6V5C

Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA complex) - partially docked state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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 Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA.

Partin, A.C.Zhang, K.Jeong, B.C.Herrell, E.Li, S.Chiu, W.Nam, Y.

(2020) Mol Cell 78: 411

  • DOI: https://doi.org/10.1016/j.molcel.2020.02.016
  • Primary Citation of Related Structures:  
    6V5B, 6V5C

  • PubMed Abstract: 

    Metazoan microRNAs require specific maturation steps initiated by Microprocessor, comprising Drosha and DGCR8. Lack of structural information for the assembled complex has hindered an understanding of how Microprocessor recognizes primary microRNA transcripts (pri-miRNAs). Here we present a cryoelectron microscopy structure of human Microprocessor with a pri-miRNA docked in the active site, poised for cleavage. The basal junction is recognized by a four-way intramolecular junction in Drosha, triggered by the Belt and Wedge regions that clamp over the ssRNA. The belt is important for efficiency and accuracy of pri-miRNA processing. Two dsRBDs form a molecular ruler to measure the stem length between the two dsRNA-ssRNA junctions. The specific organization of the dsRBDs near the apical junction is independent of Drosha core domains, as observed in a second structure in the partially docked state. Collectively, we derive a molecular model to explain how Microprocessor recognizes a pri-miRNA and accurately identifies the cleavage site.


  • Organizational Affiliation

    Laboratory of RNA Biology, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Departments of Biophysics and Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease 31,016Homo sapiensMutation(s): 2 
Gene Names: DROSHARN3RNASE3LRNASEN
EC: 3.1.26.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRR4 (Homo sapiens)
Explore Q9NRR4 
Go to UniProtKB:  Q9NRR4
PHAROS:  Q9NRR4
GTEx:  ENSG00000113360 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRR4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Microprocessor complex subunit DGCR8B [auth C],
C [auth B]
532Homo sapiensMutation(s): 0 
Gene Names: DGCR8C22orf12DGCRK6LP4941
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WYQ5 (Homo sapiens)
Explore Q8WYQ5 
Go to UniProtKB:  Q8WYQ5
PHAROS:  Q8WYQ5
GTEx:  ENSG00000128191 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WYQ5
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
Pri-miR-16-2 (66-MER)105Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14
RECONSTRUCTIONcryoSPARC2.0.5

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079429
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD021600
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM122960

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references
  • Version 1.2: 2020-05-27
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references