7FJJ

human Pol III pre-termination complex


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into RNA polymerase III-mediated transcription termination through trapping poly-deoxythymidine.

Hou, H.Li, Y.Wang, M.Liu, A.Yu, Z.Chen, K.Zhao, D.Xu, Y.

(2021) Nat Commun 12: 6135-6135

  • DOI: https://doi.org/10.1038/s41467-021-26402-9
  • Primary Citation of Related Structures:  
    7FJI, 7FJJ

  • PubMed Abstract: 

    Termination of the RNA polymerase III (Pol III)-mediated transcription requires the conversion of an elongation complex (EC) to a pre-termination complex (PTC) on poly-deoxythymidine (dT)-containing non-template strand, a mechanism distinct from Pol I and Pol II. Here, our in vitro transcription elongation assay showed that 5-7 dT-containing DNA template led to transcription termination of Pol III, but not Pol I or Pol II. We assembled human Pol III PTC on a 7 dT-containing DNA template and determined the structure at 3.6 Å resolution. The structure reveals that poly-dT are trapped in a narrow exit tunnel formed by RPC2. A hydrophobic gate of the exit tunnel separates the bases of two connected deoxythymidines and may prevent translocation of the non-template strand. The fork loop 2 stabilizes both template and non-template strands around the transcription fork, and may further prevent strand translocation. Our study shows that the Pol III-specific exit tunnel and FL2 allow for efficient translocation of non-poly-dT sequence during transcription elongation but trap poly-dT to promote DNA retention of Pol III, revealing molecular mechanism of poly-dT-dependent transcription termination of Pol III.


  • Organizational Affiliation

    Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, 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 III subunit RPC11,390Homo sapiensMutation(s): 0 
Gene Names: POLR3A
EC: 2.7.7.6
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PHAROS:  O14802
GTEx:  ENSG00000148606 
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UniProt GroupO14802
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC21,133Homo sapiensMutation(s): 0 
Gene Names: POLR3B
EC: 2.7.7.6
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PHAROS:  Q9NW08
GTEx:  ENSG00000013503 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC1346Homo sapiensMutation(s): 0 
Gene Names: POLR1CPOLR1E
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GTEx:  ENSG00000171453 
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UniProt GroupO15160
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC9148Homo sapiensMutation(s): 0 
Gene Names: CRCP
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PHAROS:  O75575
GTEx:  ENSG00000241258 
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UniProt GroupO75575
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
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PHAROS:  P19388
GTEx:  ENSG00000099817 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2127Homo sapiensMutation(s): 0 
Gene Names: POLR2FPOLRF
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PHAROS:  P61218
GTEx:  ENSG00000100142 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC8204Homo sapiensMutation(s): 0 
Gene Names: POLR3HKIAA1665RPC8
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GTEx:  ENSG00000100413 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Homo sapiensMutation(s): 0 
Gene Names: POLR2H
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GTEx:  ENSG00000163882 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC10108Homo sapiensMutation(s): 1 
Gene Names: POLR3KRPC11My010
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GTEx:  ENSG00000161980 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Homo sapiensMutation(s): 0 
Gene Names: POLR2L
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GTEx:  ENSG00000177700 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC2133Homo sapiensMutation(s): 0 
Gene Names: POLR1D
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GTEx:  ENSG00000186184 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC458Homo sapiensMutation(s): 0 
Gene Names: POLR2K
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PHAROS:  P53803
GTEx:  ENSG00000147669 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC5708Homo sapiensMutation(s): 0 
Gene Names: POLR3EKIAA1452
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GTEx:  ENSG00000058600 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC4398Homo sapiensMutation(s): 0 
Gene Names: POLR3DBN51BN51T
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GTEx:  ENSG00000168495 
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UniProt GroupP05423
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC3534Homo sapiensMutation(s): 0 
Gene Names: POLR3C
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PHAROS:  Q9BUI4
GTEx:  ENSG00000186141 
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UniProt GroupQ9BUI4
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC6316Homo sapiensMutation(s): 0 
Gene Names: POLR3F
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GTEx:  ENSG00000132664 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC7223Homo sapiensMutation(s): 0 
Gene Names: POLR3G
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GTEx:  ENSG00000113356 
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UniProt GroupO15318
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Entity ID: 18
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*CP*GP*GP*GP*UP*GP*CP*UP*G)-3')10Homo sapiens
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Entity ID: 19
MoleculeChains LengthOrganismImage
non-template DNAS [auth X]54Homo sapiens
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Entity ID: 20
MoleculeChains LengthOrganismImage
template DNAT [auth Y]54Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
CA [auth P]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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

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

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2021-10-27 
  • Deposition Author(s): Hou, H., Xu, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31821002

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary