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Yorodumi- EMDB-29552: Structure of NOT1:NOT10:NOT11 module of the chicken CCR4-NOT complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29552 | |||||||||
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Title | Structure of NOT1:NOT10:NOT11 module of the chicken CCR4-NOT complex | |||||||||
Map data | DeepEMhancer map | |||||||||
Sample |
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Keywords | mRNA degradation / gene expression / RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information Deadenylation of mRNA / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / CCR4-NOT complex / regulatory ncRNA-mediated gene silencing / mRNA catabolic process / negative regulation of translation / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.57 Å | |||||||||
Authors | Lea SM / Deme JC / Raisch T / Levdansky Y / Valkov E | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Commun Biol / Year: 2023 Title: Structure and assembly of the NOT10:11 module of the CCR4-NOT complex. Authors: Yevgen Levdansky / Tobias Raisch / Justin C Deme / Filip Pekovic / Hans Elmlund / Susan M Lea / Eugene Valkov / Abstract: NOT1, NOT10, and NOT11 form a conserved module in the CCR4-NOT complex, critical for post-transcriptional regulation in eukaryotes, but how this module contributes to the functions of the CCR4-NOT ...NOT1, NOT10, and NOT11 form a conserved module in the CCR4-NOT complex, critical for post-transcriptional regulation in eukaryotes, but how this module contributes to the functions of the CCR4-NOT remains poorly understood. Here, we present cryo-EM structures of human and chicken NOT1:NOT10:NOT11 ternary complexes to sub-3 Å resolution, revealing an evolutionarily conserved, flexible structure. Through biochemical dissection studies, which include the Drosophila orthologs, we show that the module assembly is hierarchical, with NOT11 binding to NOT10, which then organizes it for binding to NOT1. A short proline-rich motif in NOT11 stabilizes the entire module assembly. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29552.map.gz | 182.2 MB | EMDB map data format | |
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Header (meta data) | emd-29552-v30.xml emd-29552.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29552_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_29552.png | 34 KB | ||
Masks | emd_29552_msk_1.map | 216 MB | Mask map | |
Others | emd_29552_additional_1.map.gz emd_29552_additional_2.map.gz emd_29552_half_map_1.map.gz emd_29552_half_map_2.map.gz | 107.4 MB 203.7 MB 200.8 MB 200.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29552 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29552 | HTTPS FTP |
-Validation report
Summary document | emd_29552_validation.pdf.gz | 735.2 KB | Display | EMDB validaton report |
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Full document | emd_29552_full_validation.pdf.gz | 734.8 KB | Display | |
Data in XML | emd_29552_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | emd_29552_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29552 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29552 | HTTPS FTP |
-Related structure data
Related structure data | 8fy4MC 8fy3C 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_29552.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | DeepEMhancer map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.723 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29552_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_29552_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Sharpened map
File | emd_29552_additional_2.map | ||||||||||||
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Annotation | Sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_29552_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_29552_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NOT1:NOT10:NOT11
Entire | Name: NOT1:NOT10:NOT11 |
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Components |
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-Supramolecule #1: NOT1:NOT10:NOT11
Supramolecule | Name: NOT1:NOT10:NOT11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Gallus gallus (chicken) |
-Macromolecule #1: CCR4-NOT transcription complex subunit 1
Macromolecule | Name: CCR4-NOT transcription complex subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 76.422859 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNLDSLSLAL SQISYLVDNL TKKNYRASQQ EIQHIVNRHG PEADRHLLRC LFSHVDFSGD GKSSGKDFHQ TQFLIQECAS LITKPNFIS TLSYAIDNPL HYQKSLKPSP HLFAQLSKVI KLSKVQEVIF GLALLNSFSS DLRGFAAQFI KQKLPDLLRS Y IDADVSGN ...String: MNLDSLSLAL SQISYLVDNL TKKNYRASQQ EIQHIVNRHG PEADRHLLRC LFSHVDFSGD GKSSGKDFHQ TQFLIQECAS LITKPNFIS TLSYAIDNPL HYQKSLKPSP HLFAQLSKVI KLSKVQEVIF GLALLNSFSS DLRGFAAQFI KQKLPDLLRS Y IDADVSGN QEGGFQDIAI EVLHLLLSHL LFGQKGAFGV GQEQIDAFLK TLRRDFPQER CPVVLAPLLY PEKRDILMDR IL PDSGGIA KTMMESSLAD FMQEVGYGFC TSIEECRNII MQFGVREVTA AQVARVLGMM ARTHSGLTDG IPLQSISAPG SGI WSDGKD KSDGAQAHTW NVEVLIDVLK ELNPSLDFKV VTYELDHPGF QIRDSKGLHI VVFGIQRGLG MEVFPVNAIY RPWK HAEGQ LSFIQHSLIN PDIFCFADYP CHAVTTDILK APPEDDNREI ATWKSLDLIE SLLRLAEVGQ YEQVKQLFSF PIKHC PDML VLALLQINTS WHTLRHELIS TLMPIFLGNH PNSAIILHYA WHGQGQSPSI RQLIMHAMAE WYMRGEQYDQ AKLSRI LDV AQDLKALSML LNGTPFAFVI DLAALASRRE YLKLDKWLTD KIREHGEPFI QACMTFLKRR CPSILGGLAP EKDQPKS AQ LPPETLATML ACLQACAGSV SQELSETILT MVANCSNVMN UniProtKB: UNIPROTKB: E1C1B8 |
-Macromolecule #2: CCR4-NOT transcription complex subunit 10
Macromolecule | Name: CCR4-NOT transcription complex subunit 10 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 75.955148 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDQEKELSSS ALQAFLAGNY DACLQHLNTL QDINKDDYKI TLNTAVAEFC KSNQTTTDNL RQTLNQLKNQ VHSAVEEMDG LDDVENSML YYNQAVILYH LRQYTEAISV GEKLYQFIEP FEEKFAQAVC FLLVDLYLLT YQAEKALHLL AVLEKMISQG N NNSKNGKN ...String: MDQEKELSSS ALQAFLAGNY DACLQHLNTL QDINKDDYKI TLNTAVAEFC KSNQTTTDNL RQTLNQLKNQ VHSAVEEMDG LDDVENSML YYNQAVILYH LRQYTEAISV GEKLYQFIEP FEEKFAQAVC FLLVDLYLLT YQAEKALHLL AVLEKMISQG N NNSKNGKN ESGNNTNKDS SNQKAESGAL IEVAKSKIHQ YKVRAYIQMK SLKACKREIK SVMNTAGNSA PSLFLKSNFE YL RGNYRKA VKLLNSANIA EHPGFMKTGE CLRCMFWNNL GCIHFAMGKH NLGIFYFKKA LQENDNACAQ LGTGSSDPGK KFS GRPMCT LLTNKRYELL YNCGIQLLHI GRPLAAFECL IEAVQVYHSN PRLWLRIAEC CIAANKGTSE QETKGLPSKK GIVQ SIVGQ GYHRKIVLAS QSIQNVVYND GQSSAIPVAS MEFAAICLRN ALLLLPEDQQ EPKQENGSKP NNQLGGNTEN SESSE ACSN KSHEGDKFIA APPSSPLKKQ ELENLRCSIL ACSAYVALAL GDNLMALNHA DKLLQQPKLS GSLKFLGHLY AAEALI SLD RISDAITHLN PENVTDVSLT VSSNEQDQGS DKGENEAMES SGKQTPQCYP SSVTSARTMM LFNLGSAYCL RSEYDKA RK CLHQAASLIH PKEIPPEAIL LAVYLELQNG NTQLALQIIK RNQ UniProtKB: CCR4-NOT transcription complex subunit 10 |
-Macromolecule #3: CCR4-NOT transcription complex subunit 11
Macromolecule | Name: CCR4-NOT transcription complex subunit 11 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 51.950637 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLERMSLSPK ELTSLLGIVS EEAGGSTFEG LSSAFHHYFG KAEHFRLGSV LVLLLQQPDL LPSPAQRLTA LYLLWEMYRT EPLAANPFA AVFAHLLNPA PERGGDEAER TPLSGFLPPI TPPEKFFLSQ LMLAPPRELF KKTPRQIAAM DVGNMAQSLG I SGLQLALA ...String: MLERMSLSPK ELTSLLGIVS EEAGGSTFEG LSSAFHHYFG KAEHFRLGSV LVLLLQQPDL LPSPAQRLTA LYLLWEMYRT EPLAANPFA AVFAHLLNPA PERGGDEAER TPLSGFLPPI TPPEKFFLSQ LMLAPPRELF KKTPRQIAAM DVGNMAQSLG I SGLQLALA ERQSELPTQS KASFPSILSD PDPDSSNSGF DSSVASQITE ALVSGPKPPI ESHFRPEFIR PPPPLHICED EL AWLNPIE PDHTIQWDKS MCVKNSTGVE IKRIMAKAFK SPLTSPQQTQ LLGELEKDPK LVYHIGLTPA KLPDLVENNP LVA IEMLLK LMQSSQITEY FSVLVNMDMS LHSMEVVNRL TTAVDLPPEF IHLYISNCIS TCEQIKDKYM QNRLVRLVCV FLQS LIRNK IINVQDLFIE VQAFCIEFSR IREAAGLFRL LKTLDTGSEN LYFQGSGAMG SGSGHHHHHH GT UniProtKB: CCR4-NOT transcription complex subunit 11 |
-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: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.25 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |