+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23636 | ||||||||||||||||||||||||||||||||||||||||||
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Title | Open conformation of the Yeast wild-type gamma-TuRC | ||||||||||||||||||||||||||||||||||||||||||
Map data | Yeast WT gamma-TuRC open state main map | ||||||||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | microtubule nucleation / CELL CYCLE | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information gamma-tubulin complex localization to nuclear side of mitotic spindle pole body / protein localization to mitotic spindle pole body / inner plaque of spindle pole body / microtubule nucleation by spindle pole body / outer plaque of spindle pole body / central plaque of spindle pole body / gamma-tubulin small complex / regulation of microtubule nucleation / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation ...gamma-tubulin complex localization to nuclear side of mitotic spindle pole body / protein localization to mitotic spindle pole body / inner plaque of spindle pole body / microtubule nucleation by spindle pole body / outer plaque of spindle pole body / central plaque of spindle pole body / gamma-tubulin small complex / regulation of microtubule nucleation / karyogamy involved in conjugation with cellular fusion / mitotic spindle elongation / equatorial microtubule organizing center / mitotic spindle pole body / gamma-tubulin complex / positive regulation of microtubule nucleation / meiotic spindle organization / microtubule nucleation / positive regulation of cytoplasmic translation / gamma-tubulin binding / spindle pole body / mitotic sister chromatid segregation / spindle assembly / meiotic cell cycle / cytoplasmic microtubule organization / mitotic spindle organization / structural constituent of cytoskeleton / spindle pole / spindle / mitotic cell cycle / protein-containing complex assembly / microtubule / calmodulin binding / cytoskeleton / protein-containing complex binding / GTP binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | ||||||||||||||||||||||||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||||||||||||||||||||||||||
Authors | Brilot AF / Lyon AS | ||||||||||||||||||||||||||||||||||||||||||
Funding support | United States, 13 items
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Citation | Journal: Elife / Year: 2021 Title: CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. Authors: Axel F Brilot / Andrew S Lyon / Alex Zelter / Shruthi Viswanath / Alison Maxwell / Michael J MacCoss / Eric G Muller / Andrej Sali / Trisha N Davis / David A Agard / Abstract: Microtubule (MT) nucleation is regulated by the γ-tubulin ring complex (γTuRC), conserved from yeast to humans. In , γTuRC is composed of seven identical γ-tubulin small complex (γTuSC) sub- ...Microtubule (MT) nucleation is regulated by the γ-tubulin ring complex (γTuRC), conserved from yeast to humans. In , γTuRC is composed of seven identical γ-tubulin small complex (γTuSC) sub-assemblies, which associate helically to template MT growth. γTuRC assembly provides a key point of regulation for the MT cytoskeleton. Here, we combine crosslinking mass spectrometry, X-ray crystallography, and cryo-EM structures of both monomeric and dimeric γTuSCs, and open and closed helical γTuRC assemblies in complex with Spc110p to elucidate the mechanisms of γTuRC assembly. γTuRC assembly is substantially aided by the evolutionarily conserved CM1 motif in Spc110p spanning a pair of adjacent γTuSCs. By providing the highest resolution and most complete views of any γTuSC assembly, our structures allow phosphorylation sites to be mapped, surprisingly suggesting that they are mostly inhibitory. A comparison of our structures with the CM1 binding site in the human γTuRC structure at the interface between GCP2 and GCP6 allows for the interpretation of significant structural changes arising from CM1 helix binding to metazoan γTuRC. | ||||||||||||||||||||||||||||||||||||||||||
