7CNC | pdb_00007cnc

cystal structure of human ERH in complex with DGCR8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7CNC

This is version 1.2 of the entry. See complete history

Literature

ERH facilitates microRNA maturation through the interaction with the N-terminus of DGCR8.

Kwon, S.C.Jang, H.Shen, S.Baek, S.C.Kim, K.Yang, J.Kim, J.Kim, J.S.Wang, S.Shi, Y.Li, F.Kim, V.N.

(2020) Nucleic Acids Res 48: 11097-11112

  • DOI: https://doi.org/10.1093/nar/gkaa827
  • Primary Citation Related Structures: 
    7CNC

  • PubMed Abstract: 

    The microprocessor complex cleaves the primary transcript of microRNA (pri-miRNA) to initiate miRNA maturation. Microprocessor is known to consist of RNase III DROSHA and dsRNA-binding DGCR8. Here, we identify Enhancer of Rudimentary Homolog (ERH) as a new component of Microprocessor. Through a crystal structure and biochemical experiments, we reveal that ERH uses its hydrophobic groove to bind to a conserved region in the N-terminus of DGCR8, in a 2:2 stoichiometry. Knock-down of ERH or deletion of the DGCR8 N-terminus results in a reduced processing of suboptimal pri-miRNAs in polycistronic miRNA clusters. ERH increases the processing of suboptimal pri-miR-451 in a manner dependent on its neighboring pri-miR-144. Thus, the ERH dimer may mediate 'cluster assistance' in which Microprocessor is loaded onto a poor substrate with help from a high-affinity substrate in the same cluster. Our study reveals a role of ERH in the miRNA biogenesis pathway.


  • Organizational Affiliation
    • Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.

Macromolecule Content 

  • Total Structure Weight: 16.81 kDa 
  • Atom Count: 1,239 
  • Modeled Residue Count: 130 
  • Deposited Residue Count: 143 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Enhancer of rudimentary homolog112Homo sapiensMutation(s): 0 
Gene Names: ERH
UniProt & NIH Common Fund Data Resources
Find proteins for P84090 (Homo sapiens)
Explore P84090 
Go to UniProtKB:  P84090
PHAROS:  P84090
GTEx:  ENSG00000100632 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84090
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Microprocessor complex subunit DGCR831Homo 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.848α = 90
b = 45.072β = 107.44
c = 43.479γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description