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- EMDB-6783: GMPCPP-microtubule complexed with nucleotide-free KIF5C -

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Basic information

Entry
Database: EMDB / ID: EMD-6783
TitleGMPCPP-microtubule complexed with nucleotide-free KIF5C
Map dataKIF5C(nucleotide-free) and Microtubule(GMPCPP)
Sample
  • Organelle or cellular component: GMPCPP-microtubule complexed with nucleotide-free KIF5C
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: water
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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-beta mRNA autoregulation signal. / Alpha tubulin / 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) / Pig (pig)
Methodhelical reconstruction / cryo EM / Resolution: 6.43 Å
AuthorsMorikawa M / Shigematsu H / Nitta R / Hirokawa N
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)17H05897 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)16H06372 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-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 7.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5xxx
  • Surface level: 7.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6783.png

Downloads & links

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Map

FileDownload / File: emd_6783.map.gz / Format: CCP4 / Size: 30.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKIF5C(nucleotide-free) and Microtubule(GMPCPP)
Voxel sizeX=Y=Z: 1.284 Å
Density
Contour LevelBy AUTHOR: 7.4 / Movie #1: 7.4
Minimum - Maximum-4.36565 - 13.830622
Average (Standard dev.)1.018187 (±2.450797)
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-4.36613.8311.018

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Supplemental data

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Sample components

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Entire : GMPCPP-microtubule complexed with nucleotide-free KIF5C

EntireName: GMPCPP-microtubule complexed with nucleotide-free KIF5C
Components
  • Organelle or cellular component: GMPCPP-microtubule complexed with nucleotide-free KIF5C
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: water

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

SupramoleculeName: GMPCPP-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)

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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: Pig (pig)
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

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Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
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

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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 / Guanosine triphosphate

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 18 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 5 / Number of copies: 9 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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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 / Water

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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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

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Electron microscopy

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

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

6353

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 8.8632 Å
Applied symmetry - Helical parameters - Δ&Phi: -25.7541 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9) / Number images used: 5822

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-5xxx:
GMPCPP-microtubule complexed with nucleotide-free KIF5C

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