[English] 日本語
Yorodumi
- PDB-8qat: Cryo-EM structure of Fts-Hook3-FHIP1B at 3.2 A resolution. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qat
TitleCryo-EM structure of Fts-Hook3-FHIP1B at 3.2 A resolution.
Components
  • AKT-interacting protein
  • FHF complex subunit HOOK-interacting protein 1B
  • Protein Hook homolog 3
KeywordsPROTEIN TRANSPORT / motor proteins / molecular motors / cargo adaptors / bidirectional transport / microtubules / cytoskeleton.
Function / homology
Function and homology information


FHF complex / interkinetic nuclear migration / Golgi localization / protein localization to perinuclear region of cytoplasm / microtubule anchoring at centrosome / dynein light chain binding / cytoskeleton-dependent intracellular transport / neuronal stem cell population maintenance / early endosome to late endosome transport / endosome organization ...FHF complex / interkinetic nuclear migration / Golgi localization / protein localization to perinuclear region of cytoplasm / microtubule anchoring at centrosome / dynein light chain binding / cytoskeleton-dependent intracellular transport / neuronal stem cell population maintenance / early endosome to late endosome transport / endosome organization / cis-Golgi network / protein localization to centrosome / DNA damage tolerance / dynein light intermediate chain binding / lysosome organization / endosome to lysosome transport / pericentriolar material / dynein intermediate chain binding / ubiquitin conjugating enzyme activity / dynactin binding / protein K63-linked ubiquitination / positive regulation of protein binding / cytoplasmic microtubule organization / negative regulation of neurogenesis / centriolar satellite / positive regulation of protein phosphorylation / protein transport / microtubule binding / microtubule / apoptotic process / centrosome / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
FHF complex subunit HOOK interacting protein / FHF complex subunit HOOK interacting protein, KELAA motif / FHF complex subunit HOOK interacting protein, C-terminal / Retinoic acid induced 16-like protein / KELAA motif / Family of unknown function (DUF5917) / Hook, C-terminal / HOOK protein coiled-coil region / HOOK, N-terminal / HOOK domain ...FHF complex subunit HOOK interacting protein / FHF complex subunit HOOK interacting protein, KELAA motif / FHF complex subunit HOOK interacting protein, C-terminal / Retinoic acid induced 16-like protein / KELAA motif / Family of unknown function (DUF5917) / Hook, C-terminal / HOOK protein coiled-coil region / HOOK, N-terminal / HOOK domain / : / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Protein Hook homolog 3 / FHF complex subunit HOOK-interacting protein 1B / AKT-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsAbid Ali, F. / Carter, A.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
Wellcome Trust United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: KIF1C activates and extends dynein movement through the FHF cargo adapter.
Authors: Ferdos Abid Ali / Alexander J Zwetsloot / Caroline E Stone / Tomos E Morgan / Richard F Wademan / Andrew P Carter / Anne Straube /
Abstract: Cellular cargos move bidirectionally on microtubules by recruiting opposite polarity motors dynein and kinesin. These motors show codependence, where one requires the activity of the other, although ...Cellular cargos move bidirectionally on microtubules by recruiting opposite polarity motors dynein and kinesin. These motors show codependence, where one requires the activity of the other, although the mechanism is unknown. Here we show that kinesin-3 KIF1C acts as both an activator and a processivity factor for dynein, using in vitro reconstitutions of human proteins. Activation requires only a fragment of the KIF1C nonmotor stalk binding the cargo adapter HOOK3. The interaction site is separate from the constitutive factors FTS and FHIP, which link HOOK3 to small G-proteins on cargos. We provide a structural model for the autoinhibited FTS-HOOK3-FHIP1B (an FHF complex) and explain how KIF1C relieves it. Collectively, we explain codependency by revealing how mutual activation of dynein and kinesin occurs through their shared adapter. Many adapters bind both dynein and kinesins, suggesting this mechanism could be generalized to other bidirectional complexes.
History
DepositionAug 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Apr 23, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein Hook homolog 3
B: Protein Hook homolog 3
C: FHF complex subunit HOOK-interacting protein 1B
D: AKT-interacting protein


Theoretical massNumber of molelcules
Total (without water)173,6064
Polymers173,6064
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Protein Hook homolog 3


Mass: 17394.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOOK3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86VS8
#2: Protein FHF complex subunit HOOK-interacting protein 1B


Mass: 105642.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FHIP1B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8N612
#3: Protein AKT-interacting protein


Mass: 33173.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKTIP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H8T0
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: The Fts-Hook3-FHIP1B complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.305 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
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: 26000 nm / Nominal defocus min: 16000 nm
Image recordingElectron dose: 43.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 273204 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingDetails: Initial model based on alphafold prediction of FHF / Source name: AlphaFold / Type: in silico model

+
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