EncoMPASS
Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry
 Enter the 4-character identifier from the Protein Databank for your structure of interest (or XXXX_A for chain A of that structure) or use the Advanced Search to search by name or other features.
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Updated: Nov 30, 2023 9:00 |
6ytk_T
General information about
the structure of a protein chain.
The
orientation in the lipid bilayer is either taken directly from
OPM or generated using the related method, PPM; the title of the
protein is taken from the OPM database. However, the structure
and chain identifier may be modified from the coordinate file
retrievable from OPM or the PDB because of inconsistencies with
the definition of the biological unit. The processed coordinate
file of the whole protein is available for download.
General information about
the structure of a protein chain. The orientation in the lipid bilayer is either taken directly from OPM or generated using the related method, PPM; the title of the protein is taken from the OPM database. However, the structure and chain identifier may be modified from the coordinate file retrievable from OPM or the PDB because of inconsistencies with the definition of the biological unit. The processed coordinate file of the whole protein is available for download.
Calcium homeostasis modulator CALHM4, decamer
Complex:
Method:
ELECTRON MICROSCOPY
Resolution:
4.07 Ã…
Amino Acids:
267
Sequence:
Uniprot:
Coordinates
The structure shown may
be modified from the coordinate file retrievable from OPM or
from the PDB because of inconsistencies with the definition of
the biological unit.
Structure Relationships
General features of the current chain and its relationship to other structures in the database
Details include: (i) the predominant secondary structure (alpha or beta), (ii) the number of transmembrane domains according to our algorithm, and (iii-v) the number of neighbors according to comparisons using sequence (iii), structure (iv), or both (v).
Two chains are designated sequence neighbors when the sequence identity in the MUSCLE alignment is ≥0.85. Two chains are assigned as structural neighbors when the Fr-TM-Align structure alignment led to a TM-score of ≥0.6.
General features of the current chain and its relationship to other structures in the database
Details include: (i) the predominant secondary structure (alpha or beta), (ii) the number of transmembrane domains according to our algorithm, and (iii-v) the number of neighbors according to comparisons using sequence (iii), structure (iv), or both (v).
Two chains are designated sequence neighbors when the sequence identity in the MUSCLE alignment is ≥0.85. Two chains are assigned as structural neighbors when the Fr-TM-Align structure alignment led to a TM-score of ≥0.6.
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Plot of the relationships between the structural neighbors of this chain, which is placed in the center of the graph
Distances between this chain and its neighbors are scaled according to the TM-score of their structure alignment. Only chains that are classified as structural neighbors are included (TM-score of ≥0.6). The distance between neighbors also represents the corresponding TM-score, albeit in a more approximate way. Colors of dots represent the difference in the number of membrane-spanning segments in that neighbor. |
Structural and sequence relationships between the current protein chain and all other structures with a similar number of transmembrane domains
Each point shows the structural similarity, scored with the TM-score (1 for perfect match) and sequence identity between the current protein chain and another membrane protein chain. For reference, density contours from the distribution of all alignments in the database are shown. The two histograms along the axes indicate the number of alignments in each sector of the graph. Colors of dots represent the difference in the number of membrane-spanning segments in that neighbor. |
Regions of the protein that are more or less variable across structural homologues
Distances between each residue of the current chain and the corresponding residues in all structurally-aligned neighboring chains are plotted as a density of distances (in Å). Transmembrane segments of the current chain are indicated by gray boxes. |
Superpositions
Coordinates of the structure alignments.
Coordinates of all superpositions between the current protein chain and any chain with the same number of transmembrane regions. |
Cα-distances
Data for generating the Density scatter plot.
For each relationship between the current protein chain and all other structures with the same number of transmembrane regions, the distances between the aligned Cα are reported. The columns contain the residue index relative to the PDB file of the current protein and the distance between aligned Cα (in Å).
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Similarity
Sequence and structure alignment estimators.
For each structure and sequence alignment involving the current protein chain, the following are reported in this order: 1) secondary structure type and 2) number of transmembrane regions for the two chains; PDB code of 3) the first and 4) second chain; 5) sequence identity of the sequence alignment; 6) sequence identity of the sequence alignment retrieved from the structure superposition; 7) TM-score and 8) RMSD of the structure alignment. |
Standard Symmetry Detection
Raw output from two symmetry detection programs: CE-Symm and SymD
Structures were processed using CE-Symm and SymD with default options. For CE-Symm, if no symmetry was detected (reported as Order = C1), no image is provided. When symmetry is detected, different colors are used to represent the repeated elements with respect to a given symmetry axis; the PyMOL script for generating these representations is also provided. [Note that CE-Symm calculations were carried out with a random seed of 3, 5, or 10, from which the result with the highest number of repeats and/or highest number of aligned residues is reported.]
For SymD, which does not report information about the residues contributing to each repeat, the aligned residues (capital letters in the FASTA alignment files) are colored blue; the accompanying PyMOL visualization script generates this representation. [Note that SymD does not report symmetry order and so here, the order has been estimated based on the unit angle provided by the program.]
To interpret the repeat definitions, see the FAQ.
Raw output from two symmetry detection programs: CE-Symm and SymD
Structures were processed using CE-Symm and SymD with default options. For CE-Symm, if no symmetry was detected (reported as Order = C1), no image is provided. When symmetry is detected, different colors are used to represent the repeated elements with respect to a given symmetry axis; the PyMOL script for generating these representations is also provided. [Note that CE-Symm calculations were carried out with a random seed of 3, 5, or 10, from which the result with the highest number of repeats and/or highest number of aligned residues is reported.]
For SymD, which does not report information about the residues contributing to each repeat, the aligned residues (capital letters in the FASTA alignment files) are colored blue; the accompanying PyMOL visualization script generates this representation. [Note that SymD does not report symmetry order and so here, the order has been estimated based on the unit angle provided by the program.]
To interpret the repeat definitions, see the FAQ.
CE-Symm 2.2
| Order: | C1 |
| Angle: | 11.58 |
| Translation: | 9.04 |
| RMSD: | 0.0 |
| TM-Score: | 0.0 |
| Coverage: | 0.0 |
| See additional CE-Symm data |
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View
alignment(s)
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SymD 1.6
| Order: | 30.0 |
| Angle: | 12.2 |
| Translation: | -14.73 |
| RMSD: | 3.276 |
| TM-Score: | 0.24 |
| Coverage: | 0.28 |
| See additional SymD data |
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View
alignment(s)
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Multi-step Symmetry Detection
Consensus results from processing with SymD, CE-Symm, and QuatSymm with default and customized parameters
These results were obtained by from processing the SymD, CE-Symm, and QuatSymm results, and filtering using rules that take into account the restraints imposed by the membrane environment (e.g., an alpha-helical repeat should contain at least two transmembrane spans to be functionally relevant) and that consider coverage and symmetry levels. Only symmetries between repeats that are at least partially located in the membrane are considered. If independent symmetries were detected (i.e. symmetries that involve completely different and unrelated sets of repeats), the data presented for them are separated by "and".
Consensus results from processing with SymD, CE-Symm, and QuatSymm with default and customized parameters
These results were obtained by from processing the SymD, CE-Symm, and QuatSymm results, and filtering using rules that take into account the restraints imposed by the membrane environment (e.g., an alpha-helical repeat should contain at least two transmembrane spans to be functionally relevant) and that consider coverage and symmetry levels. Only symmetries between repeats that are at least partially located in the membrane are considered. If independent symmetries were detected (i.e. symmetries that involve completely different and unrelated sets of repeats), the data presented for them are separated by "and".
No symmetry found in the membrane-bound region during analysis.
Symmetry Inferred From Neighbors
Inferred symmetry from a homologous chain
If a homologous protein structure (see Structure Relationships section) contained a symmetry determined during Symmetry Analysis to be of higher coverage or higher symmetry order than that of the original protein, the symmetry of the homolog has been "transferred" to the current chain, by identifying the equivalent sections of the structure. The TM-Score, RMSD, coverage, and alignments were then re-calculated for these sections following a procedure identical to the one implemented in CE-Symm. This procedure allows for repeats and symmetries to be tracked across very different conformations of dynamic membrane proteins, as well as across protein folds.
Inferred symmetry from a homologous chain
If a homologous protein structure (see Structure Relationships section) contained a symmetry determined during Symmetry Analysis to be of higher coverage or higher symmetry order than that of the original protein, the symmetry of the homolog has been "transferred" to the current chain, by identifying the equivalent sections of the structure. The TM-Score, RMSD, coverage, and alignments were then re-calculated for these sections following a procedure identical to the one implemented in CE-Symm. This procedure allows for repeats and symmetries to be tracked across very different conformations of dynamic membrane proteins, as well as across protein folds.
| Template: | 6lyg_C |
| Template Order: | C2 |
| Angle: | 166.82 |
| Translation: | 8.3 |
| RMSD: | 3.32 |
| TM-Score: | 0.29 |
| Coverage: | 0.38 |
| Aligned Residues: | 101 |
| Number of Repeats: | 2 |
| Repeat Length: | 53 |
| Levels: | 1 |
| Topology: | Antiparallel |
| Angle with Membrane Normal: | 94.83 |
| Repeats: | |
| View alignment | |