[English] 日本語
Yorodumi
- PDB-6ian: T. brucei IFT22/74/81 GTP-bound crystal structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ian
TitleT. brucei IFT22/74/81 GTP-bound crystal structure
Components
  • (Intraflagellar transport protein ...) x 2
  • Rab-like 5
KeywordsCYTOSOLIC PROTEIN / Intraflagellar transport protein 22 / IFT74 / IFT81 / cilium formation / Rab-like / GTPase / RabL5
Function / homology
Function and homology information


intraciliary transport particle / intraciliary transport involved in cilium assembly / intraciliary transport particle B / intraciliary retrograde transport / intraciliary transport / motile cilium / : / beta-tubulin binding / proton motive force-driven ATP synthesis / proton transmembrane transporter activity ...intraciliary transport particle / intraciliary transport involved in cilium assembly / intraciliary transport particle B / intraciliary retrograde transport / intraciliary transport / motile cilium / : / beta-tubulin binding / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / cilium assembly / endomembrane system / tubulin binding / ciliary basal body / intracellular protein transport / cilium / GTPase activity / centrosome / GTP binding / cytoplasm
Similarity search - Function
Intraflagellar transport protein 74 / Intraflagellar transport protein 81 / IFT81, calponin homology domain / IFT81, N-terminal domain superfamily / Intraflagellar transport 81 calponin homology domain / Ras of Complex, Roc, domain of DAPkinase / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Rab-like 5 / Intraflagellar transport protein 22 / C2H2-type domain-containing protein / Intraflagellar transport protein-like protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
Trypanosoma brucei equiperdum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 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 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code_mod

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Intraflagellar transport protein 74
C: Intraflagellar transport protein 81
B: Intraflagellar transport protein 74
D: Intraflagellar transport protein 81
E: Rab-like 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,5577
Polymers206,0095
Non-polymers5472
Water82946
1
A: Intraflagellar transport protein 74
C: Intraflagellar transport protein 81


Theoretical massNumber of molelcules
Total (without water)90,6362
Polymers90,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16860 Å2
ΔGint-168 kcal/mol
Surface area44090 Å2
MethodPISA
2
B: Intraflagellar transport protein 74
D: Intraflagellar transport protein 81
E: Rab-like 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9205
Polymers115,3733
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18930 Å2
ΔGint-188 kcal/mol
Surface area51720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.860, 228.300, 115.710
Angle α, β, γ (deg.)90.00, 96.76, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Intraflagellar transport protein ... , 2 types, 4 molecules ABCD

#1: Protein Intraflagellar transport protein 74


Mass: 37731.594 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)
Strain: 927/4 GUTat10.1 / Gene: Tb927.7.3370 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57WF2
#2: Protein Intraflagellar transport protein 81


Mass: 52904.801 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)
Strain: 927/4 GUTat10.1 / Gene: Tb10.70.5020 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38BY1

-
Protein , 1 types, 1 molecules E

#3: Protein Rab-like 5


Mass: 24736.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei equiperdum (eukaryote)
Gene: RABL5, DPX39_110145000 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3L6KZ98, UniProt: Q381A3*PLUS

-
Non-polymers , 3 types, 48 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 4.32 Å3/Da / Density % sol: 71.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 15% (v/v) glycerol, 7.5% (w/v) PEG4000, 100 mM HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97899 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 3.2→83 Å / Num. obs: 113747 / % possible obs: 100 % / Redundancy: 19.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.21 / Net I/σ(I): 11.5
Reflection shellResolution: 3.2→3.4 Å / Rmerge(I) obs: 4.11 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 18991 / CC1/2: 0.395 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→80.982 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 33.1
RfactorNum. reflection% reflection
Rfree0.2797 5663 4.98 %
Rwork0.2412 --
obs0.2431 113665 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→80.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11964 0 33 46 12043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712117
X-RAY DIFFRACTIONf_angle_d1.05816469
X-RAY DIFFRACTIONf_dihedral_angle_d5.8087517
X-RAY DIFFRACTIONf_chiral_restr0.0552001
X-RAY DIFFRACTIONf_plane_restr0.0062189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.43691930.44263635X-RAY DIFFRACTION100
3.2364-3.27450.42291870.41343537X-RAY DIFFRACTION100
3.2745-3.31440.45411870.38753603X-RAY DIFFRACTION100
3.3144-3.35630.37531920.35873662X-RAY DIFFRACTION100
3.3563-3.40050.39691920.33973617X-RAY DIFFRACTION100
3.4005-3.44710.38871850.34363540X-RAY DIFFRACTION100
3.4471-3.49630.3571870.34683600X-RAY DIFFRACTION100
3.4963-3.54850.41191850.3273586X-RAY DIFFRACTION100
3.5485-3.6040.31981900.30873600X-RAY DIFFRACTION100
3.604-3.66310.39441880.28653582X-RAY DIFFRACTION100
3.6631-3.72620.30631950.25013686X-RAY DIFFRACTION100
3.7262-3.7940.30131840.24483569X-RAY DIFFRACTION100
3.794-3.8670.24851850.24083541X-RAY DIFFRACTION100
3.867-3.94590.27361920.23163643X-RAY DIFFRACTION100
3.9459-4.03170.35111890.24233610X-RAY DIFFRACTION100
4.0317-4.12550.29431890.2393576X-RAY DIFFRACTION100
4.1255-4.22860.28361900.23273655X-RAY DIFFRACTION100
4.2286-4.3430.23771850.21673522X-RAY DIFFRACTION100
4.343-4.47070.24681890.21193634X-RAY DIFFRACTION100
4.4707-4.6150.25141890.21263605X-RAY DIFFRACTION100
4.615-4.780.30311900.21563615X-RAY DIFFRACTION100
4.78-4.97130.25271890.21773563X-RAY DIFFRACTION100
4.9713-5.19750.26291910.22923645X-RAY DIFFRACTION100
5.1975-5.47150.38881860.27593567X-RAY DIFFRACTION100
5.4715-5.81420.39241910.3093634X-RAY DIFFRACTION100
5.8142-6.2630.30331910.28263596X-RAY DIFFRACTION100
6.263-6.89290.32291850.25433598X-RAY DIFFRACTION100
6.8929-7.88960.20321890.2143596X-RAY DIFFRACTION100
7.8896-9.93730.20081880.17583620X-RAY DIFFRACTION100
9.9373-81.0080.23531900.21673565X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 21.3313 Å / Origin y: 20.1455 Å / Origin z: 30.2711 Å
111213212223313233
T0.8833 Å20.0493 Å20.0625 Å2-0.9245 Å2-0.0138 Å2--0.8073 Å2
L0.2601 °20.0481 °20.0755 °2-0.1872 °2-0.1032 °2--0.4023 °2
S-0.0502 Å °-0.1288 Å °-0.0371 Å °-0.0448 Å °-0.0583 Å °0.0201 Å °-0.013 Å °-0.1651 Å °0.0808 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