Ortholog conservation:

The wild-type residue G27 is conserved at 98% among the CFTR orthologs

*AAPI: Alignment Average Percentage Identity
**AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 27). AAPIR appears in green if it is more than 10% compared to AAPI, in red if less than 10%.
Click here for more details on the alignment.

CYSMA's visualizing modules for Ortholog conservation:

⬇ Download the region alignment (50 residues, Fasta format)
⬇ Download the CFTR phylogenic tree

Display methods

Domain conservation:

The residue p.Gly27 belongs to the domain N-ter.

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N-ter: N-terminal region is a cytosolic region, also called the "lasso motif" because of its shape.
The first 40 residues are partially inserted into the membrane, while the end form the "lasso" helix (Zhang et al., 2016).

	N-terminal region is a cytosolic region, also called the "lasso motif" because of its shape. The first 40 residues are partially inserted into the membrane, while the end form the "lasso" helix (Zhang et al., 2016).

N-ter of CF Transmembrane conductance Regulator domain alignment including p.Gly27 residue.

***AAPID: Alignment Average Percentage Identity of the Domain (positions are indicated).
^!AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 27). AAPIR appears in green if it is more than 10% compared to AAPID, in red if less than 10%.

The wild-type residue G27 belongs to the N-ter domain and is conserved at 78.86% among the N-ter homologs (97 / 123 N-ter homologs)
The variant G27R has never been found among the N-ter homologs

Divergencies show the amino acids which have been selected in the evolution. Residues present in more than 10% of the sequences are highlighted in blue.
Please note that CYSMA does not consider splicing alterations.
Refer to the Help page for more details.

CYSMA's visualizing modules for N-ter domain conservation:

Display methods

Secondary structure analysis:

Residue p.Gly27 is predicted to belong to a loop. Probability is 0.452.

Direct environment is as follow:

I	L	R	K	G27	Y	R	Q	R

Display methods

3D analysis:

Models provided and analysed by CYSMA must be considered as predictions, therefore be careful when interpreting the results. All efforts have been made to build structures of quality, however, they are provided with NO WARRANTY as to their accuracy with the real biological molecules studied.

Wild type and predicted mutant structures have been compared. You will find the results below.

• Overall quality of the structure:
  
  

  PDB template	Sequence identity*	MolProbity bad rotamers	MolProbity Ramachandran outliers	MolProbity Ramachandran favored
  5UAK	99.8 %	18/1313 - 1.37 %	17/1478 - 1.15 %	1360/1478 - 92.2 %

  
  
  

• Click on the MolProbity logo for complete details on the structure quality
  
  
  
  

• This model is made of 37 α helices and of 20 β strands (and is mainly composed of helices (739 residues in helices against 102 in strands, for a total of 1480 amino acids)).
  
  
• 3D structures predicts G27 to be located in an α helice (which differs from PsiPred prediction) and R27 in an α helice.
  

  Observed frequencies in α helices:
  G: 0.76
  R: 1.11

  Moreover, the residue is located in the last turn (C3) of this α helice (which contains 11 residues).
  C3 propensities of wild-type and mutant residues are 0.33 and 1.25.
  A potential Side chain interaction of the type i,i-4 has been detected between mutant residue and ILE23.
  This interaction presents an attracting energy of -0.22 kcal/mol.
  
  



CYSMA's modules to download the 3D structures:



Chech 3D coverage of CFTR models ⬇ Download the wild-type 3D structure (PDB format) ⬇ Download the mutant 3D model (PDB format)





CYSMA's 3D Automatic Annotation:





WARNING!
The experimental 3D structure used for our predictions is the complete human CFTR structure which have been solved at a 3.7 Å resolution using cryo-electron microscopy (PDB: 5UAK; Liu et al. 2017).
The overall resolution is fairly low so the CYSMA's 3D Automatic Annotation pipeline might have missed some important structural effects.




• Replacement of a glycine is likely to rigidify the local structure
  
  
• Solvent accessibility: the wild-type G27 and the mutant G27R are predicted to be buried
  
  
• The two residues have a different polarity, which could interfere with hydrogen-bonding capabilities
  
  
• The two residues have different charge properties, which could interfere with ionic bonds or potential inter- or intra-molecular interactions
  
  
• Hydrogen bond network:
  

  G27	R27
  none	distance: 4.04 Å / angle: 2.02 rad between ARG 27 NE and THR 1036 O

  
  
  
• The mutant residue is not predicted to introduce steric clashes
  

  G27	R27
  none	none

  
  
  

CYSMA's 3D visualizing module:



• If you want to investigate further the structures, you can use the JSmol applets of the wild-type (left) and mutant (right) structures.
  
  Click on the JSmol applets' link to hide it.
  You have a full access to Jmol commands with a simple right click on one applet.
  
  
  
  
  

  G27 (wild-type)	R27 (mutant)

  
                Slab       Spin on/off       Show measurements       Change background       Sharper/Faster                    

  
  JSmol Legends:
  The residue at the position 27 is located in the center, labelled in yellow and surrounded by its neighboring residues (distance < 5 Å).
  Van der Waals contacts with the residue 27 are represented by dotted lines.
  Amino acids involved in H-bonds with the residue 27 are labelled in blue.
  Amino acids involved in steric clashes with the residue 27 are labelled in red.

  
  Display JSmol complete legends

  The overall structure of the complete human CFTR is represented in ribbon diagrams (click on the Reset button to visualize the overall CFTR structure).
  The membrane-spanning domain MSD1 is represented in blue and MSD2 in light blue.The nucleotide-binding domain NBD1 is represented in orange, NBD2 in light salmon.The lasso domain is shown in red and the R domain in green.

  Display Molecular Modelling methods

  The 3D structures used in CYSMA are models based on the CFTR experimental 3D structure in the channel-closed conformation (PDB: 5UAK; resolution: 3.9 Å).
  In the wild-type model, the (missing) loops and the (missing) R domain were built de novo using the software Modeller. For the variant models, the point mutation (homology modelling) are made on the fly with Modeller (more). Each structure has been assessed with MolProbity⁽¹⁹⁾. Msms⁽²⁰⁾ is used to calculate solvent accessibility, and STRIDE⁽²¹⁾ (plus stride2pdb) for secondary structure assignment.
  Secondary structure analyses in 3D models uses side chain interaction energies reviewed in ⁽²³⁾, as well as amino-acids propensities for N-caps, N1-N3, helix middle, C3-C1 and C-caps extracted from ⁽²⁴⁾(PDB values).
  Structural properties are calculated using an in-house developped program based for the USMA's 3D Automatic Annotation pipeline.

  Refer to the Help page for more details.

• SIFT prediction: variant G27R is predicted to be damaging (score: 0)


• PPH2 prediction: variant G27R is predicted to be damaging (score: 1)


• UNIPROT annotations
  

  The variation is not reported in Uniprot.

• Click on the LOVD picture to check if a variant is described at position 27    
  
  
  
  



• Graphical display of the region at NCBI (including SNPs)



• CYSMA Report:

  
  

  Report for p.Gly27Arg variant

  CFTR orthologs conservation	The wild-type residue G27 is conserved at 98% among the CFTR orthologs
  N-ter homologs conservation	The wild-type residue G27 belongs to the N-ter domain and is conserved at 78.86% among the N-ter homologs (97 / 123 N-ter homologs) The variant G27R has never been found among the N-ter homologs
  Structural effects	Replacement of a glycine is likely to rigidify the local structure Solvent accessibility: the wild-type G27 and the mutant G27R are predicted to be buried The two residues have a different polarity, which could interfere with hydrogen-bonding capabilities The two residues have different charge properties, which could interfere with ionic bonds or potential inter- or intra-molecular interactions The mutant residue is not predicted to introduce steric clashes
  Allele frequency	The variant has not been reported in gnomAD
  Clinical significance	The variant G27R has been been described as not provided - no assertion provided - (ClinVar for more details)
  CFTR-France	The variant G27R might correspond to: NM_000492.3:c.79G>A, which is reported to be unclassified ( CFTR-France for more details)
  Additional resources	SIFT prediction: variant G27R is predicted to be damaging (score: 0) PPH2 prediction: variant G27R is predicted to be damaging (score: 1)