8P4D

Structural insights into human co-transcriptional capping - structure 4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural insights into human co-transcriptional capping.

Garg, G.Dienemann, C.Farnung, L.Schwarz, J.Linden, A.Urlaub, H.Cramer, P.

(2023) Mol Cell 83: 2464-2477.e5

  • DOI: https://doi.org/10.1016/j.molcel.2023.06.002
  • Primary Citation of Related Structures:  
    8P4A, 8P4B, 8P4C, 8P4D, 8P4E, 8P4F

  • PubMed Abstract: 

    Co-transcriptional capping of the nascent pre-mRNA 5' end prevents degradation of RNA polymerase (Pol) II transcripts and suppresses the innate immune response. Here, we provide mechanistic insights into the three major steps of human co-transcriptional pre-mRNA capping based on six different cryoelectron microscopy (cryo-EM) structures. The human mRNA capping enzyme, RNGTT, first docks to the Pol II stalk to position its triphosphatase domain near the RNA exit site. The capping enzyme then moves onto the Pol II surface, and its guanylyltransferase receives the pre-mRNA 5'-diphosphate end. Addition of a GMP moiety can occur when the RNA is ∼22 nt long, sufficient to reach the active site of the guanylyltransferase. For subsequent cap(1) methylation, the methyltransferase CMTR1 binds the Pol II stalk and can receive RNA after it is grown to ∼29 nt in length. The observed rearrangements of capping factors on the Pol II surface may be triggered by the completion of catalytic reaction steps and are accommodated by domain movements in the elongation factor DRB sensitivity-inducing factor (DSIF).


  • Organizational Affiliation

    Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1C [auth A]1,970Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
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UniProt GroupA0A8D1DPV6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaD [auth B]1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
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UniProt GroupI3LGP4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3E [auth C]275Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EF [auth E]210Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FG [auth F]127Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-a117Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit K58Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit DN [auth D]142Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7O [auth G]172Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA-capping enzymeP [auth M]597Homo sapiensMutation(s): 0 
Gene Names: RNGTTCAP1A
EC: 3.6.1.74 (PDB Primary Data), 2.7.7.50 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60942 (Homo sapiens)
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PHAROS:  O60942
GTEx:  ENSG00000111880 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4Q [auth Y]117Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
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GTEx:  ENSG00000213246 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5R [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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GTEx:  ENSG00000196235 
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (32-MER)A [auth N]32synthetic construct
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (41-MER)B [auth T]41synthetic construct
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Entity ID: 13
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')M [auth P]19synthetic construct
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union693023
German Research Foundation (DFG)GermanySFB 860

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release