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Cryo-EM structure of the rc-lh core complex from roseiflexus castenholzii

Analyse Cryo-EM structure of the rc-lh core complex from roseiflexus castenholzii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YQ7
Type: protein
Length: 2,155 residues
Chains: 35
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta subunit of light-harvesting 1; Precursor for L subunits of photosynthetic reaction…
UniProt: Q83XD2, Q83XD0, Q83XC9, Q83XD1
Ligands: BCL, KGD, HEM, BPH, MQE, FE
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 7 distinct chains · 49% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, B, 0, 8, 6, 4, 2, K, I, G, W, U, S, Q, O	Beta subunit of light-harvesting 1	protein	44	64% helix, 0% strand	Q83XD2
L	Precursor for L subunits of photosynthetic reaction center	protein	309	53% helix, 0% strand	Q83XD0
C	Cytochrome subunit of photosynthetic reaction center	protein	293	33% helix, 1% strand	Q83XC9
T, V, R, P, N, J, H, F, D, A, 9, 7, 5, 3, 1	Alpha subunit of light-harvesting 1	protein	36	69% helix, 0% strand	Q83XD1
Y	Peptide from precursor for L and M subunits of photosynthetic reaction center	protein	25	80% helix, 0% strand	—
X	Subunit X	protein	23	91% helix, 0% strand	—
M	Precursor for M subunits of photosynthetic reaction center	protein	305	49% helix, 0% strand	Q83XD0

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 48 copies · chains E, G, D, B, A, 0, 9, 8, L, M, 7, 6, 5, 4, 3, 2, C, 1, K, J, I, H, F, W, T, V, X, U, S, R, Q, P, O, N
KGD · beta,psi-caroten-4-one · ligand · 14 copies · chains W, T, V, U, R, S, P, Q, N, O, J, K, H, I, F, G, D, E, A, B, 9, 0, 7, 8, 5, 6, 3, 4, 1
HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, L, M
BPH · Bacteriopheophytin A · ligand · 3 copies · chains L, M
MQE · 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3, 7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34, 38,42-undecaen-1-yl]naphthalene-1,4-dione · ligand · 2 copies · chains L, Y, M, P
FE · Fe (III) ion · metal · chains L, M

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	962	0.87	0.88	101	HEM
2	1015	0.81	0.82	120	BCL
3	948	0.79	0.80	85	empty
4	713	0.77	0.81	71	empty
5	911	0.75	0.78	80	empty

Interfaces

91 interfaces between chains.

L–M · 4526 Å² buried · 17 hydrogen bonds · protein-protein
C–M · 1099 Å² buried · 5 hydrogen bonds · protein-protein
A–M · 547 Å² buried · 1 hydrogen bond · protein-protein
L–R · 506 Å² buried · 0 hydrogen bonds · protein-protein
L–C · 481 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 covalent, 7 cofactor (covalent ligand, heme attachment).

Compared structures

5YQ7 · Cryo-EM structure of the RC-LH core complex from Roseiflexus castenholzii · the same entry in another collection · chain E against E, TM-score 1.00

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 Q83XD2
Every structure of UniProt Q83XD0
Every structure of UniProt Q83XC9
Every structure of UniProt Q83XD1
Elsewhere: RCSB PDB 5YQ7 · PDBe 5YQ7 · UniProt Q83XD2 · UniProt Q83XD0 · UniProt Q83XC9 · UniProt Q83XD1

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