Research workbench

The structure of the mitoribosome from Neurospora crassa with bound tRNA at the P-site

Analyse The structure of the mitoribosome from Neurospora crassa with bound tRNA at the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YWY
Type: protein + RNA
Length: 19,966 residues
Chains: 85
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.05
Source: Neurospora crassa
Molecule: 23S rRNA; 60S ribosomal protein L2, mitochondrial; Related to ribosomal protein L3…
EC: 3.1.2.4
UniProt: A0A0B0DJN7, Q873B3, V5IMN1, Q96U12, A0A0B0DQR9, A0A0B0DK80, Q6M9C4, A0A0B0DNH1, A0A0B0E388, A0A0B0E7L9, A0A0B0DM93, Q8X081, A0A0B0ECK1, A0A0B0DXI2, Q6MVF2, Q7S5N0, A0A0B0DT83, A0A0B0DQ90, Q8X0Q2, A0A0B0DNQ5, A0A0B0DW15, Q8X098, Q9C2E5, Q9HFL0, A0A0B0E6P7, Q96U95, Q7S4E7, A0A0B0DZ96, A0A0B0DWX0, A0A0B0E3D2, A0A0B0DUU4, A0A0B0DPP2, A0A0B0DTN8, Q7S518, Q7S711, Q6MVH6, A0A0B0E0Q5, A0A0B0E462, Q8NIR6, A0A0B0DMU6, A0A0B0EF55, A0A0B0ECJ7, A0A0B0DJR9, V5ILE0, A0A1W5YJW8, A0A0B0DXP8, Q8X048, A0A0B0DP65, A0A0B0E7P2, A0A0B0EEW5, A0A0B0ED13, A0A0B0EAU9, A0A0B0DQD8, A0A0B0DQD0, Q6MVY0, A0A0B0DHJ1, Q8X067, A0A0B0DKS9, A0A0B0DJ04, Q872A7, A0A0B0DRW6, A0A0B0DTH5, Q873E4, Q7SHR9, Q7RYW7, Q7SD06, A0A0B0DU00, Q9P5J2, A0A0B0E339, Q7SHR6, Q9HE52, A0A0B0DM95, Q7SHB2, A0A0B0DYB0, Q9C251, A0A0B0DIK4, Q870V5, Q7RWZ7
Ligands: SPM, NAD, ATP, MG, K, ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 3.05 · 85 distinct chains · 37% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S rRNA	rna	2843	—	—
B	60S ribosomal protein L2, mitochondrial	protein	315	11% helix, 28% strand	A0A0B0DJN7
C	Related to ribosomal protein L3, mitochondrial	protein	307	22% helix, 25% strand	Q873B3
D	60S ribosomal protein L4, variant	protein	254	34% helix, 15% strand	V5IMN1
E	Related to ribosomal protein L5, mitochondrial	protein	309	30% helix, 14% strand	Q96U12
F	uL6m	protein	201	18% helix, 36% strand	A0A0B0DQR9
G	RIBOSOMAL_L9 domain-containing protein	protein	74	23% helix, 16% strand	A0A0B0DK80
f	Related to ribosomal protein YmL11, mitochondrial	protein	245	43% helix, 13% strand	Q6M9C4
g	uL11m	protein	147	38% helix, 21% strand	A0A0B0DNH1
H	uL13m	protein	183	34% helix, 15% strand	A0A0B0E388
I	Ribosomal protein L14	protein	119	7% helix, 39% strand	A0A0B0E7L9
J	Ribosomal protein L15	protein	243	29% helix, 9% strand	A0A0B0DM93
K	Related to ribosomal protein L16, mitochondrial	protein	168	20% helix, 24% strand	Q8X081
L	uL17m	protein	192	52% helix, 9% strand	A0A0B0ECK1
M	bL19m	protein	194	20% helix, 28% strand	A0A0B0DXI2
N	Related to ribosomal protein YmL49, mitochondrial	protein	133	11% helix, 50% strand	Q6MVF2
O	Mitochondrial large ribosomal subunit	protein	272	43% helix, 18% strand	Q7S5N0
P	uL23m	protein	180	31% helix, 19% strand	A0A0B0DT83
Q	KOW domain-containing protein	protein	353	42% helix, 21% strand	A0A0B0DQ90
R	Related to 60s ribosomal protein L2 (Mitochondrial)	protein	249	33% helix, 18% strand	Q8X0Q2
S	bL28m	protein	179	36% helix, 14% strand	A0A0B0DNQ5
T	54S ribosomal protein L4, mitochondrial	protein	180	44% helix, 2% strand	A0A0B0DW15
U	Related to ribosomal protein L30	protein	138	28% helix, 22% strand	Q8X098
V	Related to ribosomal protein YmL36, mitochondrial	protein	94	22% helix, 18% strand	Q9C2E5
W	Related to ribosomal protein YmL32 (Mitochondrial)	protein	59	37% helix, 12% strand	Q9HFL0
X	bL33m	protein	48	0% helix, 58% strand	A0A0B0E6P7
Y	Related to ribosomal protein L34, mitochondrial	protein	46	54% helix, 0% strand	Q96U95
0	Ribosomal protein	protein	46	7% helix, 33% strand	Q7S4E7
1	PEBP-like protein	protein	367	39% helix, 20% strand	A0A0B0DZ96
2	mL40	protein	123	54% helix, 2% strand	A0A0B0DWX0
3	mL41	protein	95	15% helix, 11% strand	A0A0B0E3D2
