+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42552 | |||||||||||||||||||||
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Title | KIF1A[1-393] P305L mutant APO in complex with a microtubule | |||||||||||||||||||||
Map data | Primary map, locally refined on the central asymmetric unit. | |||||||||||||||||||||
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 / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / axon / GTPase activity / synapse / dendrite / 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: 3.4 Å | |||||||||||||||||||||
Authors | Benoit MPMH / Rao L / Asenjo AB / Gennerich A / Sosa H | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: To Be Published 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 | emd_42552.map.gz | 30.1 MB | EMDB map data format | |
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Header (meta data) | emd-42552-v30.xml emd-42552.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42552_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_42552.png | 117.5 KB | ||
Masks | emd_42552_msk_1.map emd_42552_msk_2.map emd_42552_msk_3.map emd_42552_msk_4.map | 274.6 MB 274.6 MB 274.6 MB 274.6 MB | Mask map | |
Filedesc metadata | emd-42552.cif.gz | 7.2 KB | ||
Others | emd_42552_additional_1.map.gz emd_42552_half_map_1.map.gz emd_42552_half_map_2.map.gz | 237.6 MB 218.7 MB 218.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42552 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42552 | HTTPS FTP |
-Validation report
Summary document | emd_42552_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_42552_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_42552_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | emd_42552_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42552 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42552 | HTTPS FTP |
-Related structure data
Related structure data | 8utwMC 8utnC 8utoC 8utpC 8utqC 8utrC 8utsC 8uttC 8utuC 8utvC 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_42552.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 central asymmetric unit. | ||||||||||||||||||||
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_42552_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_42552_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #3
File | emd_42552_msk_3.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #4
File | emd_42552_msk_4.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Map low pass filtered to 6 A
File | emd_42552_additional_1.map | ||||||||||||
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Annotation | Map low pass filtered to 6 A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map from the gold Standard refinement
File | emd_42552_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_42552_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[1-393] P305L mutant APO in complex with a 15R microtubule
Entire | Name: KIF1A[1-393] P305L mutant APO in complex with a 15R microtubule |
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Components |
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-Supramolecule #1: KIF1A[1-393] P305L mutant APO in complex with a 15R microtubule
Supramolecule | Name: KIF1A[1-393] P305L mutant APO in complex with a 15R microtubule 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: 49.30448 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 KKKTDFILYR 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: 1 / 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: 1 / 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: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / 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: 1 / 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: 1 / 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: 1 / 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 / Pretreatment - Type: PLASMA CLEANING | ||||||||||
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: 50.4 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: 3.0100000000000002 µm / Nominal defocus min: 0.6900000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |