7DN3

Structure of Human RNA Polymerase III elongation 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 1.2 of the entry. See complete history


Literature

Structure of human RNA polymerase III elongation complex.

Li, L.Yu, Z.Zhao, D.Ren, Y.Hou, H.Xu, Y.

(2021) Cell Res 31: 791-800

  • DOI: https://doi.org/10.1038/s41422-021-00472-2
  • Primary Citation of Related Structures:  
    7DN3, 7DU2

  • PubMed Abstract: 

    RNA polymerase III (Pol III) transcribes essential structured small RNAs, such as tRNAs, 5S rRNA and U6 snRNA. The transcriptional activity of Pol III is tightly controlled and its dysregulation is associated with human diseases, such as cancer. Human Pol III has two isoforms with difference only in one of its subunits RPC7 (α and β). Despite structural studies of yeast Pol III, structure of human Pol III remains unsolved. Here, we determined the structures of 17-subunit human Pol IIIα complex in the backtracked and post-translocation states, respectively. Human Pol III contains a generally conserved catalytic core, similar to that of yeast counterpart, and structurally unique RPC3-RPC6-RPC7 heterotrimer and RPC10. The N-ribbon of TFIIS-like RPC10 docks on the RPC4-RPC5 heterodimer and the C-ribbon inserts into the funnel of Pol III in the backtracked state but is more flexible in the post-translocation state. RPC7 threads through the heterotrimer and bridges the stalk and Pol III core module. The winged helix 1 domain of RPC6 and the N-terminal region of RPC7α stabilize each other and may prevent Maf1-mediated repression of Pol III activity. The C-terminal FeS cluster of RPC6 coordinates a network of interactions that mediate core-heterotrimer contacts and stabilize Pol III. Our structural analysis sheds new light on the molecular mechanism of human Pol IIIα-specific transcriptional regulation and provides explanations for upregulated Pol III activity in RPC7α-dominant cancer cells.


  • 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 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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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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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC8D [auth G]204Homo sapiensMutation(s): 0 
Gene Names: POLR3HKIAA1665RPC8
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GTEx:  ENSG00000100413 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC10E [auth I]108Homo sapiensMutation(s): 0 
Gene Names: POLR3KRPC11My010
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GTEx:  ENSG00000161980 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC2F [auth K]133Homo sapiensMutation(s): 0 
Gene Names: POLR1D
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GTEx:  ENSG00000186184 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4G [auth L]58Homo sapiensMutation(s): 0 
Gene Names: POLR2K
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GTEx:  ENSG00000147669 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC6H [auth P]316Homo sapiensMutation(s): 0 
Gene Names: POLR3F
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GTEx:  ENSG00000132664 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1I [auth E]210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
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GTEx:  ENSG00000099817 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2J [auth F]127Homo sapiensMutation(s): 0 
Gene Names: POLR2FPOLRF
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GTEx:  ENSG00000100142 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3K [auth H]150Homo sapiensMutation(s): 0 
Gene Names: POLR2H
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GTEx:  ENSG00000163882 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5L [auth J]67Homo sapiensMutation(s): 0 
Gene Names: POLR2L
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GTEx:  ENSG00000177700 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC3M [auth O]534Homo sapiensMutation(s): 0 
Gene Names: POLR3C
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GTEx:  ENSG00000186141 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC7N [auth Q]223Homo sapiensMutation(s): 0 
Gene Names: POLR3G
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GTEx:  ENSG00000113356 
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UniProt GroupO15318
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC9O [auth D]148Homo sapiensMutation(s): 0 
Gene Names: CRCP
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GTEx:  ENSG00000241258 
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UniProt GroupO75575
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC5P [auth M]708Homo sapiensMutation(s): 0 
Gene Names: POLR3EKIAA1452
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GTEx:  ENSG00000058600 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC4Q [auth N]398Homo sapiensMutation(s): 0 
Gene Names: POLR3DBN51BN51T
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GTEx:  ENSG00000168495 
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UniProt GroupP05423
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Entity ID: 18
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*CP*GP*TP*CP*TP*GP*AP*TP*CP*TP*CP*GP*GP*AP*A)-3')R [auth X]16Homo sapiens
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Entity ID: 19
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*CP*CP*GP*AP*GP*AP*TP*CP*AP*GP*AP*CP*GP*AP*GP*AP*TP*CP*GP*GP*G)-3')S [auth Y]23Homo sapiens
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Entity ID: 20
MoleculeChains LengthOrganismImage
RNA (5'-R(P*CP*CP*CP*GP*AP*U)-3')T [auth R]6Homo 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 
AA [auth P]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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BA [auth J]
V [auth A]
W [auth A]
X [auth B]
Y [auth I]
BA [auth J],
V [auth A],
W [auth A],
X [auth B],
Y [auth I],
Z [auth L]
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: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references