Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.52 kDa 
• Atom Count: 1267 
• Modelled Residue Count: 129 
• Deposited Residue Count: 137 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2FY1

A dual mode of RNA recognition by the RBMY protein

• PDB DOI: 10.2210/pdb2FY1/pdb
• NDB: 2FY1

• Classification: STRUCTURAL PROTEIN/RNA
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-02-07 Released: 2007-02-06 
• Deposition Author(s): Skrisovska, L., Bourgois, C., Stefl, R., Kister, L., Wenter, P., Elliot, D., Stevenin, J., Allain, F.H.T.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 17 
• Selection Criteria: structures with the least restraint violations 

Literature

The testis-specific human protein RBMY recognizes RNA through a novel mode of interaction.

Skrisovska, L., Bourgeois, C.F., Stefl, R., Grellscheid, S.N., Kister, L., Wenter, P., Elliott, D.J., Stevenin, J., Allain, F.H.

(2007) EMBO Rep 8: 372-379

• PubMed: 17318228 
• DOI: 10.1038/sj.embor.7400910
• Primary Citation of Related Structures:  
  2FY1


• PubMed Abstract: 
  

The RBMY (RNA-binding motif gene on Y chromosome) protein encoded by the human Y chromosome is important for normal sperm development. Although its precise molecular RNA targets are unknown at present, it is suggested that human RBMY (hRBMY) participates in splicing in the testis. Using systematic evolution of ligands by exponential enrichment, we found that RNA stem-loops capped by a C(A)/(U)CAA pentaloop are high-affinity binding targets for hRBMY. Subsequent nuclear magnetic resonance structural determination of the hRBMY RNA recognition motif (RRM) in complex with a high-affinity target showed two distinct modes of RNA recognition. First, the RRM beta-sheet surface binds to the RNA loop in a sequence-specific fashion. Second, the beta2-beta3 loop of the hRBMY inserts into the major groove of the RNA stem. The first binding mode might be conserved in the paralogous protein heterogeneous nuclear RNP G, whereas the second mode of binding is found only in hRBMY. This structural difference could be at the origin of the function of RBMY in spermatogenesis.

---

Organizational Affiliation: 

Institute of Molecular Biology and Biophysics, ETH Zurich, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding motif protein, Y chromosome, family 1 member A1	B [auth A]	116	Homo sapiens	Mutation(s): 0  Gene Names: RBMY1A1, RBM1, RBM2, YRRM1, YRRM2
UniProt & NIH Common Fund Data Resources
Find proteins for P0DJD3 (Homo sapiens) Explore P0DJD3  Go to UniProtKB:  P0DJD3
PHAROS:  P0DJD3 GTEx:  ENSG00000234414

Entity ID: 1
Molecule	Chains	Length	Organism	Image
S1A stem-loop RNA	A [auth B]	21	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 17 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 2FY1 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-07 
• Released Date: 2007-02-06 
Deposition Author(s): Skrisovska, L., Bourgois, C., Stefl, R., Kister, L., Wenter, P., Elliot, D., Stevenin, J., Allain, F.H.T.

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-03-06
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy