9QEQ | pdb_00009qeq

Structure of the transcribing Pol II-DSIF-SPT6-U1 snRNP complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

Structure of a transcribing Pol II-DSIF-SPT6-U1 snRNP complex.

Zhang, L., Batters, C., Aibara, S., Gordiyenko, Y., Zumer, K., Schmitzova, J., Maier, K., Cramer, P., Zhang, S.

(2025) Nat Commun 16: 5823-5823

  • DOI: https://doi.org/10.1038/s41467-025-60979-9
  • Primary Citation of Related Structures:  
    9QEQ

  • PubMed Abstract: 

    In eukaryotic cells, splicing occurs predominantly co-transcriptionally, enhancing splicing efficiency and fidelity while introducing an additional layer of regulation over gene expression. RNA polymerase II (Pol II) facilitates co-transcriptional splicing by recruiting the U1 small nuclear ribonucleoprotein particle (U1 snRNP) to the nascent transcripts. Here, we report the cryo-electron microscopy structure of a transcribing Pol II-U1 snRNP complex with elongation factors DSIF and SPT6. In addition, our biochemical analysis reveals that the phosphorylated Pol II carboxyl-terminal domain and SPT6 interact directly with U1 snRNP proteins, facilitating its recruitment to the elongation complex. This multivalent interaction between U1 snRNP and the transcription elongation complex may both allow efficient spliceosome assembly and ensure transcription processivity.

    • Organizational Affiliation: 
    • MRC Laboratory of Molecular Biology, Cambridge, UK.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,970Sus scrofa domesticusMutation(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 scrofa domesticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A0B8RVL1 (Sus scrofa domesticus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Sus scrofa domesticusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit D142Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A2Y9PTG7 (Delphinapterus leucas)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit E210Sus scrofa domesticusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2127Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit172Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Sus scrofa domesticusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-a117Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II, I and III subunit K58Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT61,726Homo sapiensMutation(s): 0 
Gene Names: SUPT6H, KIAA0162, SPT6H
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GTEx:  ENSG00000109111 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4Q [auth Y]121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1, QtsA-10763
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5R [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5H, SPT5, SPT5H
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GTEx:  ENSG00000196235 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein 70 kDaT [auth b]437Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104852 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein AU [auth c]282Homo sapiensMutation(s): 0 
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PHAROS:  P09012
GTEx:  ENSG00000077312 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2V [auth e]118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FW [auth f]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EX [auth g]92Homo sapiensMutation(s): 0 
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PHAROS:  P62304
GTEx:  ENSG00000182004 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GY [auth h]76Homo sapiensMutation(s): 0 
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PHAROS:  P62308
GTEx:  ENSG00000143977 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3Z [auth i]126Homo sapiensMutation(s): 0 
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PHAROS:  P62318
GTEx:  ENSG00000100028 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteinAA [auth j]231Homo sapiensMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1BA [auth k]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 14
MoleculeChains LengthOrganismImage
Non-template DNA48synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
Pre-mRNAO [auth P]68synthetic construct
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Entity ID: 16
MoleculeChains LengthOrganismImage
Template DNAP [auth T]48synthetic construct
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Entity ID: 19
MoleculeChains LengthOrganismImage
U1 snRNAS [auth a]164Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
CA [auth A]
DA [auth A]
FA [auth B]
GA [auth C]
HA [auth I]
CA [auth A],
DA [auth A],
FA [auth B],
GA [auth C],
HA [auth I],
IA [auth I],
JA [auth J],
KA [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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EA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX1.21.2_5419:

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-07-09 
    • Deposition Author(s): Zhang, S.
Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/30

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references