[English] 日本語
Yorodumi
- EMDB-6779: GDP-microtubule complexed with nucleotide-free KIF5C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6779
TitleGDP-microtubule complexed with nucleotide-free KIF5C
Map dataKIF5C(nucleotide-free) and Microtubule(GDP)
Sample
  • Organelle or cellular component: GDP-microtubule complexed with nucleotide-free KIF5C
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: water
KeywordsMicrotubule / KIF5C / Kinesin / STRUCTURAL PROTEIN
Function / homology
Function and homology information


structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Tubulin alpha-1A chain / Tubulin beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse) / Sus scrofa (pig)
Methodhelical reconstruction / cryo EM / Resolution: 5.35 Å
AuthorsMorikawa M / Shigematsu H / Nitta R
Funding support Japan, 4 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)23000013 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)16H06372 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H05897 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)15K08168 Japan
CitationJournal: J Cell Biol / Year: 2018
Title: Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport.
Authors: Tomohiro Shima / Manatsu Morikawa / Junichi Kaneshiro / Taketoshi Kambara / Shinji Kamimura / Toshiki Yagi / Hiroyuki Iwamoto / Sotaro Uemura / Hideki Shigematsu / Mikako Shirouzu / Taro ...Authors: Tomohiro Shima / Manatsu Morikawa / Junichi Kaneshiro / Taketoshi Kambara / Shinji Kamimura / Toshiki Yagi / Hiroyuki Iwamoto / Sotaro Uemura / Hideki Shigematsu / Mikako Shirouzu / Taro Ichimura / Tomonobu M Watanabe / Ryo Nitta / Yasushi Okada / Nobutaka Hirokawa /
Abstract: Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only a subset of microtubules for transport in living cells. This biased use of microtubules is proposed as the ...Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only a subset of microtubules for transport in living cells. This biased use of microtubules is proposed as the guidance cue for polarized transport in neurons, but the underlying mechanisms are still poorly understood. Here, we report that kinesin-1 binding changes the microtubule lattice and promotes further kinesin-1 binding. This high-affinity state requires the binding of kinesin-1 in the nucleotide-free state. Microtubules return to the initial low-affinity state by washing out the binding kinesin-1 or by the binding of non-hydrolyzable ATP analogue AMPPNP to kinesin-1. X-ray fiber diffraction, fluorescence speckle microscopy, and second-harmonic generation microscopy, as well as cryo-EM, collectively demonstrated that the binding of nucleotide-free kinesin-1 to GDP microtubules changes the conformation of the GDP microtubule to a conformation resembling the GTP microtubule.
History
Header (metadata) releaseSep 21, 2016-
Map releaseSep 28, 2016-
DepositionJul 5, 2017-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 7.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5xxt
  • Surface level: 7.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6779.png

Downloads & links

-
Map

FileDownload / File: emd_6779.map.gz / Format: CCP4 / Size: 30.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKIF5C(nucleotide-free) and Microtubule(GDP)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 220 pix.
= 282.48 Å		1.28 Å/pix.
x 192 pix.
= 246.528 Å		1.28 Å/pix.
x 192 pix.
= 246.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.284 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.2 / Movie #1: 7.2
Minimum - Maximum-2.891056 - 12.075760000000001
Average (Standard dev.)0.7925549 (±2.4194982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin370370293
Dimensions192192220
Spacing192192220
CellA: 246.52802 Å / B: 246.52802 Å / C: 282.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2841.2841.284
M x/y/z192192220
origin x/y/z0.0000.0000.000
length x/y/z246.528246.528282.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS370370293
NC/NR/NS192192220
D min/max/mean-2.89112.0760.793

-
Supplemental data

-
Sample components

-
Entire : GDP-microtubule complexed with nucleotide-free KIF5C

EntireName: GDP-microtubule complexed with nucleotide-free KIF5C
Components
  • Organelle or cellular component: GDP-microtubule complexed with nucleotide-free KIF5C
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: water

-
Supramolecule #1: GDP-microtubule complexed with nucleotide-free KIF5C

SupramoleculeName: GDP-microtubule complexed with nucleotide-free KIF5C / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Tubulin alpha-1A chain

MacromoleculeName: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Brain
Molecular weightTheoretical: 48.638793 KDa
SequenceString: RECISIHVGQ AGVQIGNACW ELYCLEHGIQ PDGQMPSDKT IGGGDDSFNT FFSETGAGKH VPRAVFVDLE PTVIDEVRTG TYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFSVFHS FGGGTGSGFT SLLMERLSVD Y GKKSKLEF ...String:
RECISIHVGQ AGVQIGNACW ELYCLEHGIQ PDGQMPSDKT IGGGDDSFNT FFSETGAGKH VPRAVFVDLE PTVIDEVRTG TYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFSVFHS FGGGTGSGFT SLLMERLSVD Y GKKSKLEF SIYPAPQVST AVVEPYNSIL TTHTTLEHSD CAFMVDNEAI YDICRRNLDI ERPTYTNLNR LIGQIVSSIT AS LRFDGAL NVDLTEFQTN LVPYPRGHFP LATYAPVISA EKAYHEQLSV AEITNACFEP ANQMVKCDPR HGKYMACCLL YRG DVVPKD VNAAIATIKT KRTIQFVDWC PTGFKVGINY EPPTVVPGGD LAKVQRAVCM LSNTTAIAEA WARLDHKFDL MYAK RAFVH WYVGEGMEEG EFSEAREDMA ALEKDYEEVG VDS

UniProtKB: Tubulin alpha-1A chain

-
Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Brain
Molecular weightTheoretical: 47.809746 KDa
SequenceString: REIVHIQAGQ CGNQIGAKFW EVISDEHGID PTGSYHGDSD LQLERINVYY NEAAGNKYVP RAILVDLEPG TMDSVRSGPF GQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP D RIMNTFSV ...String:
REIVHIQAGQ CGNQIGAKFW EVISDEHGID PTGSYHGDSD LQLERINVYY NEAAGNKYVP RAILVDLEPG TMDSVRSGPF GQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP D RIMNTFSV VPSPKVSDTV VEPYNATLSV HQLVENTDET YCIDNEALYD ICFRTLKLTT PTYGDLNHLV SATMSGVTTC LR FPGQLNA DLRKLAVNMV PFPRLHFFMP GFAPLTSRGS QQYRALTVPE LTQQMFDAKN MMAACDPRHG RYLTVAAVFR GRM SMKEVD EQMLNVQNKN SSYFVEWIPN NVKTAVCDIP PRGLKMSATF IGNSTAIQEL FKRISEQFTA MFRRKAFLHW YTGE GMDEM EFTEAESNMN DLVSEYQQYQ D

UniProtKB: Tubulin beta chain

-
Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 9 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 9 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 9 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 36 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.70662 Å
Applied symmetry - Helical parameters - Δ&Phi: -25.7617 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 5.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9) / Number images used: 17173
Startup modelType of model: EMDB MAP
EMDB ID:

6353

Final angle assignmentType: NOT APPLICABLE

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-5xxt:
GDP-microtubule complexed with nucleotide-free KIF5C

+
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