6Y31

NG domain of human SRP54 T117 deletion mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.311 
  • R-Value Observed: 0.312 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia.

Juaire, K.D.Lapouge, K.Becker, M.M.M.Kotova, I.Michelhans, M.Carapito, R.Wild, K.Bahram, S.Sinning, I.

(2021) Structure 29: 15

  • DOI: https://doi.org/10.1016/j.str.2020.09.008
  • Primary Citation of Related Structures:  
    6Y2Z, 6Y30, 6Y31, 6Y32

  • PubMed Abstract: 

    The SRP54 GTPase is a key component of co-translational protein targeting by the signal recognition particle (SRP). Point mutations in SRP54 have been recently shown to lead to a form of severe congenital neutropenia displaying symptoms overlapping with those of Shwachman-Diamond syndrome. The phenotype includes severe neutropenia, exocrine pancreatic deficiency, and neurodevelopmental as well as skeletal disorders. Using a combination of X-ray crystallography, hydrogen-deuterium exchange coupled to mass spectrometry and complementary biochemical and biophysical methods, we reveal extensive structural defects in three disease-causing SRP54 variants resulting in critical protein destabilization. GTP binding is mostly abolished as a consequence of an altered GTPase core. The mutations located in conserved sequence fingerprints of SRP54 eliminate targeting complex formation with the SRP receptor as demonstrated in yeast and human cells. These specific defects critically influence the entire SRP pathway, thereby causing this life-threatening disease.


  • Organizational Affiliation

    Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 54 kDa protein
A, B, C, D
303Homo sapiensMutation(s): 0 
Gene Names: SRP54
EC: 3.6.5.4
UniProt & NIH Common Fund Data Resources
Find proteins for P61011 (Homo sapiens)
Explore P61011 
Go to UniProtKB:  P61011
PHAROS:  P61011
GTEx:  ENSG00000100883 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61011
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.311 
  • R-Value Observed: 0.312 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.356α = 90
b = 50.607β = 99.39
c = 181.629γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySI 586/6-1

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2021-01-20
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description