EncoMPASS
Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry
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Updated: Nov 30, 2023 9:00 |
2dyr
General information about the
complete biological unit of each membrane protein structure.
The orientation in the lipid bilayer is either taken
directly from OPM or generated using the related routine PPM;
the title is taken from the OPM database. However, the structure
shown may be modified from the coordinate file retrievable from
OPM or the PDB, because of inconsistencies with the definition
of the biological unit. The coordinate file is downloadable, as
is a PyMOL script for visualizing the structure.
General information about the
complete biological unit of each membrane protein structure. The orientation in the lipid bilayer is either taken directly from OPM or generated using the related routine PPM; the title is taken from the OPM database. However, the structure shown may be modified from the coordinate file retrievable from OPM or the PDB, because of inconsistencies with the definition of the biological unit. The coordinate file is downloadable, as is a PyMOL script for visualizing the structure.
Mitochondrial cytochrome c oxidase
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
A list of chains contained in
the biological unit and their relationships to other structures
in the database.
Details include: (i) the predominant secondary
structure (alpha or beta), (ii) the number of transmembrane
regions 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.
A list of chains contained in
the biological unit and their relationships to other structures
in the database. Details include: (i) the predominant secondary structure (alpha or beta), (ii) the number of transmembrane regions 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.
| Member | Class | TM Domains | Seq Neighbors | Struct Neighbors | All Neighbors | Symmetry |
|---|---|---|---|---|---|---|
| 2dyr_A | alpha | 12 | 99 | 186 | 186 | C3 |
| 2dyr_B | alpha | 2 | 98 | 128 | 128 | na |
| 2dyr_C | alpha | 7 | 99 | 113 | 113 | C2 |
| 2dyr_D | alpha | 1 | 98 | 917 | 917 | na |
| 2dyr_G | alpha | 1 | 98 | 557 | 557 | na |
| 2dyr_I | alpha | 1 | 98 | 1258 | 1258 | na |
| 2dyr_J | alpha | 1 | 98 | 1197 | 1197 | na |
| 2dyr_K | alpha | 1 | 98 | 179 | 179 | na |
| 2dyr_L | alpha | 1 | 98 | 178 | 178 | na |
| 2dyr_M | alpha | 1 | 98 | 135 | 135 | na |
| 2dyr_N | alpha | 12 | 99 | 186 | 186 | C3 |
| 2dyr_O | alpha | 2 | 98 | 128 | 128 | na |
| 2dyr_P | alpha | 7 | 99 | 113 | 113 | C2 |
| 2dyr_Q | alpha | 1 | 98 | 917 | 917 | na |
| 2dyr_T | alpha | 1 | 98 | 557 | 557 | na |
| 2dyr_V | alpha | 1 | 98 | 1258 | 1258 | na |
| 2dyr_W | alpha | 1 | 98 | 1197 | 1197 | na |
| 2dyr_X | alpha | 1 | 98 | 179 | 179 | na |
| 2dyr_Y | alpha | 1 | 98 | 178 | 178 | na |
| 2dyr_Z | alpha | 1 | 98 | 135 | 135 | na |
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 and the PyMOL
script for generating the representations is 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 repeats information,
the aligned residues (capital letters in the FASTA files) are
colored blue and the accompanying PyMOL script generates this
representation. [Note that SymD does not report symmetry order
and so here, the order has been predicted 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 and the PyMOL script for generating the representations is 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 repeats information, the aligned residues (capital letters in the FASTA files) are colored blue and the accompanying PyMOL script generates this representation. [Note that SymD does not report symmetry order and so here, the order has been predicted based on the unit angle provided by the program.]
To interpret the repeat definitions, see the FAQ.
CE-Symm 2.2
| Order: | C1 |
| Angle: | 180.00 |
| Translation: | 0.00 |
| RMSD: | 0.0 |
| TM-Score: | 0.0 |
| Coverage: | 1.0 |
| See additional CE-Symm data |
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View
alignment(s)
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SymD 1.6
| Order: | 2 |
| Angle: | 180.0 |
| Translation: | 0.0 |
| RMSD: | 0.137 |
| TM-Score: | 1.0 |
| Coverage: | 1.0 |
| 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 filtered 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. Note that for multi-chain complexes the order of the
chains is important for symmetry detection and is therefore also
reported.
Consensus results from
processing with SymD, CE-Symm and QuatSymm with default and customized
parameters These results were filtered 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. Note that for multi-chain complexes the order of the chains is important for symmetry detection and is therefore also reported.
| Chain Order: | A;N;B;O;C;P;D;Q;G;T;I;V;J;W;K;X;L;Y;M;Z; |
| Order: | C2 |
| Angle: | 180.0 |
| Translation: | 0.0 |
| RMSD: | 0.14 |
| TM-Score: | 1.0 |
| Coverage: | 1.0 |
| Aligned Residues: | 2986 |
| Number of Repeats: | 2 |
| Repeat Length: | 1493 |
| Levels: | 1 |
| Topology: | Parallel |
| Angle with Membrane Normal: | -89.43 |
| Repeats: |
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View alignment(s)
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