[English] 日本語
Yorodumi
- EMDB-18303: Low resolution cryo-EM structure of FHF bound to KIF1C stalk Hook... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18303
TitleLow resolution cryo-EM structure of FHF bound to KIF1C stalk Hook3 binding domain
Map dataMain map for FHF-KIF1C stalk structure
Sample
  • Complex: The Fts-Hook3(451-718)-FHIP1B complex bound to KIF1C Hook3 binding domain (KIF1C 647-922)
    • Protein or peptide: Hook3(451-718)
    • Protein or peptide: FHIP1B
    • Protein or peptide: Fts
    • Protein or peptide: KIF1C(674-922)
Keywordsmotor proteins / molecular motors / cargo adaptors / bidirectional transport / microtubules / cytoskeleton. / PROTEIN TRANSPORT
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsAbid Ali F / Cartera AP
Funding support United Kingdom, 2 items
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, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18303.png

Downloads & links

-
Map

FileDownload / File: emd_18303.map.gz / Format: CCP4 / Size: 65.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map for FHF-KIF1C stalk structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.52 Å/pix.
x 258 pix.
= 392.184 Å		1.52 Å/pix.
x 258 pix.
= 392.184 Å		1.52 Å/pix.
x 258 pix.
= 392.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.52009 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00908
Minimum - Maximum-0.014492597 - 0.057999473
Average (Standard dev.)0.000098642326 (±0.0014652268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions258258258
Spacing258258258
CellA=B=C: 392.184 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18303_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 2 for FHF-KIF1C stalk structure

Fileemd_18303_half_map_1.map
AnnotationHalf-map 2 for FHF-KIF1C stalk structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 1 for FHF-KIF1C stalk structure

Fileemd_18303_half_map_2.map
AnnotationHalf-map 1 for FHF-KIF1C stalk structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The Fts-Hook3(451-718)-FHIP1B complex bound to KIF1C Hook3 bindin...

EntireName: The Fts-Hook3(451-718)-FHIP1B complex bound to KIF1C Hook3 binding domain (KIF1C 647-922)
Components
  • Complex: The Fts-Hook3(451-718)-FHIP1B complex bound to KIF1C Hook3 binding domain (KIF1C 647-922)
    • Protein or peptide: Hook3(451-718)
    • Protein or peptide: FHIP1B
    • Protein or peptide: Fts
    • Protein or peptide: KIF1C(674-922)

-
Supramolecule #1: The Fts-Hook3(451-718)-FHIP1B complex bound to KIF1C Hook3 bindin...

SupramoleculeName: The Fts-Hook3(451-718)-FHIP1B complex bound to KIF1C Hook3 binding domain (KIF1C 647-922)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 430 KDa

-
Macromolecule #1: Hook3(451-718)

MacromoleculeName: Hook3(451-718) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDSLAAEIVT PEIREKLIRL QHENKMLKLN QEGSDNEKIA LLQSLLDDAN LRKNELETEN RLVNQRLLEV QSQVEELQKS LQDQGSKAED SVLLKKKLEE HLEKLHEANN ELQKKRAIIE DLEPRFNNSS LKIEELQEAL RKKEEEMKQM EERYKKYLEK AKSVIRTLDP ...String:
SDSLAAEIVT PEIREKLIRL QHENKMLKLN QEGSDNEKIA LLQSLLDDAN LRKNELETEN RLVNQRLLEV QSQVEELQKS LQDQGSKAED SVLLKKKLEE HLEKLHEANN ELQKKRAIIE DLEPRFNNSS LKIEELQEAL RKKEEEMKQM EERYKKYLEK AKSVIRTLDP KQNQGAAPEI QALKNQLQER DRLFHSLEKE YEKTKSQREM EEKYIVSAWY NMGMTLHKKA AEDRLASTGS GQSFLARQRQ ATSSRRSYPG HVQPATAR

