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Yorodumi- EMDB-21068: Structure of GCP6 in the native human gamma-tubulin ring complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21068 | |||||||||
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Title | Structure of GCP6 in the native human gamma-tubulin ring complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | GCP / GCP6 / gamma-tubulin ring complex / gTuRC / g-TuRC / microtubule / microtubule nucleation / single particle cryo-EM structure / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information equatorial microtubule organizing center / gamma-tubulin ring complex / microtubule minus-end binding / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle assembly / cytoplasmic microtubule organization / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes ...equatorial microtubule organizing center / gamma-tubulin ring complex / microtubule minus-end binding / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle assembly / cytoplasmic microtubule organization / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / meiotic cell cycle / spindle pole / mitotic cell cycle / microtubule binding / microtubule / centrosome / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Wieczorek M / Urnavicius L | |||||||||
Funding support | United States, France, 2 items
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Citation | Journal: Cell / Year: 2020 Title: Asymmetric Molecular Architecture of the Human γ-Tubulin Ring Complex. Authors: Michal Wieczorek / Linas Urnavicius / Shih-Chieh Ti / Kelly R Molloy / Brian T Chait / Tarun M Kapoor / Abstract: The γ-tubulin ring complex (γ-TuRC) is an essential regulator of centrosomal and acentrosomal microtubule formation, yet its structure is not known. Here, we present a cryo-EM reconstruction of the ...The γ-tubulin ring complex (γ-TuRC) is an essential regulator of centrosomal and acentrosomal microtubule formation, yet its structure is not known. Here, we present a cryo-EM reconstruction of the native human γ-TuRC at ∼3.8 Å resolution, revealing an asymmetric, cone-shaped structure. Pseudo-atomic models indicate that GCP4, GCP5, and GCP6 form distinct Y-shaped assemblies that structurally mimic GCP2/GCP3 subcomplexes distal to the γ-TuRC "seam." We also identify an unanticipated structural bridge that includes an actin-like protein and spans the γ-TuRC lumen. Despite its asymmetric architecture, the γ-TuRC arranges γ-tubulins into a helical geometry poised to nucleate microtubules. Diversity in the γ-TuRC subunits introduces large (>100,000 Å) surfaces in the complex that allow for interactions with different regulatory factors. The observed compositional complexity of the γ-TuRC could self-regulate its assembly into a cone-shaped structure to control microtubule formation across diverse contexts, e.g., within biological condensates or alongside existing 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_21068.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-21068-v30.xml emd-21068.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_21068.png | 41.4 KB | ||
Filedesc metadata | emd-21068.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21068 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21068 | HTTPS FTP |
-Validation report
Summary document | emd_21068_validation.pdf.gz | 370.8 KB | Display | EMDB validaton report |
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Full document | emd_21068_full_validation.pdf.gz | 370.3 KB | Display | |
Data in XML | emd_21068_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_21068_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21068 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21068 | HTTPS FTP |
-Related structure data
Related structure data | 6v6cMC 6v5vC 6v69C 6v6bC 6v6sC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21068.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.335 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Native human gamma-tubulin ring complex
Entire | Name: Native human gamma-tubulin ring complex |
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Components |
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-Supramolecule #1: Native human gamma-tubulin ring complex
Supramolecule | Name: Native human gamma-tubulin ring complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Gamma-tubulin complex component 6
Macromolecule | Name: Gamma-tubulin complex component 6 / type: protein_or_peptide / ID: 1 Details: Please note that the full sequence for GCP6 (Uniprot accession number Q96RT7) was much longer than our modeled region, and the alignment failed to capture the domains we built, despite all ...Details: Please note that the full sequence for GCP6 (Uniprot accession number Q96RT7) was much longer than our modeled region, and the alignment failed to capture the domains we built, despite all residues being numbered accordingly in the submitted coordinates. See below for full sequence. Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 200.733641 KDa |
Sequence | String: MASITQLFDD LCEALLPAAK THLGQRSVNR KRAKRSLKKV AYNALFTNLF QDETQQLQPD MSKLPARNKI LMLSFDLRVG GLGPKADRL EELVEELEAA PCCPLLEVGS VLDLLVQLAG SGPPQVLPRK RDYFLNNKHV GRNVPYSGYD CDDLSVFEMD V QSLISREE ...String: MASITQLFDD LCEALLPAAK THLGQRSVNR KRAKRSLKKV AYNALFTNLF QDETQQLQPD MSKLPARNKI LMLSFDLRVG GLGPKADRL EELVEELEAA PCCPLLEVGS VLDLLVQLAG SGPPQVLPRK RDYFLNNKHV GRNVPYSGYD CDDLSVFEMD V QSLISREE CLCHSMIQET LQVMEAAPGT GLPTVGLFSF GDPCGDRFER DTRVSLFGAL VHSRTYDMDV RLGLPPVPDN AD LSGLAIK VPPSVDQWED EGFQSASNLT PDSQSEPSVT PDVDLWEAAL TYEASKRRCW ERVGCPPGHR EEPYLTEAGR DAF DKFCRL HQGELQLLAG GVLQAPQPVL VKECELVKDV LNVLIGVVSA TFSLCQPAQA FVVKRGVHVS GASPESISSL LSEV AEYGT CYTRLSHFSL QPVLDSLYSK GLVFQAFTSG LRRYLQYYRA CVLSTPPTLS LLTIGFLFKK LGRQLRYLAE LCGVG AVLP GTCGGGPRAA FPTGVKLLSY LYQEALHNCS NEHYPVLLSL LKTSCEPYTR FIHDWVYSGV FRDAYGEFMI QVNHEY LSF RDKLYWTHGY VLISKEVEDC VPVFLKHIAH DIYVCGKTIN LLKLCCPRHY LCWSDVPVPR ISVIFSLEEL KEIEKDC AV YVGRMERVAR HSSVSKEEKE LRMEIAKQEL IAHAREAASR VLSALSDRQM SERMALDARK REQFQRLKEQ FVKDQERR Q AARQEELDDD FSYARELRDR ERRLKSLEEE LERKARQALV DHYSKLSAEA ARREQKALWR IQRHRLESAR LRFLLEDEK HIQEMLKAVS EAHQPQEPPD VLLSVHPQVT SPGPEHPEGG QGCDSGSAEQ HSPAWDGWNR PGLLTPQPLK PLAVGAGGRG LQQAEGARP FSDSLSIGDF LPVGPGAEPS VQTGMVPLLE VALQTINLDL PPSAPGEAPA AASTQPSRPQ EYDFSTVLRP A VATSPAPG PLQAAECSLG SSGLQLWEDS CGKMDACGSA SRETLLPSHP PRRAALEEGS SQPTERLFGQ VSGGGLPTGD YA SEIAPTR PRWNTHGHVS DASIRVGENV SDVAPTQPRW NTHGHVSNAS ISLGESVSDV APTRPRWNIH GHVSNASIRV GEN VSDVAP TRPRWNTHGH VSNASIRVGE NVSDVAPTRP RWNTHGHVSD ASISLGESVS DMAPARPRWN THGHVSDASI SLGE SVSDM APTRPRWNTH GHVSDTSIRV GENVSDVAPI RSRCNTHGHV SDASISLGEP VSDVVSTRPR WNTHVPIPPP HMVLG ALSP EAEPNTPRPQ QSPPGHTSQS ALSLGAQSTV LDCGPRLPVE VGPSLSSPSS GCGEGSISVG ENVSDVAPTQ PWWPNT PGD SVSEELGPGR SGDTEDLSPN WPLNSQEDTA AQSSPGRGEE AEASAAEAQG GEQAYLAGLA GQYHLERYPD SYESMSE PP IAHLLRPVLP RAFAFPVDPQ VQSAADETAV QLSELLTLPV LMKRSITAPL AAHISLVNKA AVDYFFVELH LEAHYEAL R HFLLMEDGEF AQSLSDLLFE KLGAGQTPGE LLNPLVLNSV LSKALQCSLH GDTPHASNLS LALKYLPEVF APNAPDVLS CLELRYKVDW PLNIVITEGC VSKYSGVFSF LLQLKLMMWA LKDVCFHLKR TALLSHMAGS VQFRQLQLFK HEMQHFVKVI QGYIANQIL HVTWCEFRAR LATVGDLEEI QRAHAEYLHK AVFRGLLTEK AAPVMNVIHS IFSLVLKFRS QLISQAWGPP G GPRGAEHP NFALMQQSYN TFKYYSHFLF KVVTKLVNRG YQPHLEDFLL RINFNNYYQD A UniProtKB: Gamma-tubulin complex component 6 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Relion 3.0 initial model generation |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102613 |
Initial angle assignment | Type: OTHER / Details: Relion 3.0 |
Final angle assignment | Type: OTHER / Details: Relion 3.0 |