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- PDB-2yc4: Intraflagellar Transport Complex 25-27 from Chlamydomonas -

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Basic information

Entry
Database: PDB / ID: 2yc4
TitleIntraflagellar Transport Complex 25-27 from Chlamydomonas
Components
  • INTRAFLAGELLAR TRANSPORT PROTEIN 25
  • SMALL RAB-RELATED GTPASE
KeywordsTRANSPORT PROTEIN / CILIUM / IFT COMPLEX
Function / homology
Function and homology information


intraciliary transport particle B / intraciliary transport / motile cilium / cytoskeleton / endosome / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Intraflagellar transport protein 25 / small GTPase Rab1 family profile. / Galactose-binding domain-like / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Galactose-binding-like domain superfamily / Small GTP-binding protein domain ...Intraflagellar transport protein 25 / small GTPase Rab1 family profile. / Galactose-binding domain-like / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Galactose-binding-like domain superfamily / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Jelly Rolls / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Intraflagellar transport protein 27 / Intraflagellar transport protein 25
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBhogaraju, S. / Taschner, M. / Lorentzen, E.
CitationJournal: Embo J. / Year: 2011
Title: Crystal Structure of the Intraflagellar Transport Complex 25/27.
Authors: Bhogaraju, S. / Taschner, M. / Morawetz, M. / Basquin, C. / Lorentzen, E.
History
DepositionMar 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: INTRAFLAGELLAR TRANSPORT PROTEIN 25
B: INTRAFLAGELLAR TRANSPORT PROTEIN 25
C: SMALL RAB-RELATED GTPASE
D: SMALL RAB-RELATED GTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6628
Polymers77,5224
Non-polymers1404
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-49.7 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.020, 68.300, 93.780
Angle α, β, γ (deg.)90.00, 92.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9775, 0.193185, 0.0847), (0.185877, -0.978705, 0.087095), (0.099722, -0.069391, -0.992593)-1.58298, -6.61124, 45.6719
2given(0.983811, -0.147133, 0.10231), (-0.141925, -0.988265, -0.05648), (0.10942, 0.041045, -0.993148)-7.40766, 1.40745, 44.2976

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein INTRAFLAGELLAR TRANSPORT PROTEIN 25 / IFT25


Mass: 15690.838 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8LIX8
#2: Protein SMALL RAB-RELATED GTPASE / IFT27


Mass: 23070.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8HN58

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Non-polymers , 4 types, 30 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsC-TERMINAL TRUNCATION, ONLY RESIDUES 1-135 IN CONSTRUCT

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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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 6 / Details: 25%PEG 3350 50MM MES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.973
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15717 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 48.27 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellResolution: 2.8→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TVG

1tvg


Resolution: 2.8→46.848 Å / SU ML: 0.49 / σ(F): 2 / Phase error: 34.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3158 787 5 %
Rwork0.2254 --
obs0.2298 15717 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.813 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1-1.2698 Å20 Å2-0.3044 Å2
2--0.8346 Å20 Å2
3----2.1045 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4629 0 4 26 4659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014717
X-RAY DIFFRACTIONf_angle_d1.3696425
X-RAY DIFFRACTIONf_dihedral_angle_d16.5941626
X-RAY DIFFRACTIONf_chiral_restr0.082761
X-RAY DIFFRACTIONf_plane_restr0.006828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.97540.40341300.31452479X-RAY DIFFRACTION100
2.9754-3.20510.3711290.28612450X-RAY DIFFRACTION100
3.2051-3.52750.34361310.2482482X-RAY DIFFRACTION100
3.5275-4.03770.32631310.21052485X-RAY DIFFRACTION100
4.0377-5.08620.24851310.17742480X-RAY DIFFRACTION100
5.0862-46.85480.29261350.21512554X-RAY DIFFRACTION100

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