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- EMDB-29551: Structure of NOT1:NOT10:NOT11 module of the human CCR4-NOT complex -

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Basic information

Entry
Database: EMDB / ID: EMD-29551
TitleStructure of NOT1:NOT10:NOT11 module of the human CCR4-NOT complex
Map datasharpened volume
Sample
  • Complex: NOT1:NOT10:NOT11
    • Protein or peptide: CCR4-NOT transcription complex subunit 1
    • Protein or peptide: CCR4-NOT transcription complex subunit 10
    • Protein or peptide: CCR4-NOT transcription complex subunit 11
KeywordsmRNA degradation / gene expression / RNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / CCR4-NOT complex / armadillo repeat domain binding / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation ...positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / CCR4-NOT complex / armadillo repeat domain binding / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / 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 / 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 / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / mRNA catabolic process / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear estrogen receptor binding / P-body / molecular adaptor activity / negative regulation of translation / protein domain specific binding / negative regulation of transcription by RNA polymerase II / RNA binding / extracellular space / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
CCR4-NOT transcription complex subunit 10 / CCR4-NOT transcription complex subunit 11 / CCR4-NOT transcription complex subunit 11 / CCR4-NOT transcription complex subunit 1, N-terminal domain / CCR4-Not complex component, Not1, C-terminal / CCR4-NOT transcription complex subunit 1, domain 4 / CCR4-NOT transcription complex subunit 1, CAF1-binding domain / CCR4-NOT transcription complex subunit 1, TTP binding domain / CCR4-NOT transcription complex subunit 1, HEAT repeat / CCR4-NOT subunit 1, TTP binding domain superfamily ...CCR4-NOT transcription complex subunit 10 / CCR4-NOT transcription complex subunit 11 / CCR4-NOT transcription complex subunit 11 / CCR4-NOT transcription complex subunit 1, N-terminal domain / CCR4-Not complex component, Not1, C-terminal / CCR4-NOT transcription complex subunit 1, domain 4 / CCR4-NOT transcription complex subunit 1, CAF1-binding domain / CCR4-NOT transcription complex subunit 1, TTP binding domain / CCR4-NOT transcription complex subunit 1, HEAT repeat / CCR4-NOT subunit 1, TTP binding domain superfamily / CCR4-NOT transcription complex subunit 1 / CCR4-Not complex component, Not1 / CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819 / CCR4-NOT transcription complex subunit 1 CAF1-binding domain / CCR4-NOT transcription complex subunit 1 TTP binding domain / CCR4-NOT transcription complex subunit 1 HEAT repeat / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / CCR4-NOT transcription complex subunit 11 / CCR4-NOT transcription complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsLea SM / Deme JC / Raisch T / Pekovic F / Valkov E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: 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
DepositionJan 25, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29551.png

Downloads & links

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Map

FileDownload / File: emd_29551.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened volume
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 392 pix.
= 271.656 Å		0.69 Å/pix.
x 392 pix.
= 271.656 Å		0.69 Å/pix.
x 392 pix.
= 271.656 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.693 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.522
Minimum - Maximum-3.028964 - 4.5109
Average (Standard dev.)0.000097317046 (±0.05786596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 271.656 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29551_msk_1.map
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Additional map: DeepEMhancer volume

Fileemd_29551_additional_1.map
AnnotationDeepEMhancer volume
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Additional map: unsharpened volume

Fileemd_29551_additional_2.map
Annotationunsharpened volume
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Half map: half map A

Fileemd_29551_half_map_1.map
Annotationhalf map A
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Half map: half map B

Fileemd_29551_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : NOT1:NOT10:NOT11

EntireName: NOT1:NOT10:NOT11
Components
  • Complex: NOT1:NOT10:NOT11
    • Protein or peptide: CCR4-NOT transcription complex subunit 1
    • Protein or peptide: CCR4-NOT transcription complex subunit 10
    • Protein or peptide: CCR4-NOT transcription complex subunit 11

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Supramolecule #1: NOT1:NOT10:NOT11

SupramoleculeName: NOT1:NOT10:NOT11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CCR4-NOT transcription complex subunit 1

MacromoleculeName: CCR4-NOT transcription complex subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 111.576789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: CCR4-NOT transcription complex subunit 10

MacromoleculeName: CCR4-NOT transcription complex subunit 10 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.931148 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: CCR4-NOT transcription complex subunit 11

MacromoleculeName: CCR4-NOT transcription complex subunit 11 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.362113 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.31) / Number images used: 387942
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.31)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.31)
FSC plot (resolution estimation)

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