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- EMDB-14514: Human NEXT dimer - single protomer -

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Basic information

Entry
Database: EMDB / ID: EMD-14514
TitleHuman NEXT dimer - single protomer
Map dataNEXT_L_single_protomer_refine
Sample
  • Complex: Human NEXT dimer - single protomer
    • Complex: Human NEXT dimer - single protomer
      • Protein or peptide: Exosome RNA helicase MTR4
      • Protein or peptide: Zinc finger CCHC domain-containing protein 8
      • Protein or peptide: RNA-binding protein 7
    • Complex: RNA 5prime hairpin U60
      • RNA: RNA 5prime hairpin U60
KeywordsHELICASE / ATPASE / RNA DEGRADATION / EXOSOME / RNA BINDING PROTEIN
Function / homology
Function and homology information


snRNA catabolic process / TRAMP complex / snRNA binding / mRNA 3'-end processing / RNA catabolic process / maturation of 5.8S rRNA / regulation of alternative mRNA splicing, via spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / pre-mRNA intronic binding ...snRNA catabolic process / TRAMP complex / snRNA binding / mRNA 3'-end processing / RNA catabolic process / maturation of 5.8S rRNA / regulation of alternative mRNA splicing, via spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / pre-mRNA intronic binding / 14-3-3 protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / meiotic cell cycle / mRNA splicing, via spliceosome / rRNA processing / RNA helicase activity / single-stranded RNA binding / nuclear body / RNA helicase / nuclear speck / DNA damage response / nucleolus / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
RBM7, RNA recognition motif / : / : / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk ...RBM7, RNA recognition motif / : / : / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Exosome RNA helicase MTR4 / Zinc finger CCHC domain-containing protein 8 / RNA-binding protein 7
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsGerlach P / Lingaraju M / Salerno-Kochan A / Bonneau F / Basquin J / Conti E
Funding support Germany, European Union, 4 items
OrganizationGrant numberCountry
Max Planck Society Germany
European CommissionERC-2016-ADG 740329 EXORICOEuropean Union
German Research Foundation (DFG)SFB/TRR 237 Germany
German Research Foundation (DFG)SFB 1035 Germany
CitationJournal: Mol Cell / Year: 2022
Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome.
Authors: Piotr Gerlach / William Garland / Mahesh Lingaraju / Anna Salerno-Kochan / Fabien Bonneau / Jérôme Basquin / Torben Heick Jensen / Elena Conti /
Abstract: In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting ...In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting (NEXT) complex plays a central role in directing non-functional transcripts to exosome-mediated degradation, but the structural and molecular mechanisms remain enigmatic. Here, we elucidated the architecture of the human NEXT complex, showing that it exists as a dimer of MTR4-ZCCHC8-RBM7 heterotrimers. Dimerization preconfigures the major MTR4-binding region of ZCCHC8 and arranges the two MTR4 helicases opposite to each other, with each protomer able to function on many types of RNAs. In the inactive state of the complex, the 3' end of an RNA substrate is enclosed in the MTR4 helicase channel by a ZCCHC8 C-terminal gatekeeping domain. The architecture of a NEXT-exosome assembly points to the molecular and regulatory mechanisms with which the NEXT complex guides RNA substrates to the exosome.
History
DepositionMar 7, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14514.png

Downloads & links

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Map

FileDownload / File: emd_14514.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNEXT_L_single_protomer_refine
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.907 Å		0.85 Å/pix.
x 256 pix.
= 217.907 Å		0.85 Å/pix.
x 256 pix.
= 217.907 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.007958131 - 0.028354466
Average (Standard dev.)0.00017991319 (±0.0017164446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.9072 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14514_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: NEXT L single protomer half map 1

Fileemd_14514_half_map_1.map
AnnotationNEXT_L_single_protomer_half_map_1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: NEXT L single protomer half map 2

Fileemd_14514_half_map_2.map
AnnotationNEXT_L_single_protomer_half_map_2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human NEXT dimer - single protomer

EntireName: Human NEXT dimer - single protomer
Components
  • Complex: Human NEXT dimer - single protomer
    • Complex: Human NEXT dimer - single protomer
      • Protein or peptide: Exosome RNA helicase MTR4
      • Protein or peptide: Zinc finger CCHC domain-containing protein 8
      • Protein or peptide: RNA-binding protein 7
    • Complex: RNA 5prime hairpin U60
      • RNA: RNA 5prime hairpin U60

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Supramolecule #1: Human NEXT dimer - single protomer

SupramoleculeName: Human NEXT dimer - single protomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Human NEXT dimer - single protomer

SupramoleculeName: Human NEXT dimer - single protomer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: RNA 5prime hairpin U60

SupramoleculeName: RNA 5prime hairpin U60 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Exosome RNA helicase MTR4

MacromoleculeName: Exosome RNA helicase MTR4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPDSMADAFG DELFSVFEGD STTAAGTKKD KEKDKGKWKG PPGSADKAGK RFDGKLQSES TNNG KNKRD VDFEGTDEPI FGKKPRIEES ITEDLSLADL MPRVKVQSVE TVEGCTHEVA LPAEE DYLP LKPRVGKAAK EYPFILDAFQ REAIQCVDNN QSVLVSAHTS ...String:
GPDSMADAFG DELFSVFEGD STTAAGTKKD KEKDKGKWKG PPGSADKAGK RFDGKLQSES TNNG KNKRD VDFEGTDEPI FGKKPRIEES ITEDLSLADL MPRVKVQSVE TVEGCTHEVA LPAEE DYLP LKPRVGKAAK EYPFILDAFQ REAIQCVDNN QSVLVSAHTS AGKTVCAEYA IALALR EKQ RVIFTSPIKA LSNQKYREMY EEFQDVGLMT GDVTINPTAS CLVMTTEILR SMLYRGS EV MREVAWVIFD EIHYMRDSER GVVWEETIIL LPDNVHYVFL SATIPNARQF AEWICHLH K QPCHVIYTDY RPTPLQHYIF PAGGDGLHLV VDENGDFRED NFNTAMQVLR DAGDLAKGD QKGRKGGTKG PSNVFKIVKM IMERNFQPVI IFSFSKKDCE AYALQMTKLD FNTDEEKKMV EEVFSNAID CLSDEDKKLP QVEHVLPLLK RGIGIHHGGL LPILKETIEI LFSEGLIKAL F ATETFAMG INMPARTVLF TNARKFDGKD FRWISSGEYI QMSGRAGRRG MDDRGIVILM VD EKMSPTI GKQLLKGSAD PLNSAFHLTY NMVLNLLRVE EINPEYMLEK SFYQFQHYRA IPG VVEKVK NSEEQYNKIV IPNEESVVIY YKIRQQLAKL GKEIEEYIHK PKYCLPFLQP GRLV KVKNE GDDFGWGVVV NFSKKSNVKP NSGELDPLYV VEVLLRCSKE SLKNSATEAA KPAKP DEKG EMQVVPVLVH LLSAISSVRL YIPKDLRPVD NRQSVLKSIQ EVQKRFPDGI PLLDPI DDM GIQDQGLKKV IQKVEAFEHR MYSHPLHNDP NLETVYTLCE KKAQIAIDIK SAKRELK KA RTVLQMDELK CRKRVLRRLG FATSSDVIEM KGRVACEISS ADELLLTEMM FNGLFNDL S AEQATALLSC FVFQENSSEM PKLTEQLAGP LRQMQECAKR IAKVSAEAKL EIDEETYLS SFKPHLMDVV YTWATGATFA HICKMTDVFE GSIIRCMRRL EELLRQMCQA AKAIGNTELE NKFAEGITK IKRDIVFAAS LYL

UniProtKB: Exosome RNA helicase MTR4

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Macromolecule #2: Zinc finger CCHC domain-containing protein 8

MacromoleculeName: Zinc finger CCHC domain-containing protein 8 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: RSMAAEVYFG DLELFEPFDH PGESIPKPVH TRFKDDDGDE EDENGVGDAE LRERLRQCEE TIEQLRAENQ ELKRKLNILT RPSGILVNDT KLDGPILQIL FMNNAISKQY HQEIEEFVSN LVKRFEEQQK NDVEKTSFNL LPQPSSIVLE EDHKVEESCA IKNNKEAFSV ...String:
RSMAAEVYFG DLELFEPFDH PGESIPKPVH TRFKDDDGDE EDENGVGDAE LRERLRQCEE TIEQLRAENQ ELKRKLNILT RPSGILVNDT KLDGPILQIL FMNNAISKQY HQEIEEFVSN LVKRFEEQQK NDVEKTSFNL LPQPSSIVLE EDHKVEESCA IKNNKEAFSV VGSVLYFTNF CLDKLGQPLL NENPQLSEGW EIPKYHQVFS HIVSLEGQEI QVKAKRPKPH CFNCGSEEHQ MKDCPMPRNA ARISEKRKEY MDACGEANNQ NFQQRYHAEE VEERFGRFKP GVISEELQDA LGVTDKSLPP FIYRMRQLGY PPGWLKEAEL ENSGLALYDG KDGTDGETEV GEIQQNKSVT YDLSKLVNYP GFNISTPRGI PDEWRIFGSI PMQACQQKDV FANYLTSNFQ APGVKSGGSG AVDEDALTLE ELEEQQRRIW AALEQAESVN SDSDVPVDTP LTGNSVASSP CPNELDLPVP EGKTSEKQTL DEPEVPEIFT KKSEAGHASS PDSEVTSLCQ KEKAELAPVN TEGALLDNGS VVPNCDISNG GSQKLFPADT SPSTATKIHS PIPDMSKFAT GITPFEFENM AESTGMYLRI RSLLKNSPRN QQKNKKASE

UniProtKB: Zinc finger CCHC domain-containing protein 8

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Macromolecule #3: RNA-binding protein 7

MacromoleculeName: RNA-binding protein 7 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
RSMGAAAAEA DRTLFVGNLE TKVTEELLFE LFHQAGPVIK VKIPKDKNGK PKQFAFVNFK HEVSVPYAMN LLNGIKLYGR PIKIQFRSGS SHAPQDVSLS

UniProtKB: RNA-binding protein 7

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Macromolecule #4: RNA 5prime hairpin U60

MacromoleculeName: RNA 5prime hairpin U60 / type: rna / ID: 4
Source (natural)Organism: synthetic construct (others)
SequenceString:
CUACCCCGAG AGGGGUAGUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUU

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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-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.705 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10594
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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