EncoMPASS

Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry

National Institute of Neurological Disorders & Stroke

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Updated: August 13, 2025 9:00
6k33 : EncoMPASS

6k33
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.

Photosystem I, with light-harvesting complex

Number of Chains: 36
Number of TM Chains: 30
Amino Acids: 8454
Method: ELECTRON MICROSCOPY
Resolution: Å
Uniprot: P25936       P0A409       P0A417       P0A422       P23318      
Links: PDB      OPM      PDBTM 
MemProtMD 
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.

Member Class TM Domains Seq Neighbors Struct Neighbors All Neighbors Symmetry
6k33_A alpha 11 59 204 204 C3
6k33_B alpha 11 45 204 204 C3
6k33_F alpha 1 19 87 87 na
6k33_G alpha 1 20 375 375 na
6k33_H alpha 1 19 517 517 na
6k33_I alpha 2 19 23 27 na
6k33_J alpha 3 20 91 91 na
6k33_K alpha 1 20 226 226 na
6k33_L alpha 1 23 312 316 na
6k33_M alpha 6 11 215 215 C3
6k33_N alpha 6 11 215 215 C3
6k33_O alpha 6 11 215 215 C3
6k33_P alpha 6 11 215 215 na
6k33_Q alpha 6 11 215 215 C3
6k33_R alpha 6 11 215 215 C3
6k33_S alpha 11 59 204 204 C3
6k33_T alpha 11 45 204 204 C3
6k33_X alpha 1 19 87 87 na
6k33_Y alpha 1 20 375 375 na
6k33_Z alpha 1 19 517 517 na
6k33_a alpha 2 19 23 27 na
6k33_b alpha 3 20 91 91 na
6k33_c alpha 1 20 226 226 na
6k33_d alpha 1 23 312 316 na
6k33_e alpha 6 11 215 215 C3
6k33_f alpha 6 11 215 215 C3
6k33_g alpha 6 11 215 215 C3
6k33_h alpha 6 11 215 215 C3
6k33_i alpha 6 11 215 215 C3
6k33_j alpha 6 11 215 215 C3
Symmetry analysis has been carried out for this structure, using two different strategies named "Standard Symmetry Detection" and "Multi-step Symmetry Detection". See section titles for details.

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.

CE-Symm   2.2

Order: R
Angle: 119.89
Translation: 0.13
RMSD: 0.2
TM-Score: 1.0
Coverage: 1.0
See additional CE-Symm data
View alignment(s)

SymD   1.6

Order: 38
Angle: 9.6
Translation: -0.01
RMSD: 0.339
TM-Score: 0.5
Coverage: 0.5
See additional SymD data
View alignment(s)

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.

Chain Order: A;B;F;G;H;I;J;K;L;M;N;O;P;Q;R;S;T;X;Y;Z;a;b;c;d;e;f;g;h;i;j;
Order: R
Angle: 119.89
Translation: 0.13
RMSD: 0.2
TM-Score: 1.0
Coverage: 1.0
Aligned Residues: 7880
Number of Repeats: 2
Repeat Length: 3940
Levels: 1
Topology: Parallel
Angle with Membrane Normal: -0.06
Repeats:
View alignment(s)

 
v2.1.2