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- EMDB-19176: Microtubule-associated kinesin-1 tail complex bound to AMPPNP, tw... -

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Basic information

Entry
Database: EMDB / ID: EMD-19176
TitleMicrotubule-associated kinesin-1 tail complex bound to AMPPNP, two-headed state
Map dataMain map after focussed refinement on tubulin and kinesin
Sample
  • Complex: 13pf microtubule bound to Kif5bMoNeIAK in the presence of AMPPNP (two-headed state)
    • Complex: Kinesin-1 heavy chain
      • Protein or peptide: Kinesin-1 heavy chain
    • Complex: 13pf microtubule
      • Protein or peptide: Tubulin beta chain
      • Protein or peptide: Tubulin alpha-1B chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordsKinesin autoinhibition motor microtubules mechanochemistry intracellular transport / MOTOR PROTEIN
Function / homology
Function and homology information


plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization ...plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / 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 / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / Kinesins / RHO GTPases activate KTN1 / plus-end-directed microtubule motor activity / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / stress granule disassembly / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / centrosome localization / mitochondrion transport along microtubule / microtubule motor activity / ciliary rootlet / kinesin complex / natural killer cell mediated cytotoxicity / synaptic vesicle transport / microtubule-based movement / Insulin processing / centriolar satellite / phagocytic vesicle / axon cytoplasm / MHC class II antigen presentation / dendrite cytoplasm / regulation of membrane potential / axon guidance / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / structural constituent of cytoskeleton / cellular response to type II interferon / microtubule cytoskeleton organization / microtubule cytoskeleton / Signaling by ALK fusions and activated point mutants / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule binding / vesicle / microtubule / cadherin binding / GTPase activity / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / metal ion binding / cytosol / 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 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tubulin beta chain / Kinesin-1 heavy chain / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsAtherton J / Chegkazi MS / Steiner RA
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust206175/Z/17/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006568/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S000828/1 United Kingdom
CitationJournal: Biorxiv / Year: 2024
Title: Microtubule association induces a Mg-free apo-like ADP pre-release conformation in kinesin-1 that is unaffected by its autoinhibitory tail
Authors: Atherton J / Chegkazi MS / Peirano E / Pozzer LS / Foran T / Steiner RA
History
DepositionDec 15, 2023-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19176.png

Downloads & links

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Map

FileDownload / File: emd_19176.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map after focussed refinement on tubulin and kinesin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 259.92 Å		1.08 Å/pix.
x 240 pix.
= 259.92 Å		1.08 Å/pix.
x 240 pix.
= 259.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.015293366 - 0.034675825
Average (Standard dev.)0.00016256055 (±0.0016658106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 259.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Main map after focussed refinement on kinesin

Fileemd_19176_additional_1.map
AnnotationMain map after focussed refinement on kinesin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 after focussed refinement on tubulin and kinesin

Fileemd_19176_half_map_1.map
AnnotationHalf map 2 after focussed refinement on tubulin and kinesin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 after focussed refinement on tubulin and kinesin

Fileemd_19176_half_map_2.map
AnnotationHalf map 1 after focussed refinement on tubulin and kinesin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 13pf microtubule bound to Kif5bMoNeIAK in the presence of AMPPNP ...

EntireName: 13pf microtubule bound to Kif5bMoNeIAK in the presence of AMPPNP (two-headed state)
Components
  • Complex: 13pf microtubule bound to Kif5bMoNeIAK in the presence of AMPPNP (two-headed state)
    • Complex: Kinesin-1 heavy chain
      • Protein or peptide: Kinesin-1 heavy chain
    • Complex: 13pf microtubule
      • Protein or peptide: Tubulin beta chain
      • Protein or peptide: Tubulin alpha-1B chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: 13pf microtubule bound to Kif5bMoNeIAK in the presence of AMPPNP ...

SupramoleculeName: 13pf microtubule bound to Kif5bMoNeIAK in the presence of AMPPNP (two-headed state)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 246 kDa/nm

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Supramolecule #2: Kinesin-1 heavy chain

SupramoleculeName: Kinesin-1 heavy chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: 13pf microtubule

SupramoleculeName: 13pf microtubule / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1, #3
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 49.90777 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEGEEDEA

UniProtKB: Tubulin beta chain

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Macromolecule #2: Kinesin-1 heavy chain

MacromoleculeName: Kinesin-1 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.856102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 KQV

UniProtKB: Kinesin-1 heavy chain

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Macromolecule #3: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
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 #4: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

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Macromolecule #5: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 5 / Number of copies: 1 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy*YM

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Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / 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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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.16 mg/mL
BufferpH: 6.8 / Details: BRB80 + 5mM AMPPNP
GridModel: C-flat-2/2 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: LEICA EM GP
DetailsKinesin 1mg/ml Microtubules at 0.16mg/ml

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 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: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Kinesin decorated microtubule
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Details: Relion noise-substitution test corrected FSC / Number images used: 570836
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 2 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsPhenix Real Space refine and Coot
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8rhh:
Microtubule-associated kinesin-1 tail complex bound to AMPPNP, two-headed state

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