[English] 日本語
Yorodumi
- PDB-6iae: T. brucei IFT22 GDP-bound crystal structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6iae
TitleT. brucei IFT22 GDP-bound crystal structure
ComponentsIntraflagellar transport protein 22
KeywordsCYTOSOLIC PROTEIN / Intraflagellar transport protein 22 / cilium formation / Rab-like / GTPase / RabL5
Function / homology
Function and homology information


intraciliary transport particle B / motile cilium / cilium assembly / endomembrane system / intracellular protein transport / cilium / ciliary basal body / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Ras of Complex, Roc, domain of DAPkinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Intraflagellar transport protein 22
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsWachter, S. / Basquin, J. / Lorentzen, E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF15OC0014164 Denmark
CitationJournal: Embo J. / Year: 2019
Title: Binding of IFT22 to the intraflagellar transport complex is essential for flagellum assembly.
Authors: Wachter, S. / Jung, J. / Shafiq, S. / Basquin, J. / Fort, C. / Bastin, P. / Lorentzen, E.
History
DepositionNov 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 8, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Intraflagellar transport protein 22
B: Intraflagellar transport protein 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6656
Polymers49,5702
Non-polymers1,0954
Water27015
1
A: Intraflagellar transport protein 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3323
Polymers24,7851
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Intraflagellar transport protein 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3323
Polymers24,7851
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.015, 56.015, 263.085
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Intraflagellar transport protein 22


Mass: 24784.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Gene: IFT22, Tb11.01.8590 / Production host: Escherichia coli (E. coli) / References: UniProt: Q381A3
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 15% (w/v) PEG6000, 50 mM NaCacodylate pH 7.0 and 200 mM CaAcetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97891 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 16300 / % possible obs: 99.3 % / Redundancy: 19.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Net I/av σ(I): 18.5 / Net I/σ(I): 18.5
Reflection shellResolution: 2.49→2.57 Å / Redundancy: 17.5 % / Rmerge(I) obs: 2.8 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1558 / CC1/2: 0.363 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→48.51 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.71
RfactorNum. reflection% reflection
Rfree0.2442 820 5.05 %
Rwork0.2202 --
obs0.2234 16236 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.49→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 58 15 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062369
X-RAY DIFFRACTIONf_angle_d0.9563234
X-RAY DIFFRACTIONf_dihedral_angle_d11.7051386
X-RAY DIFFRACTIONf_chiral_restr0.05380
X-RAY DIFFRACTIONf_plane_restr0.007403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4924-2.64850.39291330.36072569X-RAY DIFFRACTION95
2.6485-2.8530.30921300.31032551X-RAY DIFFRACTION95
2.853-3.14010.26571420.26912559X-RAY DIFFRACTION95
3.1401-3.59430.26991270.2342577X-RAY DIFFRACTION95
3.5943-4.52790.22851480.19142550X-RAY DIFFRACTION94
4.5279-47.71490.22161390.2012590X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 5.5561 Å / Origin y: -3.3355 Å / Origin z: 22.2839 Å
111213212223313233
T0.8236 Å2-0.2856 Å20.0561 Å2-0.44 Å20.0198 Å2--0.5901 Å2
L1.4011 °20.1739 °20.585 °2-1.4002 °20.9311 °2--1.6747 °2
S-0.133 Å °0.1891 Å °0.1307 Å °0.1794 Å °0.167 Å °0.3412 Å °-0.1122 Å °0.1375 Å °-0.0453 Å °
Refinement TLS groupSelection details: all

+
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