8W8E

human co-transcriptional RNA capping enzyme RNGTT


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of co-transcriptional RNA capping enzymes on paused transcription complex.

Li, Y.Wang, Q.Xu, Y.Li, Z.

(2024) Nat Commun 15: 4622-4622

  • DOI: https://doi.org/10.1038/s41467-024-48963-1
  • Primary Citation of Related Structures:  
    8W8E, 8W8F

  • PubMed Abstract: 

    The 5'-end capping of nascent pre-mRNA represents the initial step in RNA processing, with evidence demonstrating that guanosine addition and 2'-O-ribose methylation occur in tandem with early steps of transcription by RNA polymerase II, especially at the pausing stage. Here, we determine the cryo-EM structures of the paused elongation complex in complex with RNGTT, as well as the paused elongation complex in complex with RNGTT and CMTR1. Our findings show the simultaneous presence of RNGTT and the NELF complex bound to RNA polymerase II. The NELF complex exhibits two conformations, one of which shows a notable rearrangement of NELF-A/D compared to that of the paused elongation complex. Moreover, CMTR1 aligns adjacent to RNGTT on the RNA polymerase II stalk. Our structures indicate that RNGTT and CMTR1 directly bind the paused elongation complex, illuminating the mechanism by which 5'-end capping of pre-mRNA during transcriptional pausing.


  • Organizational Affiliation

    Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,970Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A8D1DPV6 (Sus scrofa)
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UniProt GroupA0A8D1DPV6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,174Sus 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3271Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4142Sus 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 polymerase II subunit F127Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Sus 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
RPB1258Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa)
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UniProt GroupA0A4X1TRS6
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor AP [auth U]528Homo sapiensMutation(s): 0 
Gene Names: NELFAWHSC2P/OKcl.15
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GTEx:  ENSG00000185049 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor BQ [auth V]580Homo sapiensMutation(s): 0 
Gene Names: NELFBCOBRA1KIAA1182
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GTEx:  ENSG00000188986 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor C/DR [auth W]584Homo sapiensMutation(s): 0 
Gene Names: NELFCD
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GTEx:  ENSG00000101158 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor ES [auth X]380Homo sapiensMutation(s): 0 
Gene Names: NELFERDRDBP
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PHAROS:  P18615
GTEx:  ENSG00000204356 
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UniProt GroupP18615
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4T [auth Y]121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
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Find proteins for P63272 (Homo sapiens)
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GTEx:  ENSG00000213246 
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UniProt GroupP63272
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5U [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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GTEx:  ENSG00000196235 
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UniProt GroupO00267
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA-capping enzymeV [auth a]597Homo sapiensMutation(s): 0 
Gene Names: RNGTT
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Find proteins for O60942 (Homo sapiens)
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GTEx:  ENSG00000111880 
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UniProt GroupO60942
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Entity ID: 13
MoleculeChains LengthOrganismImage
DNA (36-MER)M [auth N]48Homo sapiens
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Entity ID: 14
MoleculeChains LengthOrganismImage
RNA (5'-D(*(GTP))-R(P*AP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')N [auth P]16Homo sapiens
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (45-MER)O [auth T]48Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
EA [auth P]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth I]
CA [auth I]
DA [auth L]
FA [auth Y]
AA [auth C],
BA [auth I],
CA [auth I],
DA [auth L],
FA [auth Y],
X [auth A],
Y [auth A],
Z [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
W [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references