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- EMDB-17763: Structure of the human nuclear cap-binding complex bound to ARS2[... -

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Basic information

Entry
Database: EMDB / ID: EMD-17763
TitleStructure of the human nuclear cap-binding complex bound to ARS2[147-871] and m7GTP
Map data
Sample
  • Complex: Structure of the human nuclear cap-binding complex bound to ARS2[147-871] and m7GTP
    • Protein or peptide: Nuclear cap-binding protein subunit 1
    • Protein or peptide: Nuclear cap-binding protein subunit 2
    • Protein or peptide: Serrate RNA effector molecule homolog
  • Ligand: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
KeywordsNuclear cap-binding complex / ARS2 / Pol II transcript metabolism / RNA BINDING PROTEIN
Function / homology
Function and homology information


mRNA cap binding complex binding / positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation ...mRNA cap binding complex binding / positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding / RNA cap binding / neuronal stem cell population maintenance / alternative mRNA splicing, via spliceosome / primary miRNA processing / miRNA-mediated post-transcriptional gene silencing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulatory ncRNA-mediated post-transcriptional gene silencing / regulation of mRNA processing / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / response to arsenic-containing substance / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / RNA catabolic process / Transport of Mature mRNA derived from an Intron-Containing Transcript / regulation of translational initiation / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / FGFR2 alternative splicing / positive regulation of neurogenesis / Signaling by FGFR2 IIIa TM / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / 7-methylguanosine mRNA capping / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Formation of HIV-1 elongation complex containing HIV-1 Tat / mRNA export from nucleus / Formation of HIV elongation complex in the absence of HIV Tat / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / mRNA processing / snRNP Assembly / positive regulation of cell growth / protein-macromolecule adaptor activity / molecular adaptor activity / defense response to virus / nuclear body / ciliary basal body / ribonucleoprotein complex / mRNA binding / regulation of DNA-templated transcription / protein-containing complex / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
SERRATE/Ars2 , C-terminal / SERRATE/Ars2, N-terminal / SERRATE/Ars2 / Arsenite-resistance protein 2 / SERRATE/Ars2, N-terminal domain / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like ...SERRATE/Ars2 , C-terminal / SERRATE/Ars2, N-terminal / SERRATE/Ars2 / Arsenite-resistance protein 2 / SERRATE/Ars2, N-terminal domain / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Nuclear cap-binding protein subunit 2 / Nuclear cap-binding protein subunit 1 / Serrate RNA effector molecule homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsDubiez E / Pellegrini E / Foucher AE / Cusack S / Kadlec J
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Cell Rep / Year: 2024
Title: Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex.
Authors: Etienne Dubiez / Erika Pellegrini / Maja Finderup Brask / William Garland / Anne-Emmanuelle Foucher / Karine Huard / Torben Heick Jensen / Stephen Cusack / Jan Kadlec /
Abstract: The nuclear cap-binding complex (CBC) coordinates co-transcriptional maturation, transport, or degradation of nascent RNA polymerase II (Pol II) transcripts. CBC with its partner ARS2 forms mutually ...The nuclear cap-binding complex (CBC) coordinates co-transcriptional maturation, transport, or degradation of nascent RNA polymerase II (Pol II) transcripts. CBC with its partner ARS2 forms mutually exclusive complexes with diverse "effectors" that promote either productive or destructive outcomes. Combining AlphaFold predictions with structural and biochemical validation, we show how effectors NCBP3, NELF-E, ARS2, PHAX, and ZC3H18 form competing binary complexes with CBC and how PHAX, NCBP3, ZC3H18, and other effectors compete for binding to ARS2. In ternary CBC-ARS2 complexes with PHAX, NCBP3, or ZC3H18, ARS2 is responsible for the initial effector recruitment but inhibits their direct binding to the CBC. We show that in vivo ZC3H18 binding to both CBC and ARS2 is required for nuclear RNA degradation. We propose that recruitment of PHAX to CBC-ARS2 can lead, with appropriate cues, to competitive displacement of ARS2 and ZC3H18 from the CBC, thus promoting a productive rather than a degradative RNA fate.
History
DepositionJun 29, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17763.png

Downloads & links

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Map

FileDownload / File: emd_17763.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.21774793 - 0.4285227
Average (Standard dev.)-0.000076382275 (±0.008672897)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17763_msk_1.map
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Half map: #1

Fileemd_17763_half_map_1.map
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Half map: #2

Fileemd_17763_half_map_2.map
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Sample components

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Entire : Structure of the human nuclear cap-binding complex bound to ARS2[...

EntireName: Structure of the human nuclear cap-binding complex bound to ARS2[147-871] and m7GTP
Components
  • Complex: Structure of the human nuclear cap-binding complex bound to ARS2[147-871] and m7GTP
    • Protein or peptide: Nuclear cap-binding protein subunit 1
    • Protein or peptide: Nuclear cap-binding protein subunit 2
    • Protein or peptide: Serrate RNA effector molecule homolog
  • Ligand: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Structure of the human nuclear cap-binding complex bound to ARS2[...

SupramoleculeName: Structure of the human nuclear cap-binding complex bound to ARS2[147-871] and m7GTP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nuclear cap-binding protein subunit 1

MacromoleculeName: Nuclear cap-binding protein subunit 1 / type: protein_or_peptide / ID: 1
Details: CBP80 construct has the N-terminal 20 residues (containing the NLS) deleted and replaced by a methionine
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.781938 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKTSDANETE DHLESLICKV GEKSACSLES NLEGLAGVLE ADLPNYKSKI LRLLCTVARL LPEKLTIYTT LVGLLNARNY NFGGEFVEA MIRQLKESLK ANNYNEAVYL VRFLSDLVNC HVIAAPSMVA MFENFVSVTQ EEDVPQVRRD WYVYAFLSSL P WVGKELYE ...String:
MKTSDANETE DHLESLICKV GEKSACSLES NLEGLAGVLE ADLPNYKSKI LRLLCTVARL LPEKLTIYTT LVGLLNARNY NFGGEFVEA MIRQLKESLK ANNYNEAVYL VRFLSDLVNC HVIAAPSMVA MFENFVSVTQ EEDVPQVRRD WYVYAFLSSL P WVGKELYE KKDAEMDRIF ANTESYLKRR QKTHVPMLQV WTADKPHPQE EYLDCLWAQI QKLKKDRWQE RHILRPYLAF DS ILCEALQ HNLPPFTPPP HTEDSVYPMP RVIFRMFDYT DDPEGPVMPG SHSVERFVIE ENLHCIIKSH WKERKTCAAQ LVS YPGKNK IPLNYHIVEV IFAELFQLPA PPHIDVMYTT LLIELCKLQP GSLPQVLAQA TEMLYMRLDT MNTTCVDRFI NWFS HHLSN FQFRWSWEDW SDCLSQDPES PKPKFVREVL EKCMRLSYHQ RILDIVPPTF SALCPANPTC IYKYGDESSN SLPGH SVAL CLAVAFKSKA TNDEIFSILK DVPNPNQDDD DDEGFSFNPL KIEVFVQTLL HLAAKSFSHS FSALAKFHEV FKTLAE SDE GKLHVLRVMF EVWRNHPQMI AVLVDKMIRT QIVDCAAVAN WIFSSELSRD FTRLFVWEIL HSTIRKMNKH VLKIQKE LE EAKEKLARQH KRRSDDDDRS SDRKDGVLEE QIERLQEKVE SAQSEQKNLF LVIFQRFIMI LTEHLVRCET DGTSVLTP W YKNCIERLQQ IFLQHHQIIQ QYMVTLENLL FTAELDPHIL AVFQQFCALQ A

UniProtKB: Nuclear cap-binding protein subunit 1

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Macromolecule #2: Nuclear cap-binding protein subunit 2

MacromoleculeName: Nuclear cap-binding protein subunit 2 / type: protein_or_peptide / ID: 2 / Details: Additional GA at the N-terminus / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.028131 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGGLLKALR SDSYVELSQY RDQHFRGDNE EQEKLLKKSC TLYVGNLSFY TTEEQIYELF SKSGDIKKII MGLDKMKKTA CGFCFVEYY SRADAENAMR YINGTRLDDR IIRTDWDAGF KEGRQYGRGR SGGQVRDEYR QDYDAGRGGY GKLAQNQ

UniProtKB: Nuclear cap-binding protein subunit 2

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Macromolecule #3: Serrate RNA effector molecule homolog

MacromoleculeName: Serrate RNA effector molecule homolog / type: protein_or_peptide / ID: 3
Details: ARS2 has N-terminal 147 residues deleted and replaced by a methionine
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.061391 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: VMKTFKEFLL SLDDSVDETE AVKRYNDYKL DFRRQQMQDF FLAHKDEEWF RSKYHPDEVG KRRQEARGAL QNRLRVFLSL METGWFDNL LLDIDKADAI VKMLDAAVIK MEGGTENDLR ILEQEEEEEQ AGKPGEPSKK EEGRAGAGLG DGERKTNDKD E KKEDGKQA ...String:
VMKTFKEFLL SLDDSVDETE AVKRYNDYKL DFRRQQMQDF FLAHKDEEWF RSKYHPDEVG KRRQEARGAL QNRLRVFLSL METGWFDNL LLDIDKADAI VKMLDAAVIK MEGGTENDLR ILEQEEEEEQ AGKPGEPSKK EEGRAGAGLG DGERKTNDKD E KKEDGKQA ENDSSNDDKT KKSEGDGDKE EKKEDSEKEA KKSSKKRNRK HSGDDSFDEG SVSESESESE SGQAEEEKEE AE EALKEKE KPKEEEWEKP KDAAGLECKP RPLHKTCSLF MRNIAPNISR AEIISLCKRY PGFMRVALSE PQPERRFFRR GWV TFDRSV NIKEICWNLQ NIRLRECELS PGVNRDLTRR VRNINGITQH KQIVRNDIKL AAKLIHTLDD RTQLWASEPG TPPL PTSLP SQNPILKNIT DYLIEEVSAE EEELLGSSGG APPEEPPKEG NPAEINVERD EKLIKVLDKL LLYLRIVHSL DYYNT CEYP NEDEMPNRCG IIHVRGPMPP NRISHGEVLE WQKTFEEKLT PLLSVRESLS EEEAQKMGRK DPEQEVEKFV TSNTQE LGK DKWLCPLSGK KFKGPEFVRK HIFNKHAEKI EEVKKEVAFF NNFLTDAKRP ALPEIKPAQP PGPAQILPPG LTPGLPY PH QTPQGLMPYG QPRPPILGYG AGAVRPAVPT GGPPYPHAPY GAGRGNYDAF RGQGGYPGKP RNRMVRGDPR AIVEYRDL D APDDVDFF

UniProtKB: Serrate RNA effector molecule homolog

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Macromolecule #4: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: MGT
Molecular weightTheoretical: 539.223 Da
Chemical component information

ChemComp-MGT:
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.13 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: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5oo6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84474
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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