6JVX

Crystal structure of RBM38 in complex with RNA

• PDB DOI: https://doi.org/10.2210/pdb6JVX/pdb
• NAKB: 6JVX

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


• Deposited: 2019-04-17 Released: 2020-01-01 
• Deposition Author(s): Qian, K., Li, M., Wang, J., Zhang, M., Wang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.221 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

Structural basis for mRNA recognition by human RBM38.

Qian, K., Li, M., Wang, J., Zhang, M., Wang, M.

(2020) Biochem J 477: 161-172

• PubMed: 31860021 
• DOI: https://doi.org/10.1042/BCJ20190652
• Primary Citation of Related Structures:  
  6JVX, 6JVY


• PubMed Abstract: 
  

  RNA-binding protein RBM38 was reported to bind the mRNA of several p53-related genes through its RRM domain and to up-regulate or down-regulate protein translation by increasing mRNA stability or recruitment of other effector proteins. The recognition mechanism, however, for RNA-binding of RBM38 remains unclear. Here, we report the crystal structure of the RRM domain of human RBM38 in complex with a single-stranded RNA. Our structural and biological results revealed that RBM38 recognizes G(U/C/A)GUG sequence single-stranded RNA in a sequence-specific and structure-specific manner. Two phenylalanine stacked with bases of RNA were crucial for RNA binding, and a series of hydrogen bonds between the base atoms of RNA and main-chain or side-chain atoms of RBM38 determine the sequence-specific recognition. Our results revealed the RNA-recognition mechanism of human RBM38 and provided structural information for understanding the RNA-binding property of RBM38.

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Organizational Affiliation: 

School of Life Sciences, Anhui University, Hefei, Anhui 230601, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 17.91 kDa 
• Atom Count: 964 
• Modelled Residue Count: 95 
• Deposited Residue Count: 140 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein 38	A	128	Homo sapiens	Mutation(s): 0  Gene Names: RBM38, RNPC1, SEB4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0Z9 (Homo sapiens) Explore Q9H0Z9  Go to UniProtKB:  Q9H0Z9
PHAROS:  Q9H0Z9 GTEx:  ENSG00000132819

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*G)-3')	B	12	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.221 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.809	α = 90
b = 78.809	β = 90
c = 66.982	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-01 
Deposition Author(s): Qian, K., Li, M., Wang, J., Zhang, M., Wang, M.

Revision History  

• Version 1.0: 2020-01-01
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description