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- PDB-2yc2: Intraflagellar Transport Complex 25-27 from Chlamydomonas -

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Basic information

Entry
Database: PDB / ID: 2yc2
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: 2.588 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)77,6026
Polymers77,5224
Non-polymers802
Water59433
1
A: INTRAFLAGELLAR TRANSPORT PROTEIN 25
D: SMALL RAB-RELATED GTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8013
Polymers38,7612
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-12.1 kcal/mol
Surface area13200 Å2
MethodPISA
2
B: INTRAFLAGELLAR TRANSPORT PROTEIN 25
C: SMALL RAB-RELATED GTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8013
Polymers38,7612
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-12.1 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.050, 96.220, 66.970
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1, -0.000257, 0.000543), (0.000257, -1, -0.000775), (0.000543, -0.000775, 1)-0.00503, -1.86547, -33.4642
2given(0.999999, -0.000361, -0.001447), (-0.000359, -0.999999, 0.001262), (-0.001447, -0.001262, -0.999998)0.06639, 46.2032, 33.5395

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Components

#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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.9 Å3/Da / Density % sol: 34 % / Description: NONE
Crystal growpH: 6 / Details: 20% PEG 3350, 50MM MES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.973
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 16992 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 36.25 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 1.59→1.74 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / % possible all: 85

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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 ENTRIES 1TVG, 2O52, 1Y2K, 2AED, 1N6H

1tvg

2o52

1y2k

2aed
PDB Unreleased entry

1n6h


Resolution: 2.588→48.11 Å / SU ML: 0.36 / σ(F): 2 / Phase error: 28.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 849 5 %
Rwork0.2036 --
obs0.2067 16991 97.27 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.311 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.808 Å2-0 Å2-1.4569 Å2
2---5.1472 Å20 Å2
3----2.6608 Å2
Refinement stepCycle: LAST / Resolution: 2.588→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 2 33 4339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014381
X-RAY DIFFRACTIONf_angle_d1.3355959
X-RAY DIFFRACTIONf_dihedral_angle_d16.6881521
X-RAY DIFFRACTIONf_chiral_restr0.087705
X-RAY DIFFRACTIONf_plane_restr0.005764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5883-2.75040.35111240.28452352X-RAY DIFFRACTION85
2.7504-2.96270.35211430.24762719X-RAY DIFFRACTION100
2.9627-3.26080.27361440.21842737X-RAY DIFFRACTION100
3.2608-3.73250.28331450.18832762X-RAY DIFFRACTION99
3.7325-4.7020.21471460.16462767X-RAY DIFFRACTION100
4.702-48.11830.24451470.20632805X-RAY DIFFRACTION99

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