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Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA

Analyse Structure of a native assembly intermediