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- EMDB-28787: Apo KIF20A[1-565] class-2 in complex with a microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-28787
TitleApo KIF20A[1-565] class-2 in complex with a microtubule
Map dataPrimary map, locally refined on the central asymmetric unit
Sample
  • Complex: KIF20A[1-565] apo in complex with a microtubule - class 2
    • Complex: KIF20A[1-565] apo
      • Protein or peptide: Kinesin-like protein KIF20AKIF20A
    • Organelle or cellular component: 15R Microtubule
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta-2B chain
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel
KeywordsKIF20A / kinesin / motility / microtubule / tubulin / MOTOR PROTEIN
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / midbody abscission / MHC class II antigen presentation / microtubule bundle formation / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport ...Mitotic Telophase/Cytokinesis / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / midbody abscission / MHC class II antigen presentation / microtubule bundle formation / 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 / 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 / COPI-mediated anterograde transport / kinesin complex / microtubule motor activity / intercellular bridge / microtubule-based movement / mitotic cytokinesis / microtubule-based process / regulation of cytokinesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / protein transport / mitotic cell cycle / midbody / microtubule binding / microtubule / GTPase activity / GTP binding / protein kinase binding / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / 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 / Kinesin-like protein KIF20A / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesMus musculus (house mouse) / Sus scrofa (pig)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBenoit MPMH / Asenjo AB / Crozet V / Ranaivoson FM / Houdusse A / Sosa H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM113164 United States
CitationJournal: Open Biol / Year: 2023
Title: Nucleotide-free structures of KIF20A illuminate atypical mechanochemistry in this kinesin-6.
Authors: Fanomezana Moutse Ranaivoson / Vincent Crozet / Matthieu P M H Benoit / Amna Abdalla Mohammed Khalid / Carlos Kikuti / Helena Sirkia / Ahmed El Marjou / Stéphanie Miserey-Lenkei / Ana B ...Authors: Fanomezana Moutse Ranaivoson / Vincent Crozet / Matthieu P M H Benoit / Amna Abdalla Mohammed Khalid / Carlos Kikuti / Helena Sirkia / Ahmed El Marjou / Stéphanie Miserey-Lenkei / Ana B Asenjo / Hernando Sosa / Christoph F Schmidt / Steven S Rosenfeld / Anne Houdusse /
Abstract: KIF20A is a critical kinesin for cell division and a promising anti-cancer drug target. The mechanisms underlying its cellular roles remain elusive. Interestingly, unusual coupling between the ...KIF20A is a critical kinesin for cell division and a promising anti-cancer drug target. The mechanisms underlying its cellular roles remain elusive. Interestingly, unusual coupling between the nucleotide- and microtubule-binding sites of this kinesin-6 has been reported, but little is known about how its divergent sequence leads to atypical motility properties. We present here the first high-resolution structure of its motor domain that delineates the highly unusual structural features of this motor, including a long L6 insertion that integrates into the core of the motor domain and that drastically affects allostery and ATPase activity. Together with the high-resolution cryo-electron microscopy microtubule-bound KIF20A structure that reveals the microtubule-binding interface, we dissect the peculiarities of the KIF20A sequence that influence its mechanochemistry, leading to low motility compared to other kinesins. Structural and functional insights from the KIF20A pre-power stroke conformation highlight the role of extended insertions in shaping the motor's mechanochemical cycle. Essential for force production and processivity is the length of the neck linker in kinesins. We highlight here the role of the sequence preceding the neck linker in controlling its backward docking and show that a neck linker four times longer than that in kinesin-1 is required for the activity of this motor.
History
DepositionNov 4, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28787.png

Downloads & links

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Map

FileDownload / File: emd_28787.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map, locally refined on the central asymmetric unit
Voxel sizeX=Y=Z: 0.844 Å
Density
Contour LevelBy AUTHOR: 0.0106
Minimum - Maximum-0.02461302 - 0.048413083
Average (Standard dev.)-0.00035328016 (±0.0028070756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 351.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28787_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_28787_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #3

Fileemd_28787_msk_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #4

Fileemd_28787_msk_4.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map from the gold Standard refinement

Fileemd_28787_half_map_1.map
AnnotationHalf map from the gold Standard refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map from the gold Standard refinement

Fileemd_28787_half_map_2.map
AnnotationHalf map from the gold Standard refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : KIF20A[1-565] apo in complex with a microtubule - class 2

EntireName: KIF20A[1-565] apo in complex with a microtubule - class 2
Components
  • Complex: KIF20A[1-565] apo in complex with a microtubule - class 2
    • Complex: KIF20A[1-565] apo
      • Protein or peptide: Kinesin-like protein KIF20AKIF20A
    • Organelle or cellular component: 15R Microtubule
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta-2B chain
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel

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Supramolecule #1: KIF20A[1-565] apo in complex with a microtubule - class 2

SupramoleculeName: KIF20A[1-565] apo in complex with a microtubule - class 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: KIF20A[1-565] apo

SupramoleculeName: KIF20A[1-565] apo / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: 15R Microtubule

SupramoleculeName: 15R Microtubule / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Sus scrofa (pig) / Organ: Brain

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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-2B chain

MacromoleculeName: Tubulin beta-2B chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 KIF20A

MacromoleculeName: Kinesin-like protein KIF20A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 64.088211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSHRILSPPA GLLSDEDVVD SPILESTAAD LRSVVRKDLL SDCSVISASL EDKQALLEDT SEKVKVYLRI RPFLTSELDR QEDQGCVCI ENTETLVLQA PKDSFALKSN ERGVGQATHK FTFSQIFGPE VGQVAFFNLT MKEMVKDVLK GQNWLIYTYG V TNSGKTYT ...String:
MSHRILSPPA GLLSDEDVVD SPILESTAAD LRSVVRKDLL SDCSVISASL EDKQALLEDT SEKVKVYLRI RPFLTSELDR QEDQGCVCI ENTETLVLQA PKDSFALKSN ERGVGQATHK FTFSQIFGPE VGQVAFFNLT MKEMVKDVLK GQNWLIYTYG V TNSGKTYT IQGTSKDAGI LPQSLALIFN SLQGQLHPTP DLKPLLSNEV IWLDSKQIRQ EEMKKLSLLI GGLQEEELST SV KKRVHTE SRIGASNSFD SGVAGLSSTS QFTSSSQLDE TSQLWAQPDT VPVSVPADIR FSVWISFFEI YNELLYDLLE PPS HQHKRQ TLRLCEDQNG NPYVKDLNWI HVRDVEEAWK LLKVGRKNQS FASTHMNQQS SRSHSIFSIR ILHLQGEGDI VPKI SELSL CDLAGSERCK HQKSGERLKE AGNINTSLHT LGRCIAALRQ NQQNRSKQNL IPFRDSKLTR VFQGFFTGRG RSCMI VNVN PCASTYDETL HAAKFSALAS QLVHAPPVHL GIPSLHSFIK KHSPQVGPGL EKEDKADSDL EDSPEDEADV SVYGKE ELL QVLEHHHHHH

UniProtKB: Kinesin-like protein KIF20A

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / 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 #6: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / 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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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
40.0 mMK-PIPES
20.0 uMPaclitaxel
1.0 mMMagnesium chloride
1.0 mMEGTA
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Average electron dose: 56.1 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: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.62 Å
Applied symmetry - Helical parameters - Δ&Phi: 168.09 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: Number of asymmetric units used is reported in "number of segments used", due to the local processing strategy employed.
Number images used: 119232
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8f18:
Apo KIF20A[1-565] class-2 in complex with a microtubule

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