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Structure of the small subunit of the mammalian mitoribosome

Analyse Structure of the small subunit of the mammalian mitoribosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AJ3
Type: protein + RNA
Length: 6,625 residues
Chains: 37
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitoribosomal 12S rRNA; Mitoribosomal protein US2M, MRPS2; Mitoribosomal protein US3M…
UniProt: F1S001, F1ST79, F1SU66, F1RVX4, F1SRT1, F1SU70, F1RIU0, I3L971, F1S8A5, F1RME2, F1S8G3, F1SG95, F1SU49, K7GKS8, Q767K8
Ligands: GDP, MG, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 36 distinct chains · 45% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mitoribosomal 12S rRNA	rna	960	—	—
B	Mitoribosomal protein US2M, MRPS2	protein	220	44% helix, 16% strand	F1S001
C	Mitoribosomal protein US3M, MRPS24	protein	132	33% helix, 22% strand	F1ST79
E	Mitoribosomal protein US5M, MRPS5	protein	328	25% helix, 23% strand	F1SU66
F	Mitoribosomal protein BS6M, MRPS6	protein	123	25% helix, 39% strand	—
G	Mitoribosomal protein US7M, MRPS7	protein	208	56% helix, 9% strand	F1RVX4
I	Mitoribosomal protein US9M, MRPS9	protein	311	43% helix, 13% strand	—
J	Mitoribosomal protein US10M, MRPS10	protein	129	23% helix, 43% strand	—
K	Mitoribosomal protein US11M, MRPS11	protein	136	22% helix, 26% strand	F1SRT1
L	Mitoribosomal protein US12M, MRPS12	protein	109	6% helix, 28% strand	—
N	Mitoribosomal protein US14M, MRPS14	protein	101	52% helix, 6% strand	—
O	Mitoribosomal protein US15M, MRPS15	protein	175	68% helix, 0% strand	—
P	Mitoribosomal protein BS16M, MRPS16	protein	117	37% helix, 27% strand	F1SU70
Q	Mitoribosomal protein US17M, MRPS17	protein	109	0% helix, 53% strand	F1RIU0
R	Mitoribosomal protein BS18M, MRPS18C	protein	97	32% helix, 3% strand	—
T	Mitoribosomal protein BL19M, MRPL19	protein	14	0% helix, 0% strand	—
U	Mitoribosomal protein BS21M, MRPS21	protein	86	60% helix, 5% strand	I3L971
V, Y	P-site and a-site tRNA	rna	64	—	—
X	MRNA	rna	13	—	—
a	Mitoribosomal protein MS22, MRPS22	protein	292	55% helix, 8% strand	—
b	Mitoribosomal protein MS23, MRPS23	protein	135	42% helix, 3% strand	—
c	Mitoribosomal protein MS25, MRPS25	protein	169	36% helix, 13% strand	—
d	Mitoribosomal protein MS26, MRPS26	protein	177	71% helix, 1% strand	F1S8A5
e	Mitoribosomal protein MS27, MRPS27	protein	336	71% helix, 0% strand	—
f	Mitoribosomal protein MS28, MRPS28	protein	99	14% helix, 36% strand	—
g	Mitoribosomal protein MS29, MRPS29	protein	346	43% helix, 16% strand	—
h	Mitoribosomal protein MS31, MRPS31	protein	103	55% helix, 0% strand	F1RME2
i	Mitoribosomal protein MS33, MRPS33	protein	99	57% helix, 0% strand	F1S8G3
j	Mitoribosomal protein MS34, MRPS34	protein	213	24% helix, 18% strand	—
k	Mitoribosomal protein MS35, MRPS35	protein	275	48% helix, 8% strand	F1SG95
m	Mitoribosomal protein MS37, MRPS37	protein	116	41% helix, 0% strand	F1SU49
n	Mitoribosomal protein MS38, MRPS38	protein	72	69% helix, 0% strand	—
o	Mitoribosomal protein MS39, MRPS39	protein	476	74% helix, 1% strand	K7GKS8
p	Mitoribosomal protein MS40, MRPS18B	protein	188	29% helix, 4% strand	Q767K8
s	Unassigned helices	protein	16	81% helix, 0% strand	—
z	Unassigned helices	protein	17	53% helix, 0% strand	—

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains g
MG · Magnesium ion · metal · 144 copies · chains A, n, E, X, N, m, L, U, d, F, I, Y, K, O, J, V, g
ZN · Zinc ion · metal · 3 copies · chains F, R, P, c, p

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	872	0.88	0.91	98	MG
2	894	0.88	0.91	111	MG
3	1159	0.86	0.88	87	MG
4	844	0.86	0.88	110	empty
5	1044	0.85	0.87	94	MG

Interfaces

130 interfaces between chains.

A–E · 3285 Å² buried · 51 hydrogen bonds · protein-nucleic
A–O · 2549 Å² buried · 43 hydrogen bonds · protein-nucleic
A–L · 2444 Å² buried · 57 hydrogen bonds · protein-nucleic
A–n · 2439 Å² buried · 33 hydrogen bonds · protein-nucleic
J–k · 2354 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 141 modified, 2 disulfide (nucleotide modification, disulfide).

Compared structures

5AJ3 · Structure of the small subunit of the mammalian mitoribosome · the same entry in another collection · chain A against A, 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 F1S001
Every structure of UniProt F1ST79
Every structure of UniProt F1SU66
Every structure of UniProt F1RVX4
Every structure of UniProt F1SRT1
Every structure of UniProt F1SU70
Every structure of UniProt F1RIU0
Every structure of UniProt I3L971
Every structure of UniProt F1S8A5
Every structure of UniProt F1RME2
Every structure of UniProt F1S8G3
Every structure of UniProt F1SG95
Every structure of UniProt F1SU49
Every structure of UniProt K7GKS8
Every structure of UniProt Q767K8
Elsewhere: RCSB PDB 5AJ3 · PDBe 5AJ3 · UniProt F1S001 · UniProt F1ST79 · UniProt F1SU66 · UniProt F1RVX4 · UniProt F1SRT1 · UniProt F1SU70 · UniProt F1RIU0 · UniProt I3L971 · UniProt F1S8A5 · UniProt F1RME2 · UniProt F1S8G3 · UniProt F1SG95 · UniProt F1SU49 · UniProt K7GKS8 · UniProt Q767K8

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