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Yorodumi- EMDB-14460: P. berghei kinesin-8B motor domain in AMPPNP state bound to tubul... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14460 | |||||||||
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Title | P. berghei kinesin-8B motor domain in AMPPNP state bound to tubulin dimer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | kinesin / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information 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 ...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 / 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 / microtubule motor activity / microtubule-based movement / 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 / GTPase activity / GTP binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Plasmodium berghei (eukaryote) / Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Liu T / Shilliday F / Cook AD / Moores CA | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Protein Sci / Year: 2018 Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin / Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14460.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-14460-v30.xml emd-14460.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14460_fsc.xml | 20.3 KB | Display | FSC data file |
Images | emd_14460.png | 78 KB | ||
Filedesc metadata | emd-14460.cif.gz | 6.7 KB | ||
Others | emd_14460_half_map_1.map.gz emd_14460_half_map_2.map.gz | 591.9 MB 592.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14460 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14460 | HTTPS FTP |
-Related structure data
Related structure data | 7z2bMC 7z2aC 7z2cC 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_14460.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map2
File | emd_14460_half_map_1.map | ||||||||||||
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Annotation | half map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map1
File | emd_14460_half_map_2.map | ||||||||||||
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Annotation | half map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : P. berghei kinesin-8B motor domain in AMPPNP state bound to tubul...
Entire | Name: P. berghei kinesin-8B motor domain in AMPPNP state bound to tubulin dimer |
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Components |
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-Supramolecule #1: P. berghei kinesin-8B motor domain in AMPPNP state bound to tubul...
Supramolecule | Name: P. berghei kinesin-8B motor domain in AMPPNP state bound to tubulin dimer type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Plasmodium berghei (eukaryote) |
-Macromolecule #1: Kinesin-8, putative
Macromolecule | Name: Kinesin-8, putative / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Plasmodium berghei (eukaryote) |
Molecular weight | Theoretical: 38.401828 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ITYNMNVVIR CRPMSNSEKN EGAKNVIKIM DNKMIVLLDP SDNTDNVLRQ NRTKEKRYCF DYVFDENSTQ EDVYNNSVKP LVDAVIKGY NSTVFAYGAT GAGKTHTIIG YKNEPGIMMM ILQDLFKKIK TLKAMNEYKI KCSFIEIYNE NICDLLNPSS E YLDLREDP ...String: ITYNMNVVIR CRPMSNSEKN EGAKNVIKIM DNKMIVLLDP SDNTDNVLRQ NRTKEKRYCF DYVFDENSTQ EDVYNNSVKP LVDAVIKGY NSTVFAYGAT GAGKTHTIIG YKNEPGIMMM ILQDLFKKIK TLKAMNEYKI KCSFIEIYNE NICDLLNPSS E YLDLREDP VKGITVSNIF EVCTTSVEEI MELIHTGNRN RTQEPTDANR TSSRSHGVLQ VIVEETEKGQ GLYQQTKKGK LC VIDLAGS ERASQTNNKG MRMLEGANIN RSLLALGNVI NALVSRSKGT SKSNFIPFRD SKLTRLLKDS LGGNCKTLMI ANI SPSHLS YEDTHNTLKY ANRAK UniProtKB: Kinesin-8, putative |
-Macromolecule #2: Detyrosinated tubulin alpha-1B chain
Macromolecule | Name: Detyrosinated 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: 47.833184 KDa |
Sequence | String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPDSF NTFFSETGAG KHVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKED AANNYARGHY TIGKEIIDLV LDRIRKLADQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE F SIYPAPQV ...String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPDSF NTFFSETGAG KHVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKED AANNYARGHY TIGKEIIDLV LDRIRKLADQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE F SIYPAPQV STAVVEPYNS ILTTHTTLEH SDCAFMVDNE AIYDICRRNL DIERPTYTNL NRLISQIVSS ITASLRFDGA LN VDLTEFQ TNLVPYPRIH FPLATYAPVI SAEKAYHEQL SVAEITNACF EPANQMVKCD PRHGKYMACC LLYRGDVVPK DVN AAIATI KTKRSIQFVD WCPTGFKVGI NYQPPTVVPG GDLAKVQRAV CMLSNTTAIA EAWARLDHKF DLMYAKRAFV HWYV GEGME EGEFSEARED MAALEKDYEE VGV UniProtKB: Tubulin alpha-1B chain |
-Macromolecule #3: Tubulin beta chain
Macromolecule | Name: Tubulin beta 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: 47.825859 KDa |
Sequence | String: 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 Q UniProtKB: Tubulin beta chain |
-Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 1 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #7: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Macromolecule | Name: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: G2P |
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Molecular weight | Theoretical: 521.208 Da |
Chemical component information | ChemComp-G2P: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |