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Yorodumi- EMDB-42546: KIF1A[1-393] AMP-PNP bound one-head-bound state in complex with a... -
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-Basic information
Entry | Database: EMDB / ID: EMD-42546 | |||||||||||||||||||||
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Title | KIF1A[1-393] AMP-PNP bound one-head-bound state in complex with a microtubule - class T1L02* | |||||||||||||||||||||
Map data | Primary map, locally refined on the two central asymmetric units | |||||||||||||||||||||
Sample |
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Keywords | KIF1A / kinesin / motility / microtubule / tubulin / MOTOR PROTEIN | |||||||||||||||||||||
Function / homology | Function and homology information neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state ...neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal 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 / 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 / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / neuronal dense core vesicle / cytoskeletal motor activity / vesicle-mediated transport / axon cytoplasm / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / axon / GTPase activity / dendrite / synapse / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) | |||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||||||||
Authors | Benoit MPMH / Rao L / Asenjo AB / Gennerich A / Sosa H | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Cryo-EM unveils kinesin KIF1A's processivity mechanism and the impact of its pathogenic variant P305L. Authors: Matthieu P M H Benoit / Lu Rao / Ana B Asenjo / Arne Gennerich / Hernando Sosa / Abstract: Mutations in the microtubule-associated motor protein KIF1A lead to severe neurological conditions known as KIF1A-associated neurological disorders (KAND). Despite insights into its molecular ...Mutations in the microtubule-associated motor protein KIF1A lead to severe neurological conditions known as KIF1A-associated neurological disorders (KAND). Despite insights into its molecular mechanism, high-resolution structures of KIF1A-microtubule complexes remain undefined. Here, we present 2.7-3.5 Å resolution structures of dimeric microtubule-bound KIF1A, including the pathogenic P305L mutant, across various nucleotide states. Our structures reveal that KIF1A binds microtubules in one- and two-heads-bound configurations, with both heads exhibiting distinct conformations with tight inter-head connection. Notably, KIF1A's class-specific loop 12 (K-loop) forms electrostatic interactions with the C-terminal tails of both α- and β-tubulin. The P305L mutation does not disrupt these interactions but alters loop-12's conformation, impairing strong microtubule-binding. Structure-function analysis reveals the K-loop and head-head coordination as major determinants of KIF1A's superprocessive motility. Our findings advance the understanding of KIF1A's molecular mechanism and provide a basis for developing structure-guided therapeutics against KAND. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42546.map.gz | 41.9 MB | EMDB map data format | |
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Header (meta data) | emd-42546-v30.xml emd-42546.xml | 25.6 KB 25.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42546_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_42546.png | 127.2 KB | ||
Masks | emd_42546_msk_1.map emd_42546_msk_2.map emd_42546_msk_3.map emd_42546_msk_4.map | 274.6 MB 274.6 MB 274.6 MB 274.6 MB | Mask map | |
Filedesc metadata | emd-42546.cif.gz | 7.4 KB | ||
Others | emd_42546_additional_1.map.gz emd_42546_additional_2.map.gz emd_42546_half_map_1.map.gz emd_42546_half_map_2.map.gz | 236 MB 236.4 MB 219 MB 219 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42546 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42546 | HTTPS FTP |
-Validation report
Summary document | emd_42546_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_42546_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_42546_validation.xml.gz | 22 KB | Display | |
Data in CIF | emd_42546_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42546 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42546 | HTTPS FTP |
-Related structure data
Related structure data | 8utqMC 8utnC 8utoC 8utpC 8utrC 8utsC 8uttC 8utuC 8utvC 8utwC 8utyC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_42546.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Primary map, locally refined on the two central asymmetric units | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.844 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_42546_msk_1.map | ||||||||||||
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-Mask #2
File | emd_42546_msk_2.map | ||||||||||||
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-Mask #3
File | emd_42546_msk_3.map | ||||||||||||
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Density Histograms |
-Mask #4
File | emd_42546_msk_4.map | ||||||||||||
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Density Histograms |
-Additional map: Map low pass filtered to 8 A
File | emd_42546_additional_1.map | ||||||||||||
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Annotation | Map low pass filtered to 8 A | ||||||||||||
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-Additional map: Map low pass filtered to 6 A
File | emd_42546_additional_2.map | ||||||||||||
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Annotation | Map low pass filtered to 6 A | ||||||||||||
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Density Histograms |
-Half map: Half map from the gold Standard refinement
File | emd_42546_half_map_1.map | ||||||||||||
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Annotation | Half map from the gold Standard refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map from the gold Standard refinement
File | emd_42546_half_map_2.map | ||||||||||||
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Annotation | Half map from the gold Standard refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : KIF1A - AMP-PNP one-head-bound state in complex with a 15R microt...
Entire | Name: KIF1A - AMP-PNP one-head-bound state in complex with a 15R microtubule - class T1L02* |
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Components |
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-Supramolecule #1: KIF1A - AMP-PNP one-head-bound state in complex with a 15R microt...
Supramolecule | Name: KIF1A - AMP-PNP one-head-bound state in complex with a 15R microtubule - class T1L02* type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Macromolecule #1: Kinesin-like protein KIF1A
Macromolecule | Name: Kinesin-like protein KIF1A / type: protein_or_peptide / ID: 1 Details: "linker" residues are comprised of a leucine zipper based on S. cerevisiae GCN4, which is followed by the C-terminal strep-tag Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 49.288438 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAGASVKVAV RVRPFNSREM SRDSKCIIQM SGSTTTIVNP KQPKETPKSF SFDYSYWSHT SPEDINYASQ KQVYRDIGEE MLQHAFEGY NVCIFAYGQT GAGKSYTMMG KQEKDQQGII PQLCEDLFSR INDTTNDNMS YSVEVSYMEI YCERVRDLLN P KNKGNLRV ...String: MAGASVKVAV RVRPFNSREM SRDSKCIIQM SGSTTTIVNP KQPKETPKSF SFDYSYWSHT SPEDINYASQ KQVYRDIGEE MLQHAFEGY NVCIFAYGQT GAGKSYTMMG KQEKDQQGII PQLCEDLFSR INDTTNDNMS YSVEVSYMEI YCERVRDLLN P KNKGNLRV REHPLLGPYV EDLSKLAVTS YNDIQDLMDS GNKARTVAAT NMNETSSRSH AVFNIIFTQK RHDAETNITT EK VSKISLV DLAGSERADS TGAKGTRLKE GANINKSLTT LGKVISALAE MDSGPNKNKK KKKTDFIPYR DSVLTWLLRE NLG GNSRTA MVAALSPADI NYDETLSTLR YADRAKQIRC NAVINEDPNN KLIRELKDEV TRLRDLLYAQ GLGDITDGAG VKQL EDKVE ELASKNYHLE NEVARLKKLV EFTSAWSHPQ FEK UniProtKB: Kinesin-like protein KIF1A |
-Macromolecule #2: Tubulin alpha-1B chain
Macromolecule | Name: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) |
Molecular weight | Theoretical: 50.204445 KDa |
Sequence | String: 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 |
-Macromolecule #3: Tubulin beta-2B chain
Macromolecule | Name: Tubulin beta-2B chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) |
Molecular weight | Theoretical: 49.999887 KDa |
Sequence | String: 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 |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #7: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Macromolecule #8: TAXOL
Macromolecule | Name: TAXOL / type: ligand / ID: 8 / Number of copies: 2 / Formula: TA1 |
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Molecular weight | Theoretical: 853.906 Da |
Chemical component information | ChemComp-TA1: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 Component:
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Grid | Model: UltrAuFoil / Material: GOLD | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.22 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |