5B16 | pdb_00005b16

X-ray structure of DROSHA in complex with the C-terminal tail of DGCR8.

• PDB DOI: https://doi.org/10.2210/pdb5B16/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2015-11-23 Released: 2016-02-03 
• Deposition Author(s): Kwon, S.C., Nguyen, T.A., Choi, Y.G., Jo, M.H., Hohng, S., Kim, V.N., Woo, J.S.
• Funding Organization(s): Institute for Basic Science

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.300 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.267 (Depositor), 0.271 (DCC) 

Literature

Structure of Human DROSHA

Kwon, S.C., Nguyen, T.A., Choi, Y.G., Jo, M.H., Hohng, S., Kim, V.N., Woo, J.S.

(2016) Cell 164: 81-90

• PubMed: 26748718 
• DOI: https://doi.org/10.1016/j.cell.2015.12.019
• Primary Citation Related Structures: 
  5B16


• PubMed Abstract: 
  

  MicroRNA maturation is initiated by RNase III DROSHA that cleaves the stem loop of primary microRNA. DROSHA functions together with its cofactor DGCR8 in a heterotrimeric complex known as Microprocessor. Here, we report the X-ray structure of DROSHA in complex with the C-terminal helix of DGCR8. We find that DROSHA contains two DGCR8-binding sites, one on each RNase III domain (RIIID), which mediate the assembly of Microprocessor. The overall structure of DROSHA is surprisingly similar to that of Dicer despite no sequence homology apart from the C-terminal part, suggesting that DROSHA may have evolved from a Dicer homolog. DROSHA exhibits unique features, including non-canonical zinc-finger motifs, a long insertion in the first RIIID, and the kinked link between Connector helix and RIIID, which explains the 11-bp-measuring "ruler" activity of DROSHA. Our study implicates the evolutionary origin of DROSHA and elucidates the molecular basis of Microprocessor assembly and primary microRNA processing.

---

Organizational Affiliation: 
• Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea; National Center for Creative Research Initiatives, Seoul National University, Seoul 08826, Korea; Institute of Applied Physics, Seoul National University, Seoul 08826, Korea.
Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea; National Center for Creative Research Initiatives, Seoul National University, Seoul 08826, Korea; Institute of Applied Physics, Seoul National University, Seoul 08826, Korea; Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea.
Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea. Electronic address: [e-mail].
Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 118 kDa 
• Atom Count: 6,159 
• Modeled Residue Count: 770 
• Deposited Residue Count: 1,064 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease 3,DROSHA,Ribonuclease 3,DROSHA,Ribonuclease 3	A	986	Homo sapiens	Mutation(s): 2  Gene Names: DROSHA, RN3, RNASE3L, RNASEN 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Microprocessor complex subunit DGCR8	B, C	39	Homo sapiens	Mutation(s): 0  Gene Names: DGCR8, C22orf12, DGCRK6, LP4941
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WYQ5 (Homo sapiens) Explore Q8WYQ5  Go to UniProtKB:  Q8WYQ5
PHAROS:  Q8WYQ5 GTEx:  ENSG00000128191

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.300 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.267 (Depositor), 0.271 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.254	α = 90
b = 118.136	β = 102.07
c = 122.296	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Kwon, S.C., Nguyen, T.A., Choi, Y.G., Jo, M.H., Hohng, S., Kim, V.N., Woo, J.S.

---

Funding Organization	Location	Grant Number
Institute for Basic Science	Korea, Republic Of	IBS-R008-D1

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary