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Yorodumi- EMDB-16321: Structure of the human nuclear cap-binding complex bound to NCBP3... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16321 | |||||||||
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Title | Structure of the human nuclear cap-binding complex bound to NCBP3(560-620) and cap-analogue m7GpppG | |||||||||
Map data | primary map | |||||||||
Sample |
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Keywords | Nuclear cap-binding complex / NCBP3 / Pol II transcript metabolism / RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information : / positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / RNA cap binding complex / mRNA metabolic process / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation ...: / positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / RNA cap binding complex / mRNA metabolic process / histone 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 / alternative mRNA splicing, via spliceosome / RNA cap binding / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / regulatory ncRNA-mediated post-transcriptional gene silencing / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / mRNA 3'-end processing / RNA catabolic process / mRNA cis splicing, via spliceosome / Abortive elongation of HIV-1 transcript in the absence of Tat / Transport of Mature mRNA derived from an Intron-Containing Transcript / regulation of translational initiation / positive regulation of mRNA splicing, via spliceosome / FGFR2 alternative splicing / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Signaling by FGFR2 IIIa TM / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 7-methylguanosine mRNA capping / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / mRNA export from nucleus / 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 / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / snRNP Assembly / positive regulation of cell growth / defense response to virus / molecular adaptor activity / nuclear speck / ribonucleoprotein complex / mRNA binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.19 Å | |||||||||
Authors | Dubiez E / Pellegrini E / Foucher AE / Cusack S / Kadlec J | |||||||||
Funding support | France, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16321.map.gz | 51.5 MB | EMDB map data format | |
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Header (meta data) | emd-16321-v30.xml emd-16321.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16321_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_16321.png | 73.4 KB | ||
Masks | emd_16321_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-16321.cif.gz | 6.2 KB | ||
Others | emd_16321_additional_1.map.gz emd_16321_half_map_1.map.gz emd_16321_half_map_2.map.gz | 3.5 MB 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16321 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16321 | HTTPS FTP |
-Validation report
Summary document | emd_16321_validation.pdf.gz | 910.8 KB | Display | EMDB validaton report |
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Full document | emd_16321_full_validation.pdf.gz | 910.4 KB | Display | |
Data in XML | emd_16321_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_16321_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16321 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16321 | HTTPS FTP |
-Related structure data
Related structure data | 8by6MC 8pmpC 8pntC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16321.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.827 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16321_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: locally filtered and sharpened map (-100 A2)
File | emd_16321_additional_1.map | ||||||||||||
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Annotation | locally filtered and sharpened map (-100 A2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_16321_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_16321_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of CBP80, CBP20 and NCBP3 with bound m7GpppG
Entire | Name: Ternary complex of CBP80, CBP20 and NCBP3 with bound m7GpppG |
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Components |
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-Supramolecule #1: Ternary complex of CBP80, CBP20 and NCBP3 with bound m7GpppG
Supramolecule | Name: Ternary complex of CBP80, CBP20 and NCBP3 with bound m7GpppG type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Nuclear cap-binding protein subunit 1
Macromolecule | Name: Nuclear cap-binding protein subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 89.809984 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 SALCPVNPTC 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 |
-Macromolecule #2: Nuclear cap-binding protein subunit 2
Macromolecule | Name: Nuclear cap-binding protein subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 18.15626 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GAMSGGLLKA LRSDSYVELS QYRDQHFRGD NEEQEKLLKK SCTLYVGNLS FYTTEEQIYE LFSKSGDIKK IIMGLDKMKK TACGFCFVE YYSRADAENA MRYINGTRLD DRIIRTDWDA GFKEGRQYGR GRSGGQVRDE YRQDYDAGRG GYGKLAQNQ UniProtKB: Nuclear cap-binding protein subunit 2 |
-Macromolecule #3: Nuclear cap-binding protein subunit 3
Macromolecule | Name: Nuclear cap-binding protein subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 6.734328 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: KKVDHRAPGA EEDDSELQRA WGALIKEKEQ SRQKKSRLDN LPSLQIEVSR ESSSGSEAES UniProtKB: Nuclear cap-binding protein subunit 3 |
-Macromolecule #4: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
Macromolecule | Name: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTG |
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Molecular weight | Theoretical: 803.44 Da |
Chemical component information | ChemComp-GTG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / 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 |