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- EMDB-24882: Human Nuclear exosome targeting (NEXT) complex homodimer bound to... -

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Basic information

Entry
Database: EMDB / ID: EMD-24882
TitleHuman Nuclear exosome targeting (NEXT) complex homodimer bound to RNA (substrate 1)
Map datahuman NEXT dimer bound to RNA - composite structure
Sample
  • Complex: human Nuclear Exosome Targeting (NEXT)-RNA substrate 1 complex
    • Protein or peptide: Exosome RNA helicase MTR4
    • Protein or peptide: Zinc finger CCHC domain-containing protein 8,Zinc finger CCHC domain-containing protein 8
    • Protein or peptide: RNA-binding protein 7
    • RNA: RNA (46-MER)
  • Ligand: ZINC ION
KeywordsHelicase / ATPase / RNA / Exosome / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / 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 / pre-mRNA intronic binding / Major pathway of rRNA processing in the nucleolus and cytosol ...co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / 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 / pre-mRNA intronic binding / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / 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 speck / nuclear body / RNA helicase / 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 / RNA-binding domain superfamily / Helicase conserved C-terminal domain / 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: 4.06 Å
AuthorsPuno MR / Lima CD
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118080 United States
CitationJournal: Cell / Year: 2022
Title: Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex.
Authors: M Rhyan Puno / Christopher D Lima /
Abstract: RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined ...RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined cryogenic electron microscopy structures of human nuclear exosome targeting (NEXT) complexes bound to RNA that reveal mechanistic insights to substrate recognition and early steps that precede RNA handover to the exosome. The structures illuminate ZCCHC8 as a scaffold, mediating homodimerization while embracing the MTR4 helicase and flexibly anchoring RBM7 to the helicase core. All three subunits collaborate to bind the RNA, with RBM7 and ZCCHC8 surveying sequences upstream of the 3' end to facilitate RNA capture by MTR4. ZCCHC8 obscures MTR4 surfaces important for RNA binding and extrusion as well as MPP6-dependent recruitment and docking onto the RNA exosome core, interactions that contribute to RNA surveillance by coordinating RNA capture, translocation, and extrusion from the helicase to the exosome for decay.
History
DepositionSep 15, 2021-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24882.png

Downloads & links

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Map

FileDownload / File: emd_24882.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman NEXT dimer bound to RNA - composite structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.09 Å/pix.
x 384 pix.
= 417.792 Å		1.09 Å/pix.
x 384 pix.
= 417.792 Å		1.09 Å/pix.
x 384 pix.
= 417.792 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 11.5
Minimum - Maximum-58.578938000000001 - 117.664664999999999
Average (Standard dev.)-0.008782573 (±1.2400491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 417.79202 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: focused refinement on protomer A MTR4 core, ZCCHC8...

Fileemd_24882_additional_1.map
Annotationfocused refinement on protomer A MTR4 core, ZCCHC8 middle region and RBM7 half map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on ZCCHC8-HD/KID MTR4-KOW half map 1

Fileemd_24882_additional_10.map
Annotationfocused refinement on ZCCHC8-HD/KID MTR4-KOW half map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on ZCCHC8-HD/KID MTR4-KOW half map 2

Fileemd_24882_additional_11.map
Annotationfocused refinement on ZCCHC8-HD/KID MTR4-KOW half map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on protomer A MTR4 half map 1

Fileemd_24882_additional_12.map
Annotationfocused refinement on protomer A MTR4 half map 1
Projections & Slices
AxesZYX

Projections

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Overall reconstruction half map 1

Fileemd_24882_additional_13.map
AnnotationOverall reconstruction half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on protomer B MTR4 core, ZCCHC8...

Fileemd_24882_additional_14.map
Annotationfocused refinement on protomer B MTR4 core, ZCCHC8 middle region and RBM7 half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Overall reconstruction half map 2

Fileemd_24882_additional_15.map
AnnotationOverall reconstruction half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on protomer A MTR4 core, ZCCHC8...

Fileemd_24882_additional_16.map
Annotationfocused refinement on protomer A MTR4 core, ZCCHC8 middle region and RBM7 half map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on protomer B MTR4 core, ZCCHC8...

Fileemd_24882_additional_17.map
Annotationfocused refinement on protomer B MTR4 core, ZCCHC8 middle region and RBM7 (component map of composite structure)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on protomer B MTR4 core, ZCCHC8...

Fileemd_24882_additional_18.map
Annotationfocused refinement on protomer B MTR4 core, ZCCHC8 middle region and RBM7 half map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on protomer B MTR4 (component map...

Fileemd_24882_additional_2.map
Annotationfocused refinement on protomer B MTR4 (component map of composite structure)
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on ZCCHC8-HD/KID MTR4-KOW (component map of...

