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- EMDB-29552: Structure of NOT1:NOT10:NOT11 module of the chicken CCR4-NOT complex -

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Basic information

Entry
Database: EMDB / ID: EMD-29552
TitleStructure of NOT1:NOT10:NOT11 module of the chicken CCR4-NOT complex
Map dataDeepEMhancer map
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


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
CCR4-NOT transcription complex subunit 10 / CCR4-NOT transcription complex subunit 11 / CCR4-NOT transcription complex subunit 11 / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 11 / : / CCR4-NOT transcription complex subunit 10
Similarity search - Component
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsLea SM / Deme JC / Raisch T / Levdansky Y / 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) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29552.png

Downloads & links

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Map

FileDownload / File: emd_29552.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer map
Voxel sizeX=Y=Z: 0.723 Å
Density
Contour LevelBy AUTHOR: 0.232
Minimum - Maximum-0.034580972 - 1.8915489
Average (Standard dev.)0.0007278938 (±0.017536482)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 277.632 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29552_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_29552_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_29552_additional_2.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_29552_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_29552_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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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: Gallus gallus (chicken)

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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: Gallus gallus (chicken)
Molecular weightTheoretical: 76.422859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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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: Gallus gallus (chicken)
Molecular weightTheoretical: 75.955148 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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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: Gallus gallus (chicken)
Molecular weightTheoretical: 51.950637 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.25 µm
Image recordingFilm 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

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.31)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.31)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.31) / Number images used: 17295060
FSC plot (resolution estimation)

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