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Yorodumi- EMDB-29551: Structure of NOT1:NOT10:NOT11 module of the human CCR4-NOT complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29551 | |||||||||
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Title | Structure of NOT1:NOT10:NOT11 module of the human CCR4-NOT complex | |||||||||
Map data | sharpened volume | |||||||||
Sample |
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Keywords | mRNA degradation / gene expression / RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / trophectodermal cell differentiation ...positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / peroxisomal membrane / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / mRNA catabolic process / nuclear estrogen receptor binding / P-body / negative regulation of translation / molecular adaptor activity / protein domain specific binding / negative regulation of transcription by RNA polymerase II / extracellular space / RNA binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.88 Å | |||||||||
Authors | Lea SM / Deme JC / Raisch T / Pekovic F / 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_29551.map.gz | 216.6 MB | EMDB map data format | |
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Header (meta data) | emd-29551-v30.xml emd-29551.xml | 21.7 KB 21.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29551_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_29551.png | 28.3 KB | ||
Masks | emd_29551_msk_1.map | 229.8 MB | Mask map | |
Others | emd_29551_additional_1.map.gz emd_29551_additional_2.map.gz emd_29551_half_map_1.map.gz emd_29551_half_map_2.map.gz | 191.7 MB 114.5 MB 213.5 MB 213.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29551 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29551 | HTTPS FTP |
-Related structure data
Related structure data | 8fy3MC 8fy4C 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_29551.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharpened volume | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.693 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29551_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: DeepEMhancer volume
File | emd_29551_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: unsharpened volume
File | emd_29551_additional_2.map | ||||||||||||
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Annotation | unsharpened volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_29551_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_29551_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: Homo sapiens (human) |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 111.576789 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNLDSLSLAL SQISYLVDNL TKKNYRASQQ EIQHIVNRHG PEADRHLLRC LFSHVDFSGD GKSSGKDFHQ TQFLIQECAL LITKPNFIS TLSYAIDNPL HYQKSLKPAP HLFAQLSKVL KLSKVQEVIF GLALLNSSSS DLRGFAAQFI KQKLPDLLRS Y IDADVSGN ...String: MNLDSLSLAL SQISYLVDNL TKKNYRASQQ EIQHIVNRHG PEADRHLLRC LFSHVDFSGD GKSSGKDFHQ TQFLIQECAL LITKPNFIS TLSYAIDNPL HYQKSLKPAP HLFAQLSKVL KLSKVQEVIF GLALLNSSSS DLRGFAAQFI KQKLPDLLRS Y IDADVSGN QEGGFQDIAI EVLHLLLSHL LFGQKGAFGV GQEQIDAFLK TLRRDFPQER CPVVLAPLLY PEKRDILMDR IL PDSGGVA KTMMESSLAD FMQEVGYGFC ASIEECRNII VQFGVREVTA AQVARVLGMM ARTHSGLTDG IPLQSISAPG SGI WSDGKD KSDGAQAHTW NVEVLIDVLK ELNPSLNFKE VTYELDHPGF QIRDSKGLHN VVYGIQRGLG MEVFPVDLIY RPWK HAEGQ LSFIQHSLIN PEIFCFADYP CHTVATDILK 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 KARQPPPGVM PKGRPPSASS LDAISPVQID PLAGMTSL S IGGSAAPHTQ SMQGFPPNLG SAFSTPQSPA KAFPPLSTPN QTTAFSGIGG LSSQLPVGGL GTGSLTGIGT GALGLPAVN NDPFVQRKLG TSGLNQPTFQ QSKMKPSDLS QVWPEANQHF SKEIDDEANS YFQRIYNHPP HPTMSVDEVL EMLQRFKDST IKREREVFN CMLRNLFEEY RFFPQYPDKE LHITACLFGG IIEKGLVTYM ALGLALRYVL EALRKPFGSK MYYFGIAALD R FKNRLKDY PQYCQHLASI SHFMQFPHHL QEYIEYGQQS RD UniProtKB: CCR4-NOT transcription complex subunit 1 |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 75.931148 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDQEKELSTN AFQAFTSGNY DACLQHLACL QDINKDDYKI ILNTAVAEFF KSNQTTTDNL RQTLNQLKNQ VHSAVEEMDG LDDVENSML YYNQAVILYH LRQYTEAISV GEKLYQFIEP FEEKFAQAVC FLLVDLYILT YQAEKALHLL AVLEKMISQG N NNKNGKNE ...String: MDQEKELSTN AFQAFTSGNY DACLQHLACL QDINKDDYKI ILNTAVAEFF KSNQTTTDNL RQTLNQLKNQ VHSAVEEMDG LDDVENSML YYNQAVILYH LRQYTEAISV GEKLYQFIEP FEEKFAQAVC FLLVDLYILT YQAEKALHLL AVLEKMISQG N NNKNGKNE TGNNNNKDGS NHKAESGALI EAAKSKIHQY KVRAYIQMKS LKACKREIKS VMNTAGNSAP SLFLKSNFEY LR GNYRKAV KLLNSSNIAE HPGFMKTGEC LRCMFWNNLG CIHFAMSKHN LGIFYFKKAL QENDNVCAQL SAGSTDPGKK FSG RPMCTL LTNKRYELLY NCGIQLLHIG RPLAAFECLI EAVQVYHANP RLWLRLAECC IAANKGTSEQ ETKGLPSKKG IVQS IVGQG YHRKIVLASQ SIQNTVYNDG QSSAIPVASM EFAAICLRNA LLLLPEEQQD PKQENGAKNS NQLGGNTESS ESSET CSSK SHDGDKFIPA PPSSPLRKQE LENLKCSILA CSAYVALALG DNLMALNHAD KLLQQPKLSG SLKFLGHLYA AEALIS LDR ISDAITHLNP ENVTDVSLGI SSNEQDQGSD KGENEAMESS GKRAPQCYPS SVNSARTVML FNLGSAYCLR SEYDKAR KC LHQAASMIHP KEVPPEAILL AVYLELQNGN TQLALQIIKR NQ 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: Homo sapiens (human) |
Molecular weight | Theoretical: 30.362113 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDSSVASQIT EALVSGPKPP IESHFRPEFI RPPPPLHICE DELAWLNPTE PDHAIQWDKS MCVKNSTGVE IKRIMAKAFK SPLSSPQQT QLLGELEKDP KLVYHIGLTP AKLPDLVENN PLVAIEMLLK LMQSSQITEY FSVLVNMDMS LHSMEVVNRL T TAVDLPPE ...String: MDSSVASQIT EALVSGPKPP IESHFRPEFI RPPPPLHICE DELAWLNPTE PDHAIQWDKS MCVKNSTGVE IKRIMAKAFK SPLSSPQQT QLLGELEKDP KLVYHIGLTP AKLPDLVENN PLVAIEMLLK LMQSSQITEY FSVLVNMDMS LHSMEVVNRL T TAVDLPPE FIHLYISNCI STCEQIKDKY MQNRLVRLVC VFLQSLIRNK IINVQDLFIE VQAFCIEFSR IREAAGLFRL LK TLDGSEN 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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.25 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |