CHOYCE: Constraining HOmologY modelling with Cryo-Electron microscopy maps

Resources

Developed by

Reda Rawi

Acknowledgments

Maya Topf
Lee Whitmore

Please address enquiries to

Choyce-help

Documentation

Tutorial

TUTORIAL

CHOYCE is used for:

Homology modelling of protein three-dimensional structures

Fitting three-dimensional structures (created in 1.) into a Cryo-Electron microscopy density map

This example will introduce the use of CHOYCE:

Target sequence is subunit III of bovine heart cytochrome c oxidase (PDB: 1OCC, Chain C, residues 74-261)
Template structure is E. coli ubiquinol oxidase (PDB: 1FFT, chain C, residues 20-203)
Target and template share a sequence identity of approx. 22%

Note that we go through this tutorial to build models knowing only the amino acid sequence of the target (in fact in this case the 3D structure is available)

Input data

User Information

E-mail address:
A valid e-mail address for communicating with the user

MODELLER access key:
Valid MODELLER access key. Available at MODELLER web page MODELLER

CHOYCE provides two options:

Upload target and template sequences already aligned
Upload just the target and template sequences, and the alignment will be made

Option 1

A possible template-target sequence alignment created by MUSCLE:

Alignment

The template sequence has to be the upper one in the alignment!

>1FFT_C 20-203 (template)
DAGGTKIFGFWIYLMSDCILFSILFATY---AVLVNGTAGG---PTG-KDIFELPFVLVE TFLLLFSSITYGMAAIAMYKNNKSQVISWLALTWLFGAGFI---GMEIYEFHHLIVNGMG PDRSGFLSAFFALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDV VWICVFTVVYLMGA
>1OCC_C 74-261 (target)
AVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIHPLNPLEVPLLN TSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYYEAPFTISDGV- -----YGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDV VWLFLYVSIYWWGS

Template structure E. coli ubiquinol oxidase (PDB: 1FFT, chain C, residues 20-203)

Template structure

Number of models to built: 50

Option 2

Target sequence subunit III of bovine heart cytochrome c oxidase (PDB: 1OCC, Chain C, residues 74-261)

Target sequence

>1OCC_C 74-261
AVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIHPLNPLEVPLLN TSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYYEAPFTISDGV- -----YGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDV VWLFLYVSIYWWGS

Template structure E. coli ubiquinol oxidase (PDB: 1FFT, chain C, residues 20-203)

Template structure

Number of alignments to built (10 models per alignment): 50

CHOYCE operates with two density map formats:

Submit density map in MRC format
Submit density map in XPLOR format

Density map

10 Å Cryo-Electron microscopy density map of the target sequence

Density Map

Map format:

Map resolution:

Map origin:

x-coordinate:

-51.644

y-coordinate:

-294.19

z-coordinate:

-157.19

Cubic grid size:

Voxel size:

1.0135

After submission of the input data CHOYCE operates as follows:

Build the specified number of comparative models

Fit the comparative models ( from step 1. ) into the submitted Cryo-EM density map

Score the fitted models

Create a result web page, containing an ordered list with the scores and the corresponding 3D-structures of the generated models

Results

After some time one gets an e-mail with a link to the results.
The results web page for this example ( using Option 2 ):

Status

Your job tmp_1258016441 is finished

Results

3D-Models	CCZ	Normalized_DOPE
target.B9999_5Superposed.pdb	7.933	0.542
target.B9999_31Superposed.pdb	7.929	0.708
target.B9999_48Superposed.pdb	7.899	0.667
target.B9999_2Superposed.pdb	7.897	0.815
target.B9999_44Superposed.pdb	7.897	0.560
target.B9999_30Superposed.pdb	7.896	0.740
target.B9999_34Superposed.pdb	7.888	0.755
target.B9999_9Superposed.pdb	7.887	0.616
target.B9999_22Superposed.pdb	7.885	0.649
target.B9999_10Superposed.pdb	7.882	0.443
target.B9999_13Superposed.pdb	7.879	0.396
target.B9999_39Superposed.pdb	7.876	0.681
target.B9999_45Superposed.pdb	7.872	0.687
target.B9999_25Superposed.pdb	7.871	0.804
target.B9999_16Superposed.pdb	7.871	0.811
target.B9999_50Superposed.pdb	7.870	0.670
target.B9999_42Superposed.pdb	7.868	0.646
target.B9999_35Superposed.pdb	7.867	0.698
target.B9999_40Superposed.pdb	7.861	0.545
target.B9999_36Superposed.pdb	7.861	0.638
target.B9999_19Superposed.pdb	7.861	0.546
target.B9999_6Superposed.pdb	7.860	0.599
target.B9999_8Superposed.pdb	7.857	0.734
target.B9999_26Superposed.pdb	7.855	0.569
target.B9999_3Superposed.pdb	7.853	0.781
target.B9999_49Superposed.pdb	7.852	0.449
target.B9999_28Superposed.pdb	7.842	0.464
target.B9999_15Superposed.pdb	7.841	0.640
target.B9999_43Superposed.pdb	7.839	0.648
target.B9999_7Superposed.pdb	7.838	0.461
target.B9999_4Superposed.pdb	7.836	0.672
target.B9999_12Superposed.pdb	7.836	0.556
target.B9999_14Superposed.pdb	7.834	0.691
target.B9999_24Superposed.pdb	7.830	0.475
target.B9999_27Superposed.pdb	7.830	0.677
target.B9999_11Superposed.pdb	7.827	0.347
target.B9999_20Superposed.pdb	7.827	0.642
target.B9999_47Superposed.pdb	7.826	0.763
target.B9999_38Superposed.pdb	7.822	0.549
target.B9999_32Superposed.pdb	7.821	0.535
target.B9999_46Superposed.pdb	7.812	0.727
target.B9999_17Superposed.pdb	7.811	0.604
target.B9999_29Superposed.pdb	7.810	0.589
target.B9999_23Superposed.pdb	7.803	0.560
target.B9999_37Superposed.pdb	7.799	0.652
target.B9999_18Superposed.pdb	7.776	0.607

Illustration of the target crystal structure 1OCC, Chain C, residues 74-261 ( green ) (in general not available) and the best model ( yellow ) from CHOYCE.