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- EMDB-4862: Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC ch... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4862 | |||||||||
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Title | Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule | |||||||||
![]() | Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule | |||||||||
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![]() | Microtubule-associated protein / neuronal migration protein / ubiquitin-like fold / microtubule nucleation and stabilisation / CYTOSOLIC PROTEIN | |||||||||
Function / homology | ![]() axoneme assembly / Neurofascin interactions / positive regulation of axon guidance / microtubule associated complex / microtubule-based process / central nervous system development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / neuron migration / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...axoneme assembly / Neurofascin interactions / positive regulation of axon guidance / microtubule associated complex / microtubule-based process / central nervous system development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / neuron migration / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / retina development in camera-type eye / mitotic cell cycle / nervous system development / microtubule binding / microtubule / cytoskeleton / intracellular signal transduction / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / protein kinase binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Manka SW | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A microtubule RELION-based pipeline for cryo-EM image processing. Authors: Alexander D Cook / Szymon W Manka / Su Wang / Carolyn A Moores / Joseph Atherton / ![]() Abstract: Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall ...Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views owing to the high structural similarity of α- and β-tubulin. The determination of the αβ-tubulin register and seam location during image processing is essential for alignment accuracy that enables determination of biologically relevant structures. Here we present a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing near-atomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 487.7 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.6 KB 14.6 KB | Display Display | ![]() |
Images | ![]() | 174.5 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rf8MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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 | Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chim...
Entire | Name: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chimera (human doublecortin sequence) bound to 13-protofilament GDP-microtubule lattice site composed of 4 tubulin subunits (two ...Name: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chimera (human doublecortin sequence) bound to 13-protofilament GDP-microtubule lattice site composed of 4 tubulin subunits (two alpha-subunits and two beta-subunits) |
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Components |
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-Supramolecule #1: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chim...
Supramolecule | Name: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chimera (human doublecortin sequence) bound to 13-protofilament GDP-microtubule lattice site composed of 4 tubulin subunits (two ...Name: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chimera (human doublecortin sequence) bound to 13-protofilament GDP-microtubule lattice site composed of 4 tubulin subunits (two alpha-subunits and two beta-subunits) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Supramolecule #2: human doublecortin
Supramolecule | Name: human doublecortin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: tubulin
Supramolecule | Name: tubulin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Neuronal migration protein doublecortin
Macromolecule | Name: Neuronal migration protein doublecortin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.441834 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QALSNEKKAK KVRFYRNGDR YFKGIVYAVS SDRFRSFDAL LADLTRSLSD NINLPQGVRY IYTIDGSRKI GSMDELEEGE SYVCSSDNF FKKVEYTKNV UniProtKB: Neuronal migration protein doublecortin |
-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: 48.113129 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 QDAT UniProtKB: Tubulin beta-2B chain |
-Macromolecule #3: Tubulin alpha-1B chain
Macromolecule | Name: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 48.263594 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 VGVDSVE UniProtKB: Tubulin alpha-1B chain |
-Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ![]() ChemComp-GDP: |
-Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ![]() ChemComp-GTP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28347 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient |
Output model | ![]() PDB-6rf8: |