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- EMDB-40780: Cryo-EM structure of the human cap binding complex (CBC) -

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Basic information

Entry
Database: EMDB / ID: EMD-40780
TitleCryo-EM structure of the human cap binding complex (CBC)
Map data
Sample
  • Complex: Cryo-EM structure of an mRNA export factor
    • Protein or peptide: Nuclear cap-binding protein subunit 1
    • Protein or peptide: Nuclear cap-binding protein subunit 2
  • Ligand: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
KeywordsmRNA nuclear export / RNA BINDING PROTEIN
Function / homology
Function and homology information


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 ...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 / 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) / 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 / snRNP Assembly / positive regulation of cell growth / molecular adaptor activity / defense response to virus / ciliary basal body / ribonucleoprotein complex / mRNA binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsXie Y / Clarke BP / Ren Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133743 United States
Citation
Journal: Elife / Year: 2024
Title: Cryo-EM structure of the CBC-ALYREF complex.
Authors: Bradley P Clarke / Alexia E Angelos / Menghan Mei / Pate S Hill / Yihu Xie / Yi Ren /
Abstract: In eukaryotes, RNAs transcribed by RNA Pol II are modified at the 5' end with a 7-methylguanosine (mG) cap, which is recognized by the nuclear cap binding complex (CBC). The CBC plays multiple ...In eukaryotes, RNAs transcribed by RNA Pol II are modified at the 5' end with a 7-methylguanosine (mG) cap, which is recognized by the nuclear cap binding complex (CBC). The CBC plays multiple important roles in mRNA metabolism, including transcription, splicing, polyadenylation, and export. It promotes mRNA export through direct interaction with a key mRNA export factor, ALYREF, which in turn links the TRanscription and EXport (TREX) complex to the 5' end of mRNA. However, the molecular mechanism for CBC-mediated recruitment of the mRNA export machinery is not well understood. Here, we present the first structure of the CBC in complex with an mRNA export factor, ALYREF. The cryo-EM structure of CBC-ALYREF reveals that the RRM domain of ALYREF makes direct contact with both the NCBP1 and NCBP2 subunits of the CBC. Comparing CBC-ALYREF with other cellular complexes containing CBC and/or ALYREF components provides insights into the coordinated events during mRNA transcription, splicing, and export.
#1: Journal: Elife / Year: 2024
Title: Cryo-EM structure of the CBC-ALYREF complex
Authors: Clarke BP / Angelos AE / Mei M / Hill PS / Xie Y / Ren Y
History
DepositionMay 14, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40780.png

Downloads & links

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Map

FileDownload / File: emd_40780.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 288 pix.
= 210.816 Å		0.73 Å/pix.
x 288 pix.
= 210.816 Å		0.73 Å/pix.
x 288 pix.
= 210.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.1198845 - 0.23891261
Average (Standard dev.)-0.00016427721 (±0.008597671)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 210.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_40780_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40780_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of an mRNA export factor

EntireName: Cryo-EM structure of an mRNA export factor
Components
  • Complex: Cryo-EM structure of an mRNA export factor
    • Protein or peptide: Nuclear cap-binding protein subunit 1
    • Protein or peptide: Nuclear cap-binding protein subunit 2
  • Ligand: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Cryo-EM structure of an mRNA export factor

SupramoleculeName: Cryo-EM structure of an mRNA export factor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.960297 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSRRRHSDEN DGGQPHKRRK TSDANETEDH LESLICKVGE KSACSLESNL EGLAGVLEAD LPNYKSKILR LLCTVARLLP EKLTIYTTL VGLLNARNYN FGGEFVEAMI RQLKESLKAN NYNEAVYLVR FLSDLVNCHV IAAPSMVAMF ENFVSVTQEE D VPQVRRDW ...String:
MSRRRHSDEN DGGQPHKRRK TSDANETEDH LESLICKVGE KSACSLESNL EGLAGVLEAD LPNYKSKILR LLCTVARLLP EKLTIYTTL VGLLNARNYN FGGEFVEAMI RQLKESLKAN NYNEAVYLVR FLSDLVNCHV IAAPSMVAMF ENFVSVTQEE D VPQVRRDW YVYAFLSSLP WVGKELYEKK DAEMDRIFAN TESYLKRRQK THVPMLQVWT ADKPHPQEEY LDCLWAQIQK LK KDRWQER HILRPYLAFD SILCEALQHN LPPFTPPPHT EDSVYPMPRV IFRMFDYTDD PEGPVMPGSH SVERFVIEEN LHC IIKSHW KERKTCAAQL VSYPGKNKIP LNYHIVEVIF AELFQLPAPP HIDVMYTTLL IELCKLQPGS LPQVLAQATE MLYM RLDTM NTTCVDRFIN WFSHHLSNFQ FRWSWEDWSD CLSQDPESPK PKFVREVLEK CMRLSYHQRI LDIVPPTFSA LCPAN PTCI YKYGDESSNS LPGHSVALCL AVAFKSKATN DEIFSILKDV PNPNQDDDDD EGFSFNPLKI EVFVQTLLHL AAKSFS HSF SALAKFHEVF KTLAESDEGK LHVLRVMFEV WRNHPQMIAV LVDKMIRTQI VDCAAVANWI FSSELSRDFT RLFVWEI LH STIRKMNKHV LKIQKELEEA KEKLARQHKR RSDDDDRSSD RKDGVLEEQI ERLQEKVESA QSEQKNLFLV IFQRFIMI L TEHLVRCETD GTSVLTPWYK NCIERLQQIF LQHHQIIQQY MVTLENLLFT AELDPHILAV FQQFCALQA

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: Trichoplusia ni (cabbage looper)
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: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: M7G
Molecular weightTheoretical: 458.235 Da
Chemical component information

ChemComp-M7G:
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE

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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: OTHER / Details: AlphaFold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78039
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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