8P4F

Structural insights into human co-transcriptional capping - structure 6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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 

  • 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1B [auth A]1,970Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0A8D1DPV6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC [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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3D [auth C]275Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit E210Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2127Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0A4X1VEK9
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3G [auth H]150Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9H [auth I]125Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5I [auth J]67Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-aJ [auth K]117Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit KK [auth L]58Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0A4X1TRS6
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4N [auth Y]117Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
UniProt & NIH Common Fund Data Resources
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PHAROS:  P63272
GTEx:  ENSG00000213246 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5O [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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GTEx:  ENSG00000196235 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7P [auth G]172Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit DQ [auth D]142Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1R [auth O]835Homo sapiensMutation(s): 0 
Gene Names: CMTR1FTSJD2KIAA0082MTR1
EC: 2.1.1.57
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GTEx:  ENSG00000137200 
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UniProt GroupQ8N1G2
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (29-MER)A [auth P]29synthetic construct
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Entity ID: 12
MoleculeChains LengthOrganismImage
DNA (38-MER)L [auth N]38synthetic construct
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Entity ID: 13
MoleculeChains LengthOrganismImage
DNA (38-MER)M [auth T]38synthetic construct
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGT
Query on MGT

Download Ideal Coordinates CCD File 
S [auth P]7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
C11 H20 N5 O14 P3
BUJQMJUTTBGELS-KQYNXXCUSA-N
SAM
Query on SAM

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CA [auth O]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN
Query on ZN

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AA [auth L]
BA [auth Y]
T [auth A]
U [auth A]
W [auth B]
AA [auth L],
BA [auth Y],
T [auth A],
U [auth A],
W [auth B],
X [auth I],
Y [auth I],
Z [auth J]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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V [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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: 2023-07-19
    Type: Initial release