4	L51_S25_CI-B8 domain-containing protein	protein	137	23% helix, 23% strand	A0A0B0DUU4
5	Ribonuclease III	protein	350	42% helix, 9% strand	A0A0B0DPP2
6	mL46	protein	273	26% helix, 22% strand	A0A0B0DTN8
7	mL49	protein	84	26% helix, 27% strand	Q7S518
8	mL50	protein	331	45% helix, 4% strand	Q7S711
h	Probable ribosomal protein YmL44, mitochondrial	protein	98	39% helix, 26% strand	Q6MVH6
i	mL54	protein	124	46% helix, 2% strand	A0A0B0E0Q5
9	RNase III domain-containing protein	protein	206	52% helix, 1% strand	A0A0B0E462
a	Related to ribosomal protein YmL20, mitochondrial	protein	161	48% helix, 6% strand	Q8NIR6
b	Mitoc_mL59 domain-containing protein	protein	161	46% helix, 2% strand	A0A0B0DMU6
c	54S ribosomal protein L31, mitochondrial	protein	98	50% helix, 6% strand	A0A0B0EF55
d	mL67	protein	235	26% helix, 17% strand	A0A0B0ECJ7
AA	bS1m	protein	372	26% helix, 13% strand	A0A0B0DJR9
BB	Mito ribosomal protein S2	protein	290	46% helix, 12% strand	V5ILE0
CC	Ribosomal protein S5	protein	438	35% helix, 17% strand	A0A1W5YJW8
DD	S4 RNA-binding domain-containing protein	protein	290	34% helix, 10% strand	A0A0B0DXP8
EE	Related to ribosomal protein S5 (Mitochondrial)	protein	367	35% helix, 20% strand	Q8X048
FF	Ribosomal protein S6	protein	117	29% helix, 38% strand	A0A0B0DP65
GG	Ribosomal_S7 domain-containing protein	protein	223	43% helix, 5% strand	A0A0B0E7P2
HH	uS8m	protein	160	29% helix, 26% strand	A0A0B0EEW5
II	uS9m	protein	247	38% helix, 14% strand	A0A0B0ED13
JJ	30S ribosomal protein S10, mitochondrial	protein	188	35% helix, 30% strand	A0A0B0EAU9
KK	Translational machinery component	protein	124	27% helix, 26% strand	A0A0B0DQD8
LL	Ribosomal protein S12	protein	128	12% helix, 27% strand	A0A0B0DQD0
MM	Probable ribosomal protein S13	protein	118	50% helix, 5% strand	Q6MVY0
NN	Mitochondrial 37S ribosomal protein MRP2	protein	112	51% helix, 7% strand	A0A0B0DHJ1
OO	Related to ribosomal protein S15 (Mitochondrial)	protein	276	60% helix, 2% strand	Q8X067
PP	bS16m	protein	98	19% helix, 32% strand	A0A0B0DKS9
QQ	uS17m	protein	158	35% helix, 27% strand	A0A0B0DJ04
RR	Ribosomal protein S18	protein	134	48% helix, 4% strand	Q872A7
SS	Ribosomal protein S19/S15	protein	81	12% helix, 19% strand	A0A0B0DRW6
TT	bS21m	protein	88	66% helix, 8% strand	A0A0B0DTH5
UU	37S ribosomal protein S25, mitochondrial	protein	224	47% helix, 1% strand	Q873E4
VV	mS26	protein	261	55% helix, 1% strand	Q7SHR9
WW	mS27	protein	353	63% helix, 1% strand	Q7RYW7
XX	Mitochondrial ribosomal protein DAP3	protein	408	37% helix, 13% strand	Q7SD06
YY	mS33	protein	99	51% helix, 4% strand	A0A0B0DU00
ZZ	37S ribosomal protein S24, mitochondrial	protein	312	46% helix, 7% strand	Q9P5J2
11	37S ribosomal protein mrp10, mitochondrial	protein	88	43% helix, 2% strand	A0A0B0E339
22	DUF1713 domain-containing protein	protein	33	79% helix, 0% strand	Q7SHR6
33	Protein FYV4, mitochondrial	protein	191	29% helix, 16% strand	Q9HE52
44	Manganese and iron superoxide dismutase	protein	260	48% helix, 8% strand	A0A0B0DM95
55	Manganese and iron superoxide dismutase	protein	232	42% helix, 12% strand	A0A0B0DM95
66	mS45	protein	283	40% helix, 8% strand	Q7SHB2
77	mS46	protein	179	47% helix, 2% strand	A0A0B0DYB0
88	3-hydroxyisobutyryl-CoA hydrolase, mitochondrial (EC 3.1.2.4)	protein	467	44% helix, 9% strand	Q9C251
00	IF1	protein	48	88% helix, 0% strand	A0A0B0DIK4
99	IF1	protein	36	94% helix, 0% strand	A0A0B0DIK4
aa	16S rRNA	rna	1435	—	—
bb	P-site-tRNA	rna	73	—	—
ee	mRNA	rna	11	—	—
cc	Poly-Peptide	protein	7	0% helix, 0% strand	—
e	60S ribosomal protein L1, mitochondrial	protein	148	24% helix, 20% strand	Q870V5
j	L51_S25_CI-B8 domain-containing protein	protein	195	44% helix, 13% strand	Q7RWZ7

Ligands and binding sites

SPM · Spermine · ligand · chains A, c
NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A, E, 2, 6
ATP · Adenosine-5'-triphosphate · ligand · chains XX
MG · Magnesium ion · metal · 250 copies · chains A, B, 3, H, b, J, L, P, C, D, Q, Y, T, c, M, S, K, AA, BB, KK, aa, QQ, XX, YY, 00, LL, 22, MM, ee
K · Potassium ion · metal · 49 copies · chains A, B, C, J, 0, E, 2, 3, ZZ, 77, 88, aa, KK
ZN · Zinc ion · metal · 2 copies · chains W, 0

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	1119	0.90	0.92	105	ATP, MG
2	1068	0.89	0.91	133	empty
3	1184	0.88	0.90	119	empty
4	954	0.88	0.91	107	MG
5	729	0.87	0.91	78	MG, SPM

Interfaces

309 interfaces between chains.

A–B · 7946 Å² buried · 219 hydrogen bonds · protein-nucleic
A–C · 7364 Å² buried · 164 hydrogen bonds · protein-nucleic
A–R · 5661 Å² buried · 114 hydrogen bonds · protein-nucleic
A–J · 5538 Å² buried · 137 hydrogen bonds · protein-nucleic
A–E · 5170 Å² buried · 111 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

Q873E4 · AlphaFold monomer V2.0 prediction for 37S ribosomal protein S25, mitochondrial (Q873E4) · a predicted model of the same protein · chain UU against A, TM-score 0.85

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.