[English] 日本語
Yorodumi
- PDB-8f5p: Structure of Leishmania tarentolae IFT-A (state 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f5p
TitleStructure of Leishmania tarentolae IFT-A (state 2)
Components
  • (Intraflagellar transport protein ...) x 2
  • (WD_REPEATS_REGION domain-containing ...) x 2
  • NET domain-containing protein
  • TPR_REGION domain-containing protein
KeywordsPROTEIN TRANSPORT / Cilia / IFT
Function / homology
Function and homology information


intraciliary transport particle A / intraciliary retrograde transport / intraciliary transport / non-motile cilium assembly / protein localization to cilium / non-motile cilium / motile cilium / axoneme / cilium assembly / ciliary basal body / cilium
Similarity search - Function
Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / Intraflagellar transport protein 122 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat profile. ...Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / Intraflagellar transport protein 122 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Uncharacterized protein / Intraflagellar transport protein 122B, putative / Wd repeat-containing protein 19 / Intraflagellar transport protein 43 / Intraflagellar transport protein 140 / Uncharacterized protein
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhou, H. / Brown, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141109 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143183 United States
CitationJournal: Cell / Year: 2022
Title: Mechanism of IFT-A polymerization into trains for ciliary transport.
Authors: Shimi Meleppattu / Haixia Zhou / Jin Dai / Miao Gui / Alan Brown /
Abstract: Intraflagellar transport (IFT) is the highly conserved process by which proteins are transported along ciliary microtubules by a train-like polymeric assembly of IFT-A and IFT-B complexes. IFT-A is ...Intraflagellar transport (IFT) is the highly conserved process by which proteins are transported along ciliary microtubules by a train-like polymeric assembly of IFT-A and IFT-B complexes. IFT-A is sandwiched between IFT-B and the ciliary membrane, consistent with its putative role in transporting transmembrane and membrane-associated cargoes. Here, we have used single-particle analysis electron cryomicroscopy (cryo-EM) to determine structures of native IFT-A complexes. We show that subcomplex rearrangements enable IFT-A to polymerize laterally on anterograde IFT trains, revealing a cooperative assembly mechanism. Surprisingly, we discover that binding of IFT-A to IFT-B shields the preferred lipid-binding interface from the ciliary membrane but orients an interconnected network of β-propeller domains with the capacity to accommodate diverse cargoes toward the ciliary membrane. This work provides a mechanistic basis for understanding IFT-train assembly and cargo interactions.
History
DepositionNov 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NET domain-containing protein
B: Intraflagellar transport protein 122B, putative
C: Intraflagellar transport protein 122 homolog
D: TPR_REGION domain-containing protein
E: WD_REPEATS_REGION domain-containing protein
F: WD_REPEATS_REGION domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)839,00210
Polymers838,7416
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 2 types, 2 molecules AD

#1: Protein NET domain-containing protein


Mass: 38742.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KKJ7
#4: Protein TPR_REGION domain-containing protein


Mass: 180805.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640K949

-
Intraflagellar transport protein ... , 2 types, 2 molecules BC

#2: Protein Intraflagellar transport protein 122B, putative


Mass: 139246.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KAU8
#3: Protein Intraflagellar transport protein 122 homolog


Mass: 144971.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KU89

-
WD REPEATS REGION domain-containing ... , 2 types, 2 molecules EF

#5: Protein WD_REPEATS_REGION domain-containing protein


Mass: 182580.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KQ11
#6: Protein WD_REPEATS_REGION domain-containing protein


Mass: 152393.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KHB7

-
Non-polymers , 1 types, 4 molecules

#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: IFT-A / Type: COMPLEX / Entity ID: #2-#6, #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
25 mMMagnesium sulfateMgSO41
31 mMCalcium chlorideCaCl21
450 mMPotassium chlorideKCl1
51 mMDTT1
SpecimenConc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 57.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.8.5image acquisition
7Coot0.9.8.3model fitting
9PHENIX1.18.2-3874model refinement
11RELION4final Euler assignment
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 563466 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00340198
ELECTRON MICROSCOPYf_angle_d0.50654499
ELECTRON MICROSCOPYf_dihedral_angle_d13.54114793
ELECTRON MICROSCOPYf_chiral_restr0.0426178
ELECTRON MICROSCOPYf_plane_restr0.0047034

+
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://pdbjlvh1.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