-
Macromolecule #2: FHIP1B

MacromoleculeName: FHIP1B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MERMNWLSRL ASRGPGHRIP QGANLQTPVM ADPETCLMVF KNHWSQVVRI LERQGPRAAP GGADDLSAVR NHTYQMLTLL AEDRAVPSAP TGPGPLLEFA LHEDLLTRVL TWQLQWDELG DGVEERRAEQ LKLFEMLVSE ARQPLLRHGP VREALLTLLD ACGRPVPSSP ...String:
MERMNWLSRL ASRGPGHRIP QGANLQTPVM ADPETCLMVF KNHWSQVVRI LERQGPRAAP GGADDLSAVR NHTYQMLTLL AEDRAVPSAP TGPGPLLEFA LHEDLLTRVL TWQLQWDELG DGVEERRAEQ LKLFEMLVSE ARQPLLRHGP VREALLTLLD ACGRPVPSSP ALDEGLVLLL SQLCVCVAQE PSLLEFFLQP PPEPGAAPRL LLFSRLVPFV HLEGTLGQQA RDALLLLMAL SAGSPTVGRY IADHSYFCPV LATGLSALYS SLPRKIEVPG DDWHCLRRED WLGVPALALF MSSLEFCNAV IQVAHPLVQK QLVDYIHNGF LVPVMGPALH KTSVEEMIAS TAYLELFLRS ISEPALLRTF LRFLLLHRHD THTILDTLVA RIGSNSRLCM VSLSLFRTLL NLSCEDVLLQ LVLRYLVPCN HVMLSQKPAV RDVDLYGRAA DKFLSLIPRC CRHHAPSPPR PEHASWARGP GSPSVDSSSV TTVPRPSTPS RLALFLRQQS LGGSESPGPA PCSPGLSASP ASSPGRRPTP AEEPGELEDN YLEYLREARR GVDRCVRACR TWSAPYDGER PSPEPSPFGS RTKKRSLLPE EDRNNVGEGE EEELGRRGRA GGAGEGPGHL PPPQLNGVPG SWPEGAKKVR LVPKEGAGEL LEGISEGMAG LEGFGQELRE LEVALSNGGT GSESPLEPPL PLEEEEAYES FTCPPEPPGP FLSSPLRTLN QLPSQPFTGP FMAVLFAKLE NMLQNSVYVN FLLTGLVAQL ACHPQPLLRS FLLNTNMVFQ PSVKSLLQVL GSVKNKIENF AASQEDFPAL LSKAKKYLIA RGKLDWAEGP AAGPAPRRSD PLVKSRRPSL GELLLRHAHS PTRARQAAQL VLQPGRDGAG LGLSGGSPGA STPVLLTRGG APERQGEALR VKNAVYCAVI FPEFLKELAA ISQAHAVTSP FLLETSEEGS GPLISGCGPL NP

-
Macromolecule #3: Fts

MacromoleculeName: Fts / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNPFWSMSTS SVRKRSEGEE KTLTGDVKTS PPRTAPKKQL PSIPKNALPI TKPTSPAPAA QSTNGTHASY GPFYLEYSLL AEFTLVVKQK LPGVYVQPSY RSALMWFGVI FIRHGLYQDG VFKFTVYIPD NYPDGDCPRL VFDIPVFHPL VDPTSGELDV KRAFAKWRRN ...String:
MNPFWSMSTS SVRKRSEGEE KTLTGDVKTS PPRTAPKKQL PSIPKNALPI TKPTSPAPAA QSTNGTHASY GPFYLEYSLL AEFTLVVKQK LPGVYVQPSY RSALMWFGVI FIRHGLYQDG VFKFTVYIPD NYPDGDCPRL VFDIPVFHPL VDPTSGELDV KRAFAKWRRN HNHIWQVLMY ARRVFYKIDT ASPLNPEAAV LYEKDIQLFK SKVVDSVKVC TARLFDQPKI EDPYAISFSP WNPSVHDEAR EKMLTQKKPE EQHNKSVHVA GLSWVKPGSV QPFSKEEKTV AT

-
Macromolecule #4: KIF1C(674-922)

MacromoleculeName: KIF1C(674-922) / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKERA EISMLEGAVL DIRYGVSRIA YSKDFETLKV DFLSKLPEML KMFEDRLCHK TYLNGDHVTH PDFMLYDALD VVLYMDPMCL ...String:
MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKERA EISMLEGAVL DIRYGVSRIA YSKDFETLKV DFLSKLPEML KMFEDRLCHK TYLNGDHVTH PDFMLYDALD VVLYMDPMCL DAFPKLVCFK KRIEAIPQID KYLKSSKYIA WPLQGWQATF GGGDHPPKSD LEVLFQGPLG SENLYFQGDY DIPTTENLYF QGESDSGDDS DKRSCEESWR LISSLREQLP PTTVQTIVKR CGLPSSGKRR APRRVYQIPQ RRRLQGKDPR WATMADLKMQ AVKEICYEVA LADFRHGRAE IEALAALKMR ELCRTYGKPD GPGDAWRAVA RDVWDTVGEE EGGGAGSGGG SEEGARGAEV EDLRAHIDKL TGILQEVKLQ NSSKDRELQA LRDRMLRMER VIPLAQDHED ENEEGGEVPW APPEGSEAAE EAAPSDRMPS ARPPSPPLSS WEAAALEHHH HHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 26.0 µm / Nominal defocus min: 16.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER / Details: de novo
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 507489
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: Initial model based on alphafold prediction of FHF
RefinementSpace: REAL / Protocol: OTHER

+
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