5OO6

Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis for mutually exclusive co-transcriptional nuclear cap-binding complexes with either NELF-E or ARS2.

Schulze, W.M.Cusack, S.

(2017) Nat Commun 8: 1302-1302

  • DOI: https://doi.org/10.1038/s41467-017-01402-w
  • Primary Citation of Related Structures:  
    5OO6, 5OOB

  • PubMed Abstract: 

    Pol II transcribes diverse classes of RNAs that need to be directed into the appropriate nuclear maturation pathway. All nascent Pol II transcripts are 5'-capped and the cap is immediately sequestered by the nuclear cap-binding complex (CBC). Mutually exclusive interactions of CBC with different partner proteins have been implicated in transcript fate determination. Here, we characterise the direct interactions between CBC and NELF-E, a subunit of the negative elongation factor complex, ARS2 and PHAX. Our biochemical and crystal structure results show that the homologous C-terminal peptides of NELF-E and ARS2 bind identically to CBC and in each case the affinity is enhanced when CBC is bound to a cap analogue. Furthermore, whereas PHAX forms a complex with CBC and ARS2, NELF-E binding to CBC is incompatible with PHAX binding. We thus define two mutually exclusive complexes CBC-NELF-E and CBC-ARS2-PHAX, which likely act in respectively earlier and later phases of transcription.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble Cedex 9, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear cap-binding protein subunit 1772Homo sapiensMutation(s): 0 
Gene Names: NCBP1CBP80NCBP
UniProt & NIH Common Fund Data Resources
Find proteins for Q09161 (Homo sapiens)
Explore Q09161 
Go to UniProtKB:  Q09161
PHAROS:  Q09161
GTEx:  ENSG00000136937 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09161
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear cap-binding protein subunit 2158Homo sapiensMutation(s): 0 
Gene Names: NCBP2CBP20PIG55
UniProt & NIH Common Fund Data Resources
Find proteins for P52298 (Homo sapiens)
Explore P52298 
Go to UniProtKB:  P52298
PHAROS:  P52298
GTEx:  ENSG00000114503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52298
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serrate RNA effector molecule homolog48Homo sapiensMutation(s): 0 
Gene Names: SRRTARS2ASR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXP5 (Homo sapiens)
Explore Q9BXP5 
Go to UniProtKB:  Q9BXP5
PHAROS:  Q9BXP5
GTEx:  ENSG00000087087 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXP5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGT
Query on MGT

Download Ideal Coordinates CCD File 
AA [auth H]
BA [auth K]
CA [auth N]
DA [auth Q]
EA [auth T]
AA [auth H],
BA [auth K],
CA [auth N],
DA [auth Q],
EA [auth T],
FA [auth W],
Y [auth B],
Z [auth E]
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
C11 H20 N5 O14 P3
BUJQMJUTTBGELS-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.52α = 90
b = 112.99β = 90.3
c = 270.98γ = 90.02
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description