Ortholog conservation:

The wild-type residue L145 is conserved at 100% among the CFTR orthologs

*AAPI: Alignment Average Percentage Identity
**AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 145). 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.Leu145 belongs to the domain MSD1.

69

422

MSD1: is the membrane-spanning domain 1, composed of six transmembrane helices (TM1-TM6).
Four of the six TMs protrude into the cytosol to form the intracellular loops ICL1 (between TM2 and TM3) and ICL2 (between TM4 and TM5). ICL1 contacts NBD1 at the level of the ATP-binding site, while ICL2 binds in a groove located at the surface of NBD2.

	is the membrane-spanning domain 1, composed of six transmembrane helices (TM1-TM6). Four of the six TMs protrude into the cytosol to form the intracellular loops ICL1 (between TM2 and TM3) and ICL2 (between TM4 and TM5). ICL1 contacts NBD1 at the level of the ATP-binding site, while ICL2 binds in a groove located at the surface of NBD2.

MSD1 of CF Transmembrane conductance Regulator domain alignment including p.Leu145 residue.

***AAPID: Alignment Average Percentage Identity of the Domain (positions are indicated).
^!AAPIR: Alignment Average Percentage Identity of the Region (20 residues surrounding position 145). AAPIR appears in green if it is more than 10% compared to AAPID, in red if less than 10%.

The wild-type residue L145 belongs to the MSD1 domain and is conserved at 26.57% among the MSD1 homologs (114 / 429 MSD1 homologs)
The variant L145V has been found among the MSD1 homologs with a non significant frequency: 4.20% (18 / 429 MSD1 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 MSD1 domain conservation:

Display methods

Secondary structure analysis:

Residue p.Leu145 is predicted to belong to an α helice. Probability is 0.993.

Direct environment is as follow:

A	I	F	G	L145	H	H	I	G

Observed frequencies in α helices:
L: 1.16
V: 0.88

Mutant residue is less observed in this type of structure.

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 L145 to be located in an α helice (which confirms PsiPred prediction) and V145 in an α helice.
  Moreover, the residue is located in the core of this α helice (which contains 50 residues).
  Helix interior propensities of wild-type and mutant residues are 1.44 and 1.03.
  Mutant residue has less affinity for the middle of helices.
  
  



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.




• Solvent accessibility: the wild-type L145 and the mutant L145V are predicted to be buried
  
  
• Hydrogen bond network:
  

  L145	V145
  none	none

  
  
  
• The mutant residue is predicted to form less hydrophobic interactions than the wild-type
  The wild-type residue LEU is buried and is likely to belong to a hydrophobic pocket or core. This hydrophobic core is reduced in the mutant residue VAL, which might slightly destabilize the region
  
  

  L145

  V145

  4.73 Å between LEU 145 CD2 and ILE 148 CD1 4.12 Å between LEU 145 CB and ALA 196 CB 4.83 Å between LEU 145 CG and ALA 196 CB 4.25 Å between LEU 145 CD1 and ALA 196 CB 4.70 Å between LEU 145 CD1 and HIS 199 CB 4.57 Å between LEU 145 CG and TYR 84 CB 4.51 Å between LEU 145 CD2 and TYR 84 CB 4.93 Å between LEU 145 CG and LEU 88 CD1 4.53 Å between LEU 145 CD1 and LEU 88 CG 4.84 Å between LEU 145 CD1 and ILE 142 CD1 4.89 Å between LEU 145 CG and PHE 81 CE1 4.58 Å between LEU 145 CD2 and PHE 81 CG

  4.46 Å between VAL 145 CB and ALA 196 CB 4.35 Å between VAL 145 CG1 and ALA 196 CB 4.08 Å between VAL 145 CG2 and TYR 84 CB 4.79 Å between VAL 145 CG2 and LEU 88 CD1 3.96 Å between VAL 145 CG1 and LEU 195 CB 4.43 Å between VAL 145 CG1 and PHE 81 CD1

  
  
  

For hydrophobic effects, the important point is the number of residues involved more than the number of interactions.



• The mutant residue is not predicted to introduce steric clashes
  

  L145	V145
  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.
  
  
  
  
  

  L145 (wild-type)	V145 (mutant)

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

  
  JSmol Legends:
  The residue at the position 145 is located in the center, labelled in yellow and surrounded by its neighboring residues (distance < 5 Å).
  Van der Waals contacts with the residue 145 are represented by dotted lines.
  Amino acids involved in H-bonds with the residue 145 are labelled in blue.
  Amino acids involved in steric clashes with the residue 145 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 L145V is predicted to be damaging (score: 0)


• PPH2 prediction: variant L145V is predicted to be possibly damaging (score: 0.811)


• UNIPROT annotations
  

  The variation is not reported in Uniprot.

• Click on the LOVD picture to check if a variant is described at position 145    
  
  
  
  



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



• CYSMA Report:

  
  

  Report for p.Leu145Val variant

  CFTR orthologs conservation	The wild-type residue L145 is conserved at 100% among the CFTR orthologs
  MSD1 homologs conservation	The wild-type residue L145 belongs to the MSD1 domain and is conserved at 26.57% among the MSD1 homologs (114 / 429 MSD1 homologs) The variant L145V has been found among the MSD1 homologs with a non significant frequency: 4.20% (18 / 429 MSD1 homologs)
  Structural effects	Solvent accessibility: the wild-type L145 and the mutant L145V are predicted to be buried The mutant residue is predicted to form less hydrophobic interactions than the wild-type The wild-type residue LEU is buried and is likely to belong to a hydrophobic pocket or core. This hydrophobic core is reduced in the mutant residue VAL, which might slightly destabilize the region The mutant residue is not predicted to introduce steric clashes
  Allele frequency	The variant has not been reported in gnomAD
  Clinical significance	The variant L145V has not been reported in ClinVar
  CFTR-France	The variant L145V might correspond to: NM_000492.3:c.433C>G, which is reported to be unclassified ( CFTR-France for more details)
  Additional resources	SIFT prediction: variant L145V is predicted to be damaging (score: 0) PPH2 prediction: variant L145V is predicted to be possibly damaging (score: 0.811)