9PQ8 | pdb_00009pq8

Crystal structure of DND1-NANOS3-RNA complex

• PDB DOI: https://doi.org/10.2210/pdb9PQ8/pdb
• NAKB: 9PQ8

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-22 Released: 2026-09-30 
• Deposition Author(s): Qiu, C., Hall, T.M.T.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: in silico

Literature

DND1-NANOS3 shapes the PGC transcriptome via a heptanucleotide sequence in mRNA 3' UTRs.

Suzawa, M., Qiu, C., Polash, A.H., Yamaji, M., Jacob, A.A., Horikawa, W., Farroha, E.M., Barua, M., Feng, X., Liu, C., Williams, J.G., Randazzo, D., Sartorelli, V., Valkov, E., Yamaji, M., Hall, T.M.T., Hafner, M.

(2026) Mol Cell 86: 4250-4266.e9

• PubMed: 42833214 
• DOI: https://doi.org/10.1016/j.molcel.2026.09.010
• Primary Citation Related Structures: 
  9PQ8


• PubMed Abstract: 
  

  Primordial germ-cell survival requires joint function of the RNA-binding proteins (RBPs) DND1 and NANOS3, yet how they collaborate has not been established. Here, we discover a paradigm of "two-factor authorization," where RBPs with low (DND1) or no (NANOS3) sequence specificity jointly repress RNAs via a unique high-information-content motif. Tandem PAR-CLIP showed that a DND1-NANOS3 complex represses mRNAs of dozens of key epigenome and cell-cycle regulators, recognizing a heptamer (AUGAAUU) in their 3' UTRs. Genome editing of this element relieved DND1-NANOS3-mediated repression of CDK1 in vivo. A high-resolution structure revealed a continuous RNA-binding surface formed by DND1 and NANOS3, and biochemical analysis indicated that a NANOS3 intrinsically disordered region contributes to high affinity and sequence specificity of the complex. RBPs are typically studied individually, thus missing new specificities imparted by ribonucleoprotein complex formation. Our study hints that two-factor authorization is an underappreciated regulatory mechanism for safeguarding against aberrant expression of post-transcriptional regulatory factors.

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Organizational Affiliation: 
• RNA Molecular Biology Group, National Institute of Arthritis and Musculoskeletal and Skin Disease, NIH, Bethesda, MD 20892, USA.
Epigenetics and RNA Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; RNA Biology Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA.
Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Disease, NIH, Bethesda, MD 20892, USA.
Transgenic Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA.
Light Imaging Section, National Institute of Arthritis and Musculoskeletal and Skin Disease, NIH, Bethesda, MD 20892, USA.
RNA Biology Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA.
Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA. Electronic address: [e-mail].
Epigenetics and RNA Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA. Electronic address: [e-mail].
RNA Molecular Biology Group, National Institute of Arthritis and Musculoskeletal and Skin Disease, NIH, Bethesda, MD 20892, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.67 kDa 
• Atom Count: 2,576 
• Modeled Residue Count: 292 
• Deposited Residue Count: 301 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dead end protein homolog 1	A	231	Homo sapiens	Mutation(s): 0  Gene Names: DND1, RBMS4
UniProt
Find proteins for Q8IYX4 (Homo sapiens) Explore Q8IYX4  Go to UniProtKB:  Q8IYX4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanos homolog 3	B	60	Homo sapiens	Mutation(s): 0  Gene Names: NANOS3, NOS3
UniProt & NIH Common Fund Data Resources
Find proteins for P60323 (Homo sapiens) Explore P60323  Go to UniProtKB:  P60323
PHAROS:  P60323 GTEx:  ENSG00000187556

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA 5'-R(AP*UP*AP*UP*GP*AP*AP*UP*UP*U)-3'	C	10	Homo sapiens

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.669	α = 90
b = 43.58	β = 95.465
c = 73.484	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-30 
Deposition Author(s): Qiu, C., Hall, T.M.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ZIA-ES050165

Revision History  

• Version 1.0: 2026-09-30
  Type: Initial release
  
• Version 1.1: 2026-10-28
  Changes: Database references