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Yorodumi- EMDB-21060: Structures of GCP4 and GCP5 in the native human gamma-tubulin rin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21060 | |||||||||
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Title | Structures of GCP4 and GCP5 in the native human gamma-tubulin ring complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | GCP / GCP4 / GCP5 / 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 / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle assembly / meiotic cell cycle / cytoplasmic microtubule organization / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes ...equatorial microtubule organizing center / gamma-tubulin ring complex / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle assembly / meiotic cell cycle / cytoplasmic microtubule organization / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / recycling endosome / structural constituent of cytoskeleton / spindle pole / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / protein-containing complex assembly / microtubule / centrosome / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 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_21060.map.gz | 4.3 MB | EMDB map data format | |
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Header (meta data) | emd-21060-v30.xml emd-21060.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
Images | emd_21060.png | 44.7 KB | ||
Filedesc metadata | emd-21060.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21060 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21060 | HTTPS FTP |
-Validation report
Summary document | emd_21060_validation.pdf.gz | 346.3 KB | Display | EMDB validaton report |
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Full document | emd_21060_full_validation.pdf.gz | 345.8 KB | Display | |
Data in XML | emd_21060_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_21060_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21060 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21060 | HTTPS FTP |
-Related structure data
Related structure data | 6v69MC 6v5vC 6v6bC 6v6cC 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_21060.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 5
Macromolecule | Name: Gamma-tubulin complex component 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 118.467547 KDa |
Sequence | String: MARHGPPWSR LDAQQERDVR ELVRGVAGLQ DEADPNFQLA LNFAWSNFRF HRFLDVNSHK IEKTIEGIYE KFVIHSDLSK AASWKRLTE EFLNAPLPSI KEIKTDAHYS ILSLLLCLSD SPSNSSYVET PRNKEVEKKD DFDWGKYLME DEEMDIGPYM D TPNWSEES ...String: MARHGPPWSR LDAQQERDVR ELVRGVAGLQ DEADPNFQLA LNFAWSNFRF HRFLDVNSHK IEKTIEGIYE KFVIHSDLSK AASWKRLTE EFLNAPLPSI KEIKTDAHYS ILSLLLCLSD SPSNSSYVET PRNKEVEKKD DFDWGKYLME DEEMDIGPYM D TPNWSEES EEENDQQPLS REDSGIQVDR TPLEEQDQNR KLDPCISWKD EPDDRSWLEH HVVHQYWTAR PSQFPHSLHL HS NLAAVWD QHLYSSDPLY VPDDRVLVTE TQVIRETLWL LSGVKKLFIF QLIDGKVTVR NNIIVTHLTH SCLRSVLEQI AAY GQVVFR LQEFIDEVMG HSSESMLPGS GSVPKKSTEA PFRTYQAFMW ALYKYFISFK EELAEIEKCI INNDTTITLA IVVD KLAPR LSQLKVLHKV FSTGVAEVPP DTRNVVRASH LLNTLYKAIL EYDNVGEASE QTVSLLFSLW VETVRPYLQT VDEWI VHGH LWDGAREFII QRNKNVPVNH RDFWYATYTL YSVSEKTENE EKMSDNASAS SGSDQGPSSR QHTMVSFLKP VLKQII MAG KSMQLLKNLQ CAESTTCQAG ARDAERKSLY TLFLESVQSR LRHGEDSTPQ VLTEQQATKE NLMKMQSIAE SHLELDD VH DPLLAINFAR MYLEQSDFHE KFAGGDVCVD RSSESVTCQT FELTLRSCLY PHIDKQYLDC CGNLMQTLKK DYRLVEYL Q AMRNFFLMEG GDTMYDFYTS IFDKIREKET WQNVSFLNVQ LQEAVGQRYP EDSSRLSISF ENVDTAKKKL PVHILDGLT LSYKVPWPVD IVISLECQKI YNQVFLLLLQ IKWAKYSLDV LLFGELVSTA EKPRLKEGLI HEQDTVAQFG PQKEPVRQQI HRMFLLRVK LMHFVNSLHN YIMTRILHST GLEFQHQVEE AKDLDQLIKI HYRYLSTIHD RCLLREKVSF VKEAIMKVLN L ALMFADGW QAGLGTWRME SIEKMESDFK NCHMFLVTIL NKAVCRGSFP HLESLALSLM AGMEQS UniProtKB: Gamma-tubulin complex component 5 |
-Macromolecule #2: Gamma-tubulin complex component 4
Macromolecule | Name: Gamma-tubulin complex component 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 76.179969 KDa |
Sequence | String: MIHELLLALS GYPGSIFTWN KRSGLQVSQD FPFLHPSETS VLNRLCRLGT DYIRFTEFIE QYTGHVQQQD HHPSQQGQGG LHGIYLRAF CTGLDSVLQP YRQALLDLEQ EFLGDPHLSI SHVNYFLDQF QLLFPSVMVV VEQIKSQKIH GCQILETVYK H SCGGLPPV ...String: MIHELLLALS GYPGSIFTWN KRSGLQVSQD FPFLHPSETS VLNRLCRLGT DYIRFTEFIE QYTGHVQQQD HHPSQQGQGG LHGIYLRAF CTGLDSVLQP YRQALLDLEQ EFLGDPHLSI SHVNYFLDQF QLLFPSVMVV VEQIKSQKIH GCQILETVYK H SCGGLPPV RSALEKILAV CHGVMYKQLS AWMLHGLLLD QHEEFFIKQG PSSGNVSAQP EEDEEDLGIG GLTGKQLREL QD LRLIEEE NMLAPSLKQF SLRVEILPSY IPVRVAEKIL FVGESVQMFE NQNVNLTRKG SILKNQEDTF AAELHRLKQQ PLF SLVDFE QVVDRIRSTV AEHLWKLMVE ESDLLGQLKI IKDFYLLGRG ELFQAFIDTA QHMLKTPPTA VTEHDVNVAF QQSA HKVLL DDDNLLPLLH LTIEYHGKEH KADATQAREG PSRETSPREA PASGWAALGL SYKVQWPLHI LFTPAVLEKY NVVFK YLLS VRRVQAELQH CWALQMQRKH LKSNQTDAIK WRLRNHMAFL VDNLQYYLQV DVLESQFSQL LHQINSTRDF ESIRLA HDH FLSNLLAQSF ILLKPVFHCL NEILDLCHSF CSLVSQNLGP LDERGAAQLS ILVKGFSRQS SLLFKILSSV RNHQINS DL AQLLLRLDYN KYYTQAGGTL GSFGM UniProtKB: Gamma-tubulin complex component 4 |
-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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103172 |
Initial angle assignment | Type: OTHER / Details: Relion 3.0 |
Final angle assignment | Type: OTHER / Details: Relion 3.0 |