4WNF

Crystal structure of the oxidized TPR domain of LGN in complex with Frmpd4/Preso1 at 2.9 Angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for the recognition of the scaffold protein Frmpd4/Preso1 by the TPR domain of the adaptor protein LGN

Takayanagi, H., Yuzawa, S., Sumimoto, H.

(2015) Acta Crystallogr F Struct Biol Commun 71: 175-183

  • DOI: 10.1107/S2053230X14028143
  • Primary Citation of Related Structures:  
    4WND, 4WNE, 4WNF, 4WNG

  • PubMed Abstract: 

    • The adaptor protein LGN interacts via the N-terminal domain comprising eight tetratricopeptide-repeat (TPR) motifs with its partner proteins mInsc, NuMA, Frmpd1 and Frmpd4 in a mutually exclusive manner. Here, the crystal structure of the LGN TPR domain ...

    The adaptor protein LGN interacts via the N-terminal domain comprising eight tetratricopeptide-repeat (TPR) motifs with its partner proteins mInsc, NuMA, Frmpd1 and Frmpd4 in a mutually exclusive manner. Here, the crystal structure of the LGN TPR domain in complex with human Frmpd4 is described at 1.5 Å resolution. In the complex, the LGN-binding region of Frmpd4 (amino-acid residues 990-1011) adopts an extended structure that runs antiparallel to LGN along the concave surface of the superhelix formed by the TPR motifs. Comparison with the previously determined structures of the LGN-Frmpd1, LGN-mInsc and LGN-NuMA complexes reveals that these partner proteins interact with LGN TPR1-6 via a common core binding region with consensus sequence (E/Q)XEX4-5(E/D/Q)X1-2(K/R)X0-1(V/I). In contrast to Frmpd1, Frmpd4 makes additional contacts with LGN via regions N- and C-terminal to the core sequence. The N-terminal extension is replaced by a specific α-helix in mInsc, which drastically increases the direct contacts with LGN TPR7/8, consistent with the higher affinity of mInsc for LGN. A crystal structure of Frmpd4-bound LGN in an oxidized form is also reported, although oxidation does not appear to strongly affect the interaction with Frmpd4.

    Organizational Affiliation: 

    Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
G-protein-signaling modulator 2 A406Homo sapiensMutation(s): 0 
Gene Names: GPSM2, LGN
Find proteins for P81274 (Homo sapiens)
Explore P81274 
Go to UniProtKB:  P81274
NIH Common Fund Data Resources
PHAROS:  P81274
GTEx:  ENSG00000121957
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FERM and PDZ domain-containing protein 4 B53Homo sapiensMutation(s): 0 
Gene Names: FRMPD4, KIAA0316, PDZD10, PDZK10
Find proteins for Q14CM0 (Homo sapiens)
Explore Q14CM0 
Go to UniProtKB:  Q14CM0
NIH Common Fund Data Resources
PHAROS:  Q14CM0
GTEx:  ENSG00000169933
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.599α = 90
b = 92.599β = 90
c = 175.238γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Derived calculations, Refinement description