Fileemd_24882_additional_3.map
Annotationfocused refinement on ZCCHC8-HD/KID MTR4-KOW (component map of composite structure)
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on protomer A MTR4 core, ZCCHC8...

Fileemd_24882_additional_4.map
Annotationfocused refinement on protomer A MTR4 core, ZCCHC8 middle region and RBM7 (component map of composite structure)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on protomer B MTR4 half map 1

Fileemd_24882_additional_5.map
Annotationfocused refinement on protomer B MTR4 half map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on protomer A MTR4 half map 2

Fileemd_24882_additional_6.map
Annotationfocused refinement on protomer A MTR4 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on protomer B MTR4 half map 2

Fileemd_24882_additional_7.map
Annotationfocused refinement on protomer B MTR4 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Overall reconstruction (component map of composite structure)

Fileemd_24882_additional_8.map
AnnotationOverall reconstruction (component map of composite structure)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement on protomer A MTR4 (component map...

Fileemd_24882_additional_9.map
Annotationfocused refinement on protomer A MTR4 (component map of composite structure)
Projections & Slices
AxesZYX

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Sample components

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Entire : human Nuclear Exosome Targeting (NEXT)-RNA substrate 1 complex

EntireName: human Nuclear Exosome Targeting (NEXT)-RNA substrate 1 complex
Components
  • Complex: human Nuclear Exosome Targeting (NEXT)-RNA substrate 1 complex
    • Protein or peptide: Exosome RNA helicase MTR4
    • Protein or peptide: Zinc finger CCHC domain-containing protein 8,Zinc finger CCHC domain-containing protein 8
    • Protein or peptide: RNA-binding protein 7
    • RNA: RNA (46-MER)
  • Ligand: ZINC ION

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Supramolecule #1: human Nuclear Exosome Targeting (NEXT)-RNA substrate 1 complex

SupramoleculeName: human Nuclear Exosome Targeting (NEXT)-RNA substrate 1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Exosome RNA helicase MTR4

MacromoleculeName: Exosome RNA helicase MTR4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.224961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGDMADAFGD ELFSVFEGDS TTAAGTKKDK EKDKGKWKGP PGSADKAGKR FDGKLQSEST NNGKNKRDVD FEGTDEPIFG KKPRIEESI TEDLSLADLM PRVKVQSVET VEGCTHEVAL PAEEDYLPLK PRVGKAAKEY PFILDAFQRE AIQCVDNNQS V LVSAHTSA ...String:
SGDMADAFGD ELFSVFEGDS TTAAGTKKDK EKDKGKWKGP PGSADKAGKR FDGKLQSEST NNGKNKRDVD FEGTDEPIFG KKPRIEESI TEDLSLADLM PRVKVQSVET VEGCTHEVAL PAEEDYLPLK PRVGKAAKEY PFILDAFQRE AIQCVDNNQS V LVSAHTSA GKTVCAEYAI ALALREKQRV IFTSPIKALS NQKYREMYEE FQDVGLMTGD VTINPTASCL VMTTEILRSM LY RGSEVMR EVAWVIFDEI HYMRDSERGV VWEETIILLP DNVHYVFLSA TIPNARQFAE WICHLHKQPC HVIYTDYRPT PLQ HYIFPA GGDGLHLVVD ENGDFREDNF NTAMQVLRDA GDLAKGDQKG RKGGTKGPSN VFKIVKMIME RNFQPVIIFS FSKK DCEAY ALQMTKLDFN TDEEKKMVEE VFSNAIDCLS DEDKKLPQVE HVLPLLKRGI GIHHGGLLPI LKETIEILFS EGLIK ALFA TETFAMGINM PARTVLFTNA RKFDGKDFRW ISSGEYIQMS GRAGRRGMDD RGIVILMVDE KMSPTIGKQL LKGSAD PLN SAFHLTYNMV LNLLRVEEIN PEYMLEKSFY QFQHYRAIPG VVEKVKNSEE QYNKIVIPNE ESVVIYYKIR QQLAKLG KE IEEYIHKPKY CLPFLQPGRL VKVKNEGDDF GWGVVVNFSK KSNVKPNSGE LDPLYVVEVL LRCSKESLKN SATEAAKP A KPDEKGEMQV VPVLVHLLSA ISSVRLYIPK DLRPVDNRQS VLKSIQEVQK RFPDGIPLLD PIDDMGIQDQ GLKKVIQKV EAFEHRMYSH PLHNDPNLET VYTLCEKKAQ IAIDIKSAKR ELKKARTVLQ MDELKCRKRV LRRLGFATSS DVIEMKGRVA CEISSADEL LLTEMMFNGL FNDLSAEQAT ALLSCFVFQE NSSEMPKLTE QLAGPLRQMQ ECAKRIAKVS AEAKLEIDEE T YLSSFKPH LMDVVYTWAT GATFAHICKM TDVFEGSIIR CMRRLEELLR QMCQAAKAIG NTELENKFAE GITKIKRDIV FA ASLYL

