+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8546 | |||||||||
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Title | Dimeric Kinesin-1 on Microtubules with ADP-AlFx | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Bos taurus (cattle) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.3 Å | |||||||||
Authors | Liu D / Liu X / Shang Z / Sindelar CV | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Elife / Year: 2017 Title: Structural basis of cooperativity in kinesin revealed by 3D reconstruction of a two-head-bound state on microtubules. Authors: Daifei Liu / Xueqi Liu / Zhiguo Shang / Charles V Sindelar / Abstract: The detailed basis of walking by dimeric molecules of kinesin along microtubules has remained unclear, partly because available structural methods have been unable to capture microtubule-bound ...The detailed basis of walking by dimeric molecules of kinesin along microtubules has remained unclear, partly because available structural methods have been unable to capture microtubule-bound intermediates of this process. Utilizing novel electron cryomicroscopy methods, we solved structures of microtubule-attached, dimeric kinesin bound to an ATP analog. We find that under these conditions, the kinesin dimer can attach to the microtubule with either one or two motor domains, and we present sub-nanometer resolution reconstructions of both states. The former structure reveals a novel kinesin conformation that revises the current understanding of how ATP binding is coupled to forward stepping of the motor. The latter structure indicates how tension between the two motor domains keeps their cycles out of phase in order to stimulate directional motility. The methods presented here pave the way for future structural studies of a variety of challenging macromolecules that bind to microtubules and other filaments. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8546.map.gz | 145.1 MB | EMDB map data format | |
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Header (meta data) | emd-8546-v30.xml emd-8546.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_8546.png | 78.7 KB | ||
Others | emd_8546_half_map_1.map.gz emd_8546_half_map_2.map.gz | 86.7 MB 86.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8546 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8546 | HTTPS FTP |
-Validation report
Summary document | emd_8546_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
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Full document | emd_8546_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_8546_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8546 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8546 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8546.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 2.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_8546_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_8546_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dimeric Kinesin-1 (1-420) on microtubules in the presence of ADP-AlFx
Entire | Name: Dimeric Kinesin-1 (1-420) on microtubules in the presence of ADP-AlFx |
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Components |
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-Supramolecule #1: Dimeric Kinesin-1 (1-420) on microtubules in the presence of ADP-AlFx
Supramolecule | Name: Dimeric Kinesin-1 (1-420) on microtubules in the presence of ADP-AlFx type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bos taurus (cattle) |
-Macromolecule #1: Kinesin-1
Macromolecule | Name: Kinesin-1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MADLAESNIK VMSRFRPLNE SEVNRGDKYI AKFQGEDTVV IASKPYAFDR VFQSSTSQEQ VYNDSAKKIV KDVLEGYNGT IFAYGQTSSG KTHTMEGKLH DPEGMGIIPR IVQDIFNYIY SMDENLEFHI KVSYFEIYLD KIRDLLDVSK TNLSVHEDKN RVPYVKGSTE ...String: MADLAESNIK VMSRFRPLNE SEVNRGDKYI AKFQGEDTVV IASKPYAFDR VFQSSTSQEQ VYNDSAKKIV KDVLEGYNGT IFAYGQTSSG KTHTMEGKLH DPEGMGIIPR IVQDIFNYIY SMDENLEFHI KVSYFEIYLD KIRDLLDVSK TNLSVHEDKN RVPYVKGSTE RFVSSPDEVM DTIDEGKSNR HVAVTNMNEH SSRSHSIFLI NVKQENTQTE QKLSGKLYLV DLAGSEKVSK TGAEGAVLDE AKNINKSLSA LGNVISALAE GSTYVPYRDS KMTRILQDSL GGNSRTTIVI SSSPSSYNES ETKSTLLFGQ RAKTIKNTVS VNVELTAEQW KKKYEKEKEK NKILRNTIQW LENELNRWRN GETVPIDEQF DKEKANLEAF TVDKDITLTN DKPATAIGVI GNFTDAERRK |
-Macromolecule #2: Alpha-tubulin
Macromolecule | Name: Alpha-tubulin / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Sequence | String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS ...String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS IYPAPQVSTA VVEPYNSILT THTTLEHSDC AFMVDNEAIY DICRRNLDIE RPTYTNLNRL ISQIVSSITA SLRFDGALNV DLTEFQTNLV PYPRIHFPLA TYAPVISAEK AYHEQLSVAE ITNACFEPAN QMVKCDPRHG KYMACCLLYR GDVVPKDVNA AIATIKTKRS IQFVDWCPTG FKVGINYQPP TVVPGGDLAK VQRAVCMLSN TTAIAEAWAR LDHKFDLMYA KRAFVHWYVG EGMEEGEFSE AREDMAALEK DYEEVGVDSV EGEGEEEGEE Y |
-Macromolecule #3: Beta-tubulin
Macromolecule | Name: Beta-tubulin / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Sequence | String: MREIVHLQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGNYV PRAVLVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDAVLDVV RKEAESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEFP DRIMNTFSVV ...String: MREIVHLQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGNYV PRAVLVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDAVLDVV RKEAESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEFP DRIMNTFSVV PSPKVSDTVV EPYNATLSVH QLVENTDETY CIDNEALYDI CFRTLKLTTP TYGDLNHLVS ATMSGVTTCL RFPGQLNADL RKLAVNMVPF PRLHFFMPGF APLTSRGSQQ YRALTVPELT QQMFDAKNMM AACDPRHGRY LTVAAVFRGR MSMKEVDEQM LSVQSKNSSY FVEWIPNNVK TAVCDIPPRG LKMAATFIGN STAIQELFKR ISEQFTAMFR RKAFLHWYTG EGMDEMEFTE AESNMNDLVS EYQQYQDATA EEGEFEEEAE EEVA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Average electron dose: 1.65 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF Details: a modified version of frealign was used for reconstruction, kinesin dimer was masked before FSC calculation using half maps. Number images used: 17862 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |