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- EMDB-7026: KLP10A-AMPPNP in complex with curved tubulin and a microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-7026
TitleKLP10A-AMPPNP in complex with curved tubulin and a microtubule
Map dataMap filtered with a B-factor of -100 A^2
Sample
  • Complex: KLP10A-AMPPNP motor in complex with curved tubulin and a microtubule
    • Complex: KLP10A-AMPPNP motor
      • Protein or peptide: Kinesin-like protein Klp10A
    • Organelle or cellular component: microtubule
      • Protein or peptide: Tubulin beta chain
      • Protein or peptide: Tubulin alpha-1B chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Keywordskinesin 13 / microtubule / tubulin / depolymerization / MOTOR PROTEIN-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


establishment of mitotic spindle asymmetry / establishment of meiotic spindle orientation / cortical microtubule / plus-end specific microtubule depolymerization / asymmetric protein localization involved in cell fate determination / meiotic spindle pole / mitotic spindle astral microtubule / centriole assembly / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins ...establishment of mitotic spindle asymmetry / establishment of meiotic spindle orientation / cortical microtubule / plus-end specific microtubule depolymerization / asymmetric protein localization involved in cell fate determination / meiotic spindle pole / mitotic spindle astral microtubule / centriole assembly / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / mitotic chromosome movement towards spindle pole / kinetochore microtubule / meiotic spindle organization / spindle assembly involved in female meiosis I / non-motile cilium assembly / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / plus-end-directed microtubule motor activity / Recruitment of NuMA to mitotic centrosomes / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / meiotic spindle / COPI-mediated anterograde transport / microtubule depolymerization / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement / mitotic spindle pole / cytoskeletal motor activity / centrosome duplication / chromosome, centromeric region / microtubule-based process / mitotic spindle organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / spindle pole / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / cell division / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tubulin beta chain / Tubulin beta chain / Tubulin alpha-1B chain / Kinesin-like protein Klp10A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly) / Sus scrofa (pig)
Methodhelical reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsBenoit MPMH / Asenjo AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM113164 United States
CitationJournal: Nat Commun / Year: 2018
Title: Cryo-EM reveals the structural basis of microtubule depolymerization by kinesin-13s.
Authors: Matthieu P M H Benoit / Ana B Asenjo / Hernando Sosa /
Abstract: Kinesin-13s constitute a distinct group within the kinesin superfamily of motor proteins that promote microtubule depolymerization and lack motile activity. The molecular mechanism by which kinesin- ...Kinesin-13s constitute a distinct group within the kinesin superfamily of motor proteins that promote microtubule depolymerization and lack motile activity. The molecular mechanism by which kinesin-13s depolymerize microtubules and are adapted to perform a seemingly very different activity from other kinesins is still unclear. To address this issue, here we report the near atomic resolution cryo-electron microscopy (cryo-EM) structures of Drosophila melanogaster kinesin-13 KLP10A protein constructs bound to curved or straight tubulin in different nucleotide states. These structures show how nucleotide induced conformational changes near the catalytic site are coupled with movement of the kinesin-13-specific loop-2 to induce tubulin curvature leading to microtubule depolymerization. The data highlight a modular structure that allows similar kinesin core motor-domains to be used for different functions, such as motility or microtubule depolymerization.
History
DepositionSep 14, 2017-
Header (metadata) releaseNov 1, 2017-
Map releaseMay 2, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0675
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0675
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6b0c
  • Surface level: 0.0675
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6b0c
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_7026.map.gz / Format: CCP4 / Size: 891.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap filtered with a B-factor of -100 A^2
Voxel sizeX=Y=Z: 1.073 Å
Density
Contour LevelBy AUTHOR: 0.0675 / Movie #1: 0.0675
Minimum - Maximum-0.3483273 - 0.6051997
Average (Standard dev.)0.003076309 (±0.030299673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions616616616
Spacing616616616
CellA=B=C: 660.96796 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0731.0731.073
M x/y/z616616616
origin x/y/z0.0000.0000.000
length x/y/z660.968660.968660.968
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS616616616
D min/max/mean-0.3480.6050.003

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Supplemental data

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Mask #1

Fileemd_7026_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map (1) from the Gold Standard refinement

Fileemd_7026_half_map_1.map
AnnotationHalf map (1) from the Gold Standard refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map (2) from the Gold Standard refinement

Fileemd_7026_half_map_2.map
AnnotationHalf map (2) from the Gold Standard refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : KLP10A-AMPPNP motor in complex with curved tubulin and a microtubule

EntireName: KLP10A-AMPPNP motor in complex with curved tubulin and a microtubule
Components
  • Complex: KLP10A-AMPPNP motor in complex with curved tubulin and a microtubule
    • Complex: KLP10A-AMPPNP motor
      • Protein or peptide: Kinesin-like protein Klp10A
    • Organelle or cellular component: microtubule
      • Protein or peptide: Tubulin beta chain
      • Protein or peptide: Tubulin alpha-1B chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: KLP10A-AMPPNP motor in complex with curved tubulin and a microtubule

SupramoleculeName: KLP10A-AMPPNP motor in complex with curved tubulin and a microtubule
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: KLP10A-AMPPNP motor

SupramoleculeName: KLP10A-AMPPNP motor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Supramolecule #3: microtubule

SupramoleculeName: microtubule / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2, #1
Details: Chains A and B make up a curved microtubule protofilament.
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: brain
Molecular weightTheoretical: 50.204445 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: brain
Molecular weightTheoretical: 49.999887 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VMPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDSK NMMAACDPRH GRYLTVAAIF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEEGEDEA

UniProtKB: Tubulin beta chain

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Macromolecule #3: Kinesin-like protein Klp10A

MacromoleculeName: Kinesin-like protein Klp10A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 41.810918 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDPSSRSITV CVRKRPISRK EVNRKEIDVI SVPRKDMLIV HEPRSKVDLT KFLENHKFR FDYAFNDTCD NAMVYKYTAK PLVKTIFEGG MATCFAYGQT GSGKTHTMGG EFNGKVQDCK NGIYAMAAKD V FVTLNMPR ...String:
MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDPSSRSITV CVRKRPISRK EVNRKEIDVI SVPRKDMLIV HEPRSKVDLT KFLENHKFR FDYAFNDTCD NAMVYKYTAK PLVKTIFEGG MATCFAYGQT GSGKTHTMGG EFNGKVQDCK NGIYAMAAKD V FVTLNMPR YRAMNLVVSA SFFEIYSGKV FDLLSDKQKL RVLEDGKQQV QVVGLTEKVV DGVEEVLKLI QHGNAARTSG QT SANSNSS RSHAVFQIVL RPQGSTKIHG KFSFIDLAGN ERGVDTSSAD RQTRMEGAEI NKSLLALKEC IRALGKQSAH LPF RVSKLT QVLRDSFIGE KSKTCMIAMI SPGLSSCEHT LNTLRYADRV KELVVKDI

UniProtKB: Kinesin-like protein Klp10A

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / 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 #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

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Macromolecule #7: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 7 / Number of copies: 1 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy*YM / Paclitaxel

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Macromolecule #8: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 8 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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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: 6.8
Component:
ConcentrationName
80.0 mMK-PIPES
20.0 uMPaclitaxel
3.0 mMMagnesium chloride
1.0 mMEGTA
2.0 mMAMP-PNP
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 46598 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Average electron dose: 1.25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionDetails: manual picking of filaments
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE / Software - Name: FREALIGN (ver. 9.11)
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.57 Å
Applied symmetry - Helical parameters - Δ&Phi: 168.089 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11)
Details: 2 independent reconstructions, each using a distinct half of every filament.
Number images used: 16942
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6b0c:
KLP10A-AMPPNP in complex with curved tubulin and a microtubule

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