5F5S

Crystal structure of the Prp38-MFAP1 complex of Homo sapiens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Scaffolding in the Spliceosome via Single alpha Helices.

Ulrich, A.K.C.Seeger, M.Schutze, T.Bartlick, N.Wahl, M.C.

(2016) Structure 24: 1972-1983

  • DOI: https://doi.org/10.1016/j.str.2016.09.007
  • Primary Citation of Related Structures:  
    5F5S, 5F5T, 5F5U, 5F5V

  • PubMed Abstract: 

    The spliceosomal B complex-specific protein Prp38 forms a complex with the intrinsically unstructured proteins MFAP1 and Snu23. Our binding and crystal structure analyses show that MFAP1 and Snu23 contact Prp38 via ER/K motif-stabilized single α helices, which have previously been recognized only as rigid connectors or force springs between protein domains. A variant of the Prp38-binding single α helix of MFAP1, in which ER/K motifs not involved in Prp38 binding were mutated, was less α-helical in isolation and showed a reduced Prp38 affinity, with opposing tendencies in interaction enthalpy and entropy. Our results indicate that the strengths of single α helix-based interactions can be tuned by the degree of helix stabilization in the unbound state. MFAP1, Snu23, and several other spliceosomal proteins contain multiple regions that likely form single α helices via which they might tether several binding partners and act as intermittent scaffolds that facilitate remodeling steps during assembly of an active spliceosome.


  • Organizational Affiliation

    Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany; Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489 Berlin, Germany. Electronic address: mwahl@zedat.fu-berlin.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38A181Homo sapiensMutation(s): 0 
Gene Names: PRPF38A
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NAV1 (Homo sapiens)
Explore Q8NAV1 
Go to UniProtKB:  Q8NAV1
PHAROS:  Q8NAV1
GTEx:  ENSG00000134748 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NAV1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Microfibrillar-associated protein 180Homo sapiensMutation(s): 0 
Gene Names: MFAP1
UniProt & NIH Common Fund Data Resources
Find proteins for P55081 (Homo sapiens)
Explore P55081 
Go to UniProtKB:  P55081
PHAROS:  P55081
GTEx:  ENSG00000140259 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55081
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.79α = 90
b = 66.79β = 90
c = 242.54γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyWA1126/7-1

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description