[English] 日本語
Yorodumi
- EMDB-71734: Kinesin-1 heterotetramer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71734
TitleKinesin-1 heterotetramer
Map dataKinesin-1 heterotetramer
Sample
  • Complex: Heterotetramer of Kinesin-1 KIF5B/KLC1
    • Protein or peptide: Kinesin light chain 1
    • Protein or peptide: Kinesin-1 heavy chain
KeywordsAutoinhibited Kinesin-1 heterotetramer / MOTOR PROTEIN
Function / homology
Function and homology information


regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / ciliary rootlet ...regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde axonal protein transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / ciliary rootlet / lysosome localization / positive regulation of potassium ion transport / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / Kinesins / vesicle transport along microtubule / centrosome localization / natural killer cell mediated cytotoxicity / microtubule motor activity / kinesin complex / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / stress granule disassembly / Insulin processing / synaptic vesicle transport / cytoskeletal motor activity / kinesin binding / postsynaptic cytosol / centriolar satellite / phagocytic vesicle / axon cytoplasm / MHC class II antigen presentation / dendrite cytoplasm / positive regulation of synaptic transmission, GABAergic / axon guidance / sperm end piece / positive regulation of protein localization to plasma membrane / regulation of membrane potential / cellular response to type II interferon / Signaling by ALK fusions and activated point mutants / growth cone / nuclear membrane / cytoplasmic vesicle / microtubule binding / vesicle / microtubule / cell adhesion / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / : / Tetratricopeptide repeat / Tetratricopeptide repeat / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain ...Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / : / Tetratricopeptide repeat / Tetratricopeptide repeat / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-1 heavy chain / Kinesin light chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsAshaduzzaman M / Al-Bassam J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM110283 United States
CitationJournal: To Be Published
Title: Kinesin-1 heterotetramer
Authors: Ashaduzzaman M / Al-Bassam J
History
DepositionJul 16, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71734.png

Downloads & links

-
Map

FileReleased
AnnotationKinesin-1 heterotetramer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.85 Å/pix.
x 302 pix.
= 559.304 Å		1.85 Å/pix.
x 302 pix.
= 559.304 Å		1.85 Å/pix.
x 302 pix.
= 559.304 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.852 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.0002768185 - 2.6389925
Average (Standard dev.)0.0013967339 (±0.026436266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-77-76-76
Dimensions302302302
Spacing302302302
CellA=B=C: 559.304 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Heterotetramer of Kinesin-1 KIF5B/KLC1

EntireName: Heterotetramer of Kinesin-1 KIF5B/KLC1
Components
  • Complex: Heterotetramer of Kinesin-1 KIF5B/KLC1
    • Protein or peptide: Kinesin light chain 1
    • Protein or peptide: Kinesin-1 heavy chain

-
Supramolecule #1: Heterotetramer of Kinesin-1 KIF5B/KLC1

SupramoleculeName: Heterotetramer of Kinesin-1 KIF5B/KLC1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: 2:2 complex of KIF5B/KLC1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

-
Macromolecule #1: Kinesin light chain 1

MacromoleculeName: Kinesin light chain 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.969688 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QDEIISKTKQ VIQGLEALKN EHNSILQSLL ETLKCLKKDD ESNLVEEKSN MIRKSLEMLE LGLSEAQVMM ALSNHLNAVE SEKQKLRAQ VRRLCQENQW LRDELANTQQ KLQKSEQSVA QLEEEKKHLE FMNQLKKYDD DISPSEDKDT DSTKEPLDDL F PNDEDDPG ...String:
QDEIISKTKQ VIQGLEALKN EHNSILQSLL ETLKCLKKDD ESNLVEEKSN MIRKSLEMLE LGLSEAQVMM ALSNHLNAVE SEKQKLRAQ VRRLCQENQW LRDELANTQQ KLQKSEQSVA QLEEEKKHLE FMNQLKKYDD DISPSEDKDT DSTKEPLDDL F PNDEDDPG QGIQQQHSSA AAAAQQGGYE IPARLRTLHN LVIQYASQGR YEVAVPLCKQ ALEDLEKTSG HDHPDVATML NI LALVYRD QNKYKDAANL LNDALAIREK TLGKDHPAVA ATLNNLAVLY GKRGKYKEAE PLCKRALEIR EKVLGKDHPD VAK QLNNLA LLCQNQGKYE EVEYYYQRAL EIYQTKLGPD DPNVAKTKNN LASCYLKQGK FKQAETLYKE ILTRAHEREF GSVD DENKP IWMHAEEREE CKGKQKDGTS FGEYGGWYKA CKVDSPTVTT TLKNLGALYR RQGKFEAAET LEEAAMRSRK QGLDN VHKQ RVAEVLNDPE NMEKRRSRES LNVDVVKYES GPDGGEEVSM SVEWNGGVSG RASFCGKRQQ QQWPGRRHR

UniProtKB: Kinesin light chain 1

-
Macromolecule #2: Kinesin-1 heavy chain

MacromoleculeName: Kinesin-1 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 136.384703 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADLAECNIK VMCRFRPLNE SEVNRGDKYI AKFQGEDTVV IASKPYAFDR VFQSSTSQEQ VYNDCAKKIV KDVLEGYNGT IFAYGQTSS GKTHTMEGKL HDPEGMGIIP RIVQDIFNYI YSMDENLEFH IKVSYFEIYL DKIRDLLDVS KTNLSVHEDK N RVPYVKGC ...String:
MADLAECNIK VMCRFRPLNE SEVNRGDKYI AKFQGEDTVV IASKPYAFDR VFQSSTSQEQ VYNDCAKKIV KDVLEGYNGT IFAYGQTSS GKTHTMEGKL HDPEGMGIIP RIVQDIFNYI YSMDENLEFH IKVSYFEIYL DKIRDLLDVS KTNLSVHEDK N RVPYVKGC TERFVCSPDE VMDTIDEGKS NRHVAVTNMN EHSSRSHSIF LINVKQENTQ TEQKLSGKLY LVDLAGSEKV SK TGAEGAV LDEAKNINKS LSALGNVISA LAEGSTYVPY RDSKMTRILQ DSLGGNCRTT IVICCSPSSY NESETKSTLL FGQ RAKTIK NTVCVNVELT AEQWKKKYEK EKEKNKILRN TIQWLENELN RWRNGETVPI DEQFDKEKAN LEAFTVDKDI TLTN DKPAT AIGVIGNFTD AERRKCEEEI AKLYKQLDDK DEEINQQSQL VEKLKTQMLD QEELLASTRR DQDNMQAELN RLQAE NDAS KEEVKEVLQA LEELAVNYDQ KSQEVEDKTK EYELLSDELN QKSATLASID AELQKLKEMT NHQKKRAAEM MASLLK DLA EIGIAVGNND VKQPEGTGMI DEEFTVARLY ISKMKSEVKT MVKRCKQLES TQTESNKKME ENEKELAACQ LRISQHE AK IKSLTEYLQN VEQKKRQLEE SVDALSEELV QLRAQEKVHE MEKEHLNKVQ TANEVKQAVE QQIQSHRETH QKQISSLR D EVEAKAKLIT DLQDQNQKMM LEQERLRVEH EKLKATDQEK SRKLHELTVM QDRREQARQD LKGLEETVAK ELQTLHNLR KLFVQDLATR VKKSAEIDSD DTGGSAAQKQ KISFLENNLE QLTKVHKQLV RDNADLRCEL PKLEKRLRAT AERVKALESA LKEAKENAS RDRKRYQQEV DRIKEAVRSK NMARRGHSAQ IAKPIRPGQH PAASPTHPSA IRGGGAFVQN SQPVAVRGGG G KQVGSGSV SKGEAVIKEF MRFKVHMEGS MNGHEFEIEG EGEGRPYEGT QTAKLKVTKG GPLPFSWDIL SPQFMYGSRA FT KHPADIP DYYKQSFPEG FKWERVMNFE DGGAVTVTQD TSLEDGTLIY KVKLRGTNFP PDGPVMQKKT MGWEASTERL YPE DGVLKG DIKMALRLKD GGRYLADFKT TYKAKKPVQM PGAYNVDRKL DITSHNEDYT VVEQYERSEG RHSTGGMDEL YK

UniProtKB: Kinesin-1 heavy chain

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.3 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30746
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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