44820.37070.06540.14240.61340.20340.415629.174126.67022.2949
20.245-0.39680.08381.85280.77030.77610.25310.23920.58830.5397-0.3443-0.4370.46451.01620.10710.3371-0.03520.05970.46850.01350.406325.83823.917311.8455
30.3502-0.1676-0.26780.33020.51150.8167-0.0821-0.48780.070.2371-0.01170.17950.95860.81270.02750.5330.15840.09890.31530.03070.331924.578715.71133.788
41.86260.45421.38340.10770.33521.00810.40180.1937-0.1329-0.12370.47740.19110.447-0.1060.87151.0979-0.13420.53830.12960.06630.712412.99813.05539.627
50.00530.0031-0.00820.0073-0.01690.0526-0.1071-0.19270.05350.1765-0.16830.12310.03740.18740.00081.2833-0.08160.17720.4229-0.06050.601516.66674.02223.0473
60.29810.1071-0.08530.0723-0.02990.08510.01030.82760.1261-0.3224-0.11061.24130.5908-0.6342-0.01480.6417-0.02920.00730.43730.00860.555912.977817.3154-5.828
70.46090.06910.0782-0.00420.02030.2669-0.26250.67790.33040.14770.01770.09530.26840.6647-0.04420.44180.11960.17040.49160.05560.405820.7717.6714-6.795
80.0143-0.02930.12670.0969-0.44511.9878-0.2859-0.23431.0642-0.3205-0.5959-0.76340.5656-0.0333-0.1220.3099-0.0096-0.04650.3109-0.02510.669112.764629.28127.0051
90.9463-0.3751-0.35430.76070.00470.16710.2610.68720.7456-0.6097-0.16490.0268-0.34810.06390.29490.3914-0.1264-0.03960.5959-0.10950.30661.467227.75216.2533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and ( resseq 0:12 )A0 - 12
2X-RAY DIFFRACTION2chain A and ( resseq 13:21 )A13 - 21
3X-RAY DIFFRACTION3chain A and ( resseq 22:44 )A22 - 44
4X-RAY DIFFRACTION4chain A and ( resseq 45:52 )A45 - 52
5X-RAY DIFFRACTION5chain A and ( resseq 53:57 )A53 - 57
6X-RAY DIFFRACTION6chain A and ( resseq 58:80 )A58 - 80
7X-RAY DIFFRACTION7chain A and ( resseq 81:104 )A81 - 104
8X-RAY DIFFRACTION8chain A and ( resseq 105:114 )A105 - 114
9X-RAY DIFFRACTION9chain A and ( resseq 115:125 )A115 - 125

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