[English] 日本語
Yorodumi
- PDB-2yc2: Intraflagellar Transport Complex 25-27 from Chlamydomonas -

+
Open data


ID or keywords:

Loading...

-
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 / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Intraflagellar transport protein 25 / Small GTPase Rab domain profile. / Galactose-binding domain-like / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Galactose-binding-like domain superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain ...Intraflagellar transport protein 25 / Small GTPase Rab domain profile. / Galactose-binding domain-like / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Galactose-binding-like domain superfamily / Rab subfamily of small GTPases / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more