Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.92 kDa 
• Atom Count: 2627 
• Residue Count: 306 
• Unique protein chains: 2

2F9D

2.5 angstrom resolution structure of the spliceosomal protein p14 bound to region of SF3b155

• DOI: 10.2210/pdb2F9D/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-12-05 Released: 2006-01-24 
• Deposition Author(s): Schellenberg, M.J., Edwards, R.A., Ritchie, D.B., Glover, J.N.M., Macmillan, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.276 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 

Literature

Crystal structure of a core spliceosomal protein interface

Schellenberg, M.J., Edwards, R.A., Ritchie, D.B., Kent, O.A., Golas, M.M., Stark, H., Glover, J.N.M., Macmillan, A.M.

(2006) Proc Natl Acad Sci U S A 103: 1266-1271

• PubMed: 16432215 
• DOI: 10.1073/pnas.0508048103
• Primary Citation of Related Structures:  
  2F9D, 2F9J


• PubMed Abstract: 
  

The precise excision of introns from precursor mRNAs (pre-mRNAs) in eukaryotes is accomplished by the spliceosome, a complex assembly containing five small nuclear ribonucleoprotein (snRNP) particles. Human p14, a component of the spliceosomal U2 and U11/U12 snRNPs, has been shown to associate directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. Here we report the 2.5-A crystal structure of a complex containing p14 and a peptide derived from the p14-associated U2 snRNP component SF3b155. p14 contains an RNA recognition motif (RRM), the surface of which is largely occluded by a C-terminal alpha-helix and a portion of the SF3b155 peptide. An analysis of RNA.protein crosslinking to wild-type and mutant p14 shows that the branch adenosine directly interacts with a conserved aromatic within a pocket on the surface of the complex. This result, combined with a comparison of the structure with known RRMs and pseudoRRMs as well as model-building by using the electron cryomicroscopy structure of a spliceosomal U11/U12 di-snRNP, suggests that p14.SF3b155 presents a noncanonical surface for RNA recognition at the heart of the mammalian spliceosome.

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Organizational Affiliation: 

Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-mRNA branch site protein p14	A, B	125	Homo sapiens	Mutation(s): 0  Gene Names: SF3B14, SF3B6, SAP14, SF3B14A, CGI-110, HSPC175, HT006
Find proteins for Q9Y3B4 (Homo sapiens) Explore Q9Y3B4  Go to UniProtKB:  Q9Y3B4
NIH Common Fund Data Resources
PHAROS:  Q9Y3B4 GTEx:  ENSG00000115128

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Splicing factor 3B subunit 1	P, Q	43	Homo sapiens	Mutation(s): 3  Gene Names: SF3B1, SAP155
Find proteins for O75533 (Homo sapiens) Explore O75533  Go to UniProtKB:  O75533
NIH Common Fund Data Resources
PHAROS:  O75533 GTEx:  ENSG00000115524

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	P,Q	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.276 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.87	α = 90
b = 115.227	β = 90
c = 82.536	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-05 
• Released Date: 2006-01-24 
Deposition Author(s): Schellenberg, M.J., Edwards, R.A., Ritchie, D.B., Glover, J.N.M., Macmillan, A.M.

Revision History 

• Version 1.0: 2006-01-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description