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_23636.map.gz | 318.2 MB | EMDB map data format | |
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Header (meta data) | emd-23636-v30.xml emd-23636.xml | 28.2 KB 28.2 KB | Display Display | EMDB header |
Images | emd_23636.png | 178.5 KB | ||
Filedesc metadata | emd-23636.cif.gz | 8.4 KB | ||
Others | emd_23636_additional_1.map.gz emd_23636_additional_2.map.gz | 66.8 MB 66.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23636 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23636 | HTTPS FTP |
-Validation report
Summary document | emd_23636_validation.pdf.gz | 663.5 KB | Display | EMDB validaton report |
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Full document | emd_23636_full_validation.pdf.gz | 663.1 KB | Display | |
Data in XML | emd_23636_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | emd_23636_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23636 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23636 | HTTPS FTP |
-Related structure data
Related structure data | 7m2xMC 7m2wC 7m2yC 7m2zC 7m3pC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23636.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Yeast WT gamma-TuRC open state main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4183 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Yeast WT gamma-TuRC open state half map 1
File | emd_23636_additional_1.map | ||||||||||||
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Annotation | Yeast WT gamma-TuRC open state half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Yeast WT gamma-TuRC open state half map 2
File | emd_23636_additional_2.map | ||||||||||||
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Annotation | Yeast WT gamma-TuRC open state half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Open conformation of the Yeast wild-type gamma-TuRC
Entire | Name: Open conformation of the Yeast wild-type gamma-TuRC |
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Components |
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-Supramolecule #1: Open conformation of the Yeast wild-type gamma-TuRC
Supramolecule | Name: Open conformation of the Yeast wild-type gamma-TuRC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Organelle: Nucleus / Location in cell: Spindle Pole Body |
-Macromolecule #1: Tubulin gamma chain
Macromolecule | Name: Tubulin gamma chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 52.671188 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MGGEIITLQA GQCGNHVGKF LWSQLAKEHA IGTDGLSQLP DSSTERDDDT KPFFRENSRN KFTPRAIMMD SEPSVIADVE NTFRGFFDP RNTWVASDGA SAGNSWANGY DIGTRNQDDI LNKIDKEIDS TDNFEGFQLL HSVAGGTGSG LGSNLLEALC D RYPKKILT ...String: MGGEIITLQA GQCGNHVGKF LWSQLAKEHA IGTDGLSQLP DSSTERDDDT KPFFRENSRN KFTPRAIMMD SEPSVIADVE NTFRGFFDP RNTWVASDGA SAGNSWANGY DIGTRNQDDI LNKIDKEIDS TDNFEGFQLL HSVAGGTGSG LGSNLLEALC D RYPKKILT TYSVFPARSS EVVVQSYNTI LALRRLIEDS DATVVFDNAS LLNISGKVFR NPNIDLQHTN QLISTIISSV TN SIRFPSY MYSSMSSIYS TLIPSPELHF LSPSFTPFTS DYIHDDIAHK GHSSYDVMLD LLDPSNSLVS TAMNNPTYFN VYN TIIGNV EPRQISRAMT KLQQRIKFPS WSSSAMHVNI GRRSPYLPLQ PNENEVSGMM LSNMSTVVNV FENACNTFDK VFAK GAFLN NYNVGDLFQS MQNVQDEFAE SREVVQSLME DYVAAEQDSY LDDVLVDDEN MVGELEEDLD ADGDHKLV UniProtKB: Tubulin gamma chain |
-Macromolecule #2: Spindle pole body component SPC97
Macromolecule | Name: Spindle pole body component SPC97 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 96.940594 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MEIKEVDDRA ELLRYTNNIP LLGKLVNHQP LWSTNPKLKS FSLEKISAPD QRRVQEALVV KDLLNVLIGL EGTYIRYFND YEPSDPETP IEFKIAKKMD PSFKTFSRRI VRYGKQYMIL TRAYEKWSDT SFGMVLQRFA YEIRRFLEDV YLKTLVERLE R DFNKVPNF ...String: MEIKEVDDRA ELLRYTNNIP LLGKLVNHQP LWSTNPKLKS FSLEKISAPD QRRVQEALVV KDLLNVLIGL EGTYIRYFND YEPSDPETP IEFKIAKKMD PSFKTFSRRI VRYGKQYMIL TRAYEKWSDT SFGMVLQRFA YEIRRFLEDV YLKTLVERLE R DFNKVPNF SIRELEQIIN ETEVNKQMEL LYNIYEEIFR EIEERRTNQS SQEDFNNFMD SMKNESSLHL RLMVAFDTTV YP VPKGGAI LKIFQQKILE NLGDRSSVMF LKKLLNNISQ DYCTMLYEWL TQGILNDPYQ EFMTYDDLEG KTDNIFDTRD RAW DTQYFI RKDVLLRDCD SEEDKNLLFK MLRTGILLKV VRASLQIPTI PSNSSDITIQ EINDFADLME GSNLELYVDK CYSR ANEIF LKLFFQGYDL INVLKHLQQI FLGYQSGHNV LKFLTKNMGE LTKHYRNDNN ANYDKLLQNF ELERQSENPN NLMRQ LLMI QFDTETLPQV LSHYLQIYPE VPENNSANDD SDPLMHANNF KNMNAILFDE LSKERTGAYH GSNLELYTPK SAIYHL KFD INIPYPLNII ISRTCMIKYQ IILRYQLVLQ YHSRLLDETW MDLNKTPSWK YRGYSHTVKR RIVRATRVLH AKMNHFI KT IMEYFNQNVI DKEVYSLEKC YRNPTLAVAI QNELEGGLTN IMTNRCLSDL IPLQLQIFDI VYKFCKFIKS MRAKLCQL D PVLYEKHKSG MMKTLNEGYR TNNGGQEDVG YQEDAALELI QKLIEYISNA SSIFRKCLIN FTQELSTEKF DFYDSSSVD AAGIERVLYS IVPPRSASAS SQR UniProtKB: Spindle pole body component SPC97 |
-Macromolecule #3: Spindle pole body component SPC98
Macromolecule | Name: Spindle pole body component SPC98 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 98.336211 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MELEPTLFGI IEALAPQLLS QSHLQTFVSD VVNLLRSSTK SATQLGPLID FYKLQSLDSP ETTIMWHKIE KFLDALFGIQ NTDDMVKYL SVFQSLLPSN YRAKIVQKSS GLNMENLANH EHLLSPVRAP SIYTEASFEN MDRFSERRSM VSSPNRYVPS S TYSSVTLR ...String: MELEPTLFGI IEALAPQLLS QSHLQTFVSD VVNLLRSSTK SATQLGPLID FYKLQSLDSP ETTIMWHKIE KFLDALFGIQ NTDDMVKYL SVFQSLLPSN YRAKIVQKSS GLNMENLANH EHLLSPVRAP SIYTEASFEN MDRFSERRSM VSSPNRYVPS S TYSSVTLR QLSNPYYVNT IPEEDILKYV SYTLLATTSA LFPFDHEQIQ IPSKIPNFES GLLHLIFEAG LLYQSLGYKV EK FRMLNIS PMKKALIIEI SEELQNYTAF VNNLVSSGTV VSLKSLYREI YENIIRLRIY CRFTEHLEEL SGDTFLIELN IFK SHGDLT IRKIATNLFN SMISLYYEYL MNWLTKGLLR ATYGEFFIAE NTDTNGTDDD FIYHIPIEFN QERVPAFIPK ELAY KIFMI GKSYIFLEKY CKEVQWTNEF SKKYHVLYQS NSYRGISTNF FEIINDQYSE IVNHTNQILN QKFHYRDVVF ALKNI LLMG KSDFMDALIE KANDILATPS DSLPNYKLTR VLQEAVQLSS LRHLMNSPRN SSVINGLDAR VLDLGHGSVG WDVFTL DYI LYPPLSLVLN VNRPFGRKEY LRIFNFLWRF KKNNYFYQKE MLKSNDIIRS FKKIRGYNPL IRDIINKLSR ISILRTQ FQ QFNSKMESYY LNCIIEENFK EMTRKLQRTE NKSQNQFDLI RLNNGTIELN GILTPKAEVL TKSSSSKPQK HAIEKTLN I DELESVHNTF LTNILSHKLF ATNTSEISVG DYSGQPYPTS LVLLLNSVYE FVKVYCNLND IGYEIFIKMN LNDHEASNG LLGKFNTNLK EIVSQYKNFK DRLYIFRADL KNDGDEELFL LSKSLR UniProtKB: Spindle pole body component SPC98 |
-Macromolecule #4: Spindle pole body component 110
Macromolecule | Name: Spindle pole body component 110 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 25.449555 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MDEASHLPNG SLKNMEFTPV GFIKSKRNTT QTQVVSPTKV PNANNGDENE GPVKKRQRRS IDDTIDSTRL FSEASQFDDS FPEIKANIP PSPRSGNVDK SRKRNLIDDL KKDVPMSQPL KEQEVREHQM KKERFDRALE SKLLGKRHIT YANSDISNKE L YINEIKSL ...String: MDEASHLPNG SLKNMEFTPV GFIKSKRNTT QTQVVSPTKV PNANNGDENE GPVKKRQRRS IDDTIDSTRL FSEASQFDDS FPEIKANIP PSPRSGNVDK SRKRNLIDDL KKDVPMSQPL KEQEVREHQM KKERFDRALE SKLLGKRHIT YANSDISNKE L YINEIKSL KHEIKELRKE KNDTLNNYDT LEEETDDLKN RLQALEKELD AKNKIVNSRK VD UniProtKB: Spindle pole body component 110 |
-Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: Whatman #1 Filter papers used.. |
-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 exposure time: 15.0 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 47214 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 0.01 Å Applied symmetry - Helical parameters - Δ&Phi: 0 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0 Beta) / Number images used: 36251 |
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Segment selection | Number selected: 28753 / Software - Name: EMAN2 / Software - details: e2helixboxer.py Details: Boxed approximately every 3 asymmetric units using a rise of 21 Angstroms, with a box size of 600 physical pixels (635.4A). |
Startup model | Type of model: EMDB MAP EMDB ID: |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: cisTEM (ver. 1.0 Beta) / Details: Projection matching in cisTEM |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 115 |
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Output model | PDB-7m2x: |