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Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A

Analyse Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PIL
Type: protein
Length: 2,291 residues
Chains: 33
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.5
Molecule: Light-harvesting protein B-875 alpha chain; Light-harvesting protein B-875 beta chain…
UniProt: Q3J1A4, Q3J1A3, Q3J170, Q3J1A5, Q3J1A6, U5NME9, P13402
Ligands: BCL, SPO, 3PE, BPH, U10, UQ1, CD4, FE
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · resolution 2.5 · 11 distinct chains · 59% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
AA	Light-harvesting protein B-875 alpha chain	protein	46	65% helix, 0% strand	Q3J1A4
AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM	Light-harvesting protein B-875 alpha chain	protein	55	69% helix, 0% strand	Q3J1A4
AN	Light-harvesting protein B-875 alpha chain	protein	51	71% helix, 0% strand	Q3J1A4
BA, BB, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM	Light-harvesting protein B-875 beta chain	protein	43	74% helix, 0% strand	Q3J1A3
BC	Light-harvesting protein B-875 beta chain	protein	42	76% helix, 0% strand	Q3J1A3
BN	Light-harvesting protein B-875 beta chain	protein	38	84% helix, 0% strand	Q3J1A3
H	Reaction center protein H chain	protein	246	24% helix, 26% strand	Q3J170
L	Reaction center protein L chain	protein	281	63% helix, 4% strand	Q3J1A5
M	Reaction center protein M chain	protein	307	64% helix, 4% strand	Q3J1A6
UU	Rc-Y	protein	49	82% helix, 0% strand	U5NME9
X	Intrinsic membrane protein PufX	protein	55	76% helix, 0% strand	P13402

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 32 copies · chains AA, BA, X, AB, BB, AC, BC, AD, BD, AE, BE, AF, BF, AG, BG, AH, BH, AI, BI, AJ, BJ, AK, BK, AL, BL, AM, BM, AN, BN, L, M
SPO · Spheroidene · ligand · 26 copies · chains AA, AB, AC, BA, BB, AD, BC, AE, BD, AF, BE, AG, BF, AH, BG, AI, BH, AJ, BI, AK, BJ, AL, BK, AM, BL, AN, BM, X, M
3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 4 copies · chains AB, AC, AD, H, L, M
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M, UU, AB, AC
UQ1 · Ubiquinone-1 · ligand · chains L, M
CD4 · (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate · ligand · chains AE, AG, H, L, M
FE · Fe (III) ion · metal · chains L, M
LMT · Dodecyl-beta-D-maltoside · additive · 4 copies · chains AA, L, AB, AJ, AK, M, X

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	992	0.84	0.84	89	BCL
2	1164	0.83	0.84	96	SPO, LMT
3	991	0.81	0.82	94	3PE, SPO
4	939	0.80	0.81	61	empty
5	297	0.79	0.89	30	SPO

Interfaces

92 interfaces between chains.

L–M · 4784 Å² buried · 69 hydrogen bonds · protein-protein
H–M · 2911 Å² buried · 37 hydrogen bonds · protein-protein
H–L · 1592 Å² buried · 14 hydrogen bonds · protein-protein
L–X · 971 Å² buried · 11 hydrogen bonds · protein-protein
AM–BM · 803 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

Q3J1A5 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (Q3J1A5) · a predicted model of the same protein · chain L against A, TM-score 0.99
Q3J1A6 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (Q3J1A6) · a predicted model of the same protein · chain M against A, TM-score 0.99
Q3J170 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (Q3J170) · a predicted model of the same protein · chain H against A, TM-score 0.98
Q3J1A3 · AlphaFold monomer V2.0 prediction for light-harvesting protein B-875 beta chain (Q3J1A3) · a predicted model of the same protein · chain BN against A, TM-score 0.88

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q3J1A4
Every structure of UniProt Q3J1A3
Every structure of UniProt Q3J170
Every structure of UniProt Q3J1A5
Every structure of UniProt Q3J1A6
Every structure of UniProt U5NME9
Every structure of UniProt P13402
Elsewhere: RCSB PDB 7PIL · PDBe 7PIL · UniProt Q3J1A4 · UniProt Q3J1A3 · UniProt Q3J170 · UniProt Q3J1A5 · UniProt Q3J1A6 · UniProt U5NME9 · UniProt P13402

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