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- EMDB-42553: KIF1A[1-393] P364L mutant AMP-PNP bound two-heads-bound state in ... -
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Open data
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Basic information
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Title | KIF1A[1-393] P364L mutant AMP-PNP bound two-heads-bound state in complex with a microtubule | ||||||||||||||||||
![]() | Primary map, locally refined on the two central asymmetric units | ||||||||||||||||||
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![]() | KIF1A / ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | helical reconstruction / ![]() | ||||||||||||||||||
![]() | Benoit MPMH / Rao L / Asenjo AB / Gennerich A / Sosa H | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM of human KIF1A reveals its mechanism of motility and the effect of its pathogenic variant P305L Authors: Benoit MPMH / Rao L / Asenjo AB / Gennerich A / Sosa H | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 15.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.6 KB 22.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.2 KB | Display | ![]() |
Images | ![]() | 106.3 KB | ||
Masks | ![]() ![]() ![]() ![]() | 91.1 MB 91.1 MB 91.1 MB 91.1 MB | ![]() | |
Filedesc metadata | ![]() | 7.2 KB | ||
Others | ![]() ![]() ![]() | 80.1 MB 71.5 MB 71.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8utyMC ![]() 8utnC ![]() 8utoC ![]() 8utpC ![]() 8utqC ![]() 8utrC ![]() 8utsC ![]() 8uttC ![]() 8utuC ![]() 8utvC ![]() 8utwC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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: 1.3 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Mask #2
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-Mask #3
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-Mask #4
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-Additional map: Map low pass filtered to 6 A
File | emd_42553_additional_1.map | ||||||||||||
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Annotation | Map low pass filtered to 6 A | ||||||||||||
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-Half map: Half map from the gold Standard refinement
File | emd_42553_half_map_1.map | ||||||||||||
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Annotation | Half map from the gold Standard refinement | ||||||||||||
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Density Histograms |
-Half map: Half map from the gold Standard refinement
File | emd_42553_half_map_2.map | ||||||||||||
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Annotation | Half map from the gold Standard refinement | ||||||||||||
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Sample components
-Entire : KIF1A-P364L AMP-PNP - two-heads-bound state in complex with a mic...
Entire | Name: KIF1A-P364L AMP-PNP - two-heads-bound state in complex with a microtubule |
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Components |
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-Supramolecule #1: KIF1A-P364L AMP-PNP - two-heads-bound state in complex with a mic...
Supramolecule | Name: KIF1A-P364L AMP-PNP - two-heads-bound state in complex with a microtubule type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Macromolecule #1: Tubulin alpha-1B chain
Macromolecule | Name: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
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 #2: Tubulin beta-2B chain
Macromolecule | Name: Tubulin beta-2B chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
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 #3: Kinesin-like protein KIF1A
Macromolecule | Name: Kinesin-like protein KIF1A / type: protein_or_peptide / ID: 3 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: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 49.30448 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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 NAVINEDLNN KLIRELKDEV TRLRDLLYAQ GLGDITDGAG VKQL EDKVE ELASKNYHLE NEVARLKKLV EFTSAWSHPQ FEK UniProtKB: Kinesin-like protein KIF1A |
-Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ![]() ChemComp-GTP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ![]() ChemComp-GDP: |
-Macromolecule #7: TAXOL
Macromolecule | Name: TAXOL / type: ligand / ID: 7 / Number of copies: 2 / Formula: TA1 |
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Molecular weight | Theoretical: 853.906 Da |
Chemical component information | ![]() ChemComp-TA1: |
-Macromolecule #8: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 8 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ![]() ChemComp-ANP: |
-Experimental details
-Structure determination
Method | ![]() |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 6.8 Component:
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.22 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |