5ZAM

Cryo-EM structure of human Dicer and its complexes with a pre-miRNA substrate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate.

Liu, Z.Wang, J.Cheng, H.Ke, X.Sun, L.Zhang, Q.C.Wang, H.W.

(2018) Cell 173: 1191-1203.e12

  • DOI: https://doi.org/10.1016/j.cell.2018.03.080

  • PubMed Abstract: 

    Human Dicer (hDicer) is a multi-domain protein belonging to the RNase III family. It plays pivotal roles in small RNA biogenesis during the RNA interference (RNAi) pathway by processing a diverse range of double-stranded RNA (dsRNA) precursors to generate ∼22 nt microRNA (miRNA) or small interfering RNA (siRNA) products for sequence-directed gene silencing. In this work, we solved the cryoelectron microscopy (cryo-EM) structure of hDicer in complex with its cofactor protein TRBP and revealed the precise spatial arrangement of hDicer's multiple domains. We further solved structures of the hDicer-TRBP complex bound with pre-let-7 RNA in two distinct conformations. In combination with biochemical analysis, these structures reveal a property of the hDicer-TRBP complex to promote the stability of pre-miRNA's stem duplex in a pre-dicing state. These results provide insights into the mechanism of RNA processing by hDicer and illustrate the regulatory role of hDicer's N-terminal helicase domain.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoribonuclease Dicer1,922Homo sapiensMutation(s): 0 
Gene Names: DICER1DICERHERNAKIAA0928
EC: 3.1.26.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPY3 (Homo sapiens)
Explore Q9UPY3 
Go to UniProtKB:  Q9UPY3
PHAROS:  Q9UPY3
GTEx:  ENSG00000100697 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UPY3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RISC-loading complex subunit TARBP2366Homo sapiensMutation(s): 0 
Gene Names: TARBP2TRBP
UniProt & NIH Common Fund Data Resources
Find proteins for Q15633 (Homo sapiens)
Explore Q15633 
Go to UniProtKB:  Q15633
PHAROS:  Q15633
GTEx:  ENSG00000139546 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15633
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (73-mer)73Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.11

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation of ChinaChina31530018

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 1.3: 2020-08-05
    Changes: Data collection