5HO4 | pdb_00005ho4

Crystal structure of hnRNPA2B1 in complex with 10-mer RNA

• PDB DOI: https://doi.org/10.2210/pdb5HO4/pdb
• NAKB: 5HO4

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens, synthetic construct
• Mutation(s): No 


• Deposited: 2016-01-19 Released: 2017-02-08 
• Deposition Author(s): Wu, B.X., Su, S.C., Gan, J.H., Ma, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1.

Wu, B.X., Su, S.C., Patil, D.P., Liu, H., Gan, J.H., Jaffrey, S.R., Ma, J.B.

(2018) Nat Commun 9: 420-420

• PubMed: 29379020 
• DOI: https://doi.org/10.1038/s41467-017-02770-z
• Primary Citation of Related Structures:  
  5HO4, 5WWE, 5WWF, 5WWG


• PubMed Abstract: 
  

  Human hnRNP A2/B1 is an RNA-binding protein that plays important roles in many biological processes, including maturation, transport, and metabolism of mRNA, and gene regulation of long noncoding RNAs. hnRNP A2/B1 was reported to control the microRNAs sorting to exosomes and promote primary microRNA processing as a potential m ⁶ A "reader." hnRNP A2/B1 contains two RNA recognition motifs that provide sequence-specific recognition of RNA substrates. Here, we determine crystal structures of tandem RRM domains of hnRNP A2/B1 in complex with various RNA substrates, elucidating specific recognitions of AGG and UAG motifs by RRM1 and RRM2 domains, respectively. Further structural and biochemical results demonstrate multivariant binding modes for sequence-diversified RNA substrates, supporting a RNA matchmaker mechanism in hnRNP A2/B1 function. Moreover, our studies in combination with bioinformatic analysis suggest that hnRNP A2/B1 may mediate effects of m ⁶ A through a "m ⁶ A switch" mechanism, instead of acting as a direct "reader" of m ⁶ A modification.

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Organizational Affiliation: 
• State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.76 kDa 
• Atom Count: 1,777 
• Modeled Residue Count: 189 
• Deposited Residue Count: 189 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterogeneous nuclear ribonucleoproteins A2/B1	A	179	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P22626 (Homo sapiens) Explore P22626  Go to UniProtKB:  P22626
PHAROS:  P22626 GTEx:  ENSG00000122566

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*AP*GP*GP*AP*CP*UP*AP*GP*C)-3')	B	10	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.604	α = 90
b = 38.959	β = 116.26
c = 70.442	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data processing
d*TREK	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-08 
Deposition Author(s): Wu, B.X., Su, S.C., Gan, J.H., Ma, J.B.

Revision History  

• Version 1.0: 2017-02-08
  Type: Initial release
  
• Version 1.1: 2017-03-01
  Changes: Structure summary
• Version 1.2: 2018-02-07
  Changes: Database references
• Version 1.3: 2019-05-22
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references