UniProtKB: Exosome RNA helicase MTR4

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

MacromoleculeName: Zinc finger CCHC domain-containing protein 8,Zinc finger CCHC domain-containing protein 8
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.259805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGDMAAEVYF GDLELFEPFD HPEESIPKPV HTRFKDDDGD EEDENGVGDA ELRERLRQCE ETIEQLRAEN QELKRKLNIL TRPSGILVN DTKLDGPILQ ILFMNNAISK QYHQEIEEFV SNLVKRFEEQ QKNDVEKTSF NLLPQPSSIV LEEDHKVEES C AIKNNKEA ...String:
SGDMAAEVYF GDLELFEPFD HPEESIPKPV HTRFKDDDGD EEDENGVGDA ELRERLRQCE ETIEQLRAEN QELKRKLNIL TRPSGILVN DTKLDGPILQ ILFMNNAISK QYHQEIEEFV SNLVKRFEEQ QKNDVEKTSF NLLPQPSSIV LEEDHKVEES C AIKNNKEA FSVVGSVLYF TNFCLDKLGQ PLLNENPQLS EGWEIPKYHQ VFSHIVSLEG QEIQVKAKRP KPHCFNCGSE EH QMKDCPM PRNAARISEK RKEYMDACGE ANNQNFQQRY HAEEVEERFG RFKPGVISEE LQDALGVTDK SLPPFIYRMR QLG YPPGWL KEAELENSGL ALYDGKDGTD GETEVGEIQQ NKSVTYDLSK LVNYPGFNIS TPRGIPDEWR IFGSIPMQAC QQKD VFANY LTSNFQAPGV KSGGAVDEDA LTLEELEEQQ RRIWAALEQA ESVNSDSDVP VDTPLTGNSV ASSPCPNELD LPVPE GKTS EKQTLDEPEV PEIFTKKSEA GHASSPDSEV TSLCQKEKAE LAPVNTEGAL LDNGSVVPNC DISNGGSQKL FPADTS PST ATKIHSPIPD MSKFATGITP FEFENMAEST GMYLRIRSLL KNSPRNQQKN KKASE

UniProtKB: Zinc finger CCHC domain-containing protein 8, 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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.462986 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGDEADRTLF VGNLETKVTE ELLFELFHQA GPVIKVKIPK DKDGKPKQFA FVNFKHEVSV PYAMNLLNGI KLYGRPIKIQ FRS

UniProtKB: RNA-binding protein 7

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Macromolecule #4: RNA (46-MER)

MacromoleculeName: RNA (46-MER) / type: rna / ID: 4
Details: The actual RNA sequence is: ACAUGAGGAUCACCCAUGUAAUCUCUUUCAAAAAA(2PU)ACAAAAAAAA. (2PU) is represented by "N" (any nucleotide. This residue is missing in the coordinates and the chemical is an ...Details: The actual RNA sequence is: ACAUGAGGAUCACCCAUGUAAUCUCUUUCAAAAAA(2PU)ACAAAAAAAA. (2PU) is represented by "N" (any nucleotide. This residue is missing in the coordinates and the chemical is an internal 2' pyrene modified uridine
Number of copies: 2
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.605818 KDa
SequenceString:
ACAUGAGGAU CACCCAUGUA AUCUCUUUCA AAAAA(N)ACAA AAAAAA

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration8 mg/mL
BufferpH: 8
Details: 20 mM Tris-Cl pH 8.0, 50 mM NaCl, 0.1 mM TCEP supplemented with 0.02% (v/v) IGEPAL CA-630
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 30 s wait time, blot for 2.5 s before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 67.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model from cryosparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION
Details: A total of 618,412 particles were used for the consensus reconstruction with an overall resolution of 4.06 Angstrom (FSC 0.143 cut off). Focused 3D classification and local refinement were ...Details: A total of 618,412 particles were used for the consensus reconstruction with an overall resolution of 4.06 Angstrom (FSC 0.143 cut off). Focused 3D classification and local refinement were performed in several regions of the complex. A composite map was generated using focused reconstructions of ZCCHC8 HD/KID-MTR4 KOW (3.26 Angstrom, FSC = 0.143; 117,561 particles), protomer A MTR4 (3.42 Angstrom, FSC = 0.143; 225,213 particles), protomer B MTR4 (3.54 Angstrom, FSC = 0.143; 236,602 particles), protomer A MTR4 core-ZCCHC8 PSP-RBM7 RRM (4.06 Angstrom, FSC = 0.143; 44,800 particles), and protomer B MTR4 core-ZCCHC8 PSP-RBM7 RRM (4.4 Angstrom, FSC = 0.143 37,088 particles).
Number images used: 618412
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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