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- EMDB-17784: Structure of the human nuclear cap-binding complex bound to PHAX ... -

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Entry
Database: EMDB / ID: EMD-17784
TitleStructure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA
Map data
Sample
  • Complex: Structure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA
    • Protein or peptide: Nuclear cap-binding protein subunit 1
    • Protein or peptide: Nuclear cap-binding protein subunit 2
    • Protein or peptide: Phosphorylated adapter RNA export protein
  • Ligand: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
KeywordsNuclear cap-binding complex / PHAX / 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 / RNA stabilization / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus ...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 / RNA stabilization / 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 / 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 / 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 / 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) / toxic substance binding / 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 / Cajal body / 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 / protein transport / snRNP Assembly / positive regulation of cell growth / molecular adaptor activity / defense response to virus / ciliary basal body / ribonucleoprotein complex / neuronal cell body / mRNA binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Phosphorylated adapter RNA export protein / Phosphorylated adapter RNA export protein, RNA-binding domain / Phosphorylated adapter RNA export protein, RNA-binding domain superfamily / Phosphorylated adapter RNA export protein, RNA-binding 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 ...Phosphorylated adapter RNA export protein / Phosphorylated adapter RNA export protein, RNA-binding domain / Phosphorylated adapter RNA export protein, RNA-binding domain superfamily / Phosphorylated adapter RNA export protein, RNA-binding 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 / Phosphorylated adapter RNA export protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 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
DepositionJul 1, 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_17784.png

Downloads & links

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Map

FileDownload / File: emd_17784.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.784 Å		0.84 Å/pix.
x 256 pix.
= 214.784 Å		0.84 Å/pix.
x 256 pix.
= 214.784 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.16261068 - 0.35710016
Average (Standard dev.)0.0006378991 (±0.013368398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17784_msk_1.map
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Half map: #2

Fileemd_17784_half_map_1.map
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Half map: #1

Fileemd_17784_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 PHAX ...

EntireName: Structure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA
Components
  • Complex: Structure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA
    • Protein or peptide: Nuclear cap-binding protein subunit 1
    • Protein or peptide: Nuclear cap-binding protein subunit 2
    • Protein or peptide: Phosphorylated adapter RNA export protein
  • Ligand: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE

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

SupramoleculeName: Structure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA
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 / 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: Phosphorylated adapter RNA export protein

MacromoleculeName: Phosphorylated adapter RNA export protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.468574 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALEVGDMED GQLSDSDSDM TVAPSDRPLQ LPKVLGGDSA MRAFQNTATA CAPVSHYRAV ESVDSSEESF SDSDDDSCLW KRKRQKCFN PPPKPEPFQF GQSSQKPPVA GGKKINNIWG AVLQEQNQDA VATELGILGM EGTIDRSRQS ETYNYLLAKK L RKESQEHT ...String:
MALEVGDMED GQLSDSDSDM TVAPSDRPLQ LPKVLGGDSA MRAFQNTATA CAPVSHYRAV ESVDSSEESF SDSDDDSCLW KRKRQKCFN PPPKPEPFQF GQSSQKPPVA GGKKINNIWG AVLQEQNQDA VATELGILGM EGTIDRSRQS ETYNYLLAKK L RKESQEHT KDLDKELDEY MHGGKKMGSK EEENGQGHLK RKRPVKDRLG NRPEMNYKGR YEITAEDSQE KVADEISFRL QE PKKDLIA RVVRIIGNKK AIELLMETAE VEQNGGLFIM NGSRRRTPGG VFLNLLKNTP SISEEQIKDI FYIENQKEYE NKK AARKRR TQVLGKKMKQ AIKSLNFQED DDTSRETFAS DTNEALASLD ESQEGHAEAK LEAEEAIEVD HSHDLDIF

UniProtKB: Phosphorylated adapter RNA export protein

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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: 41.67 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: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 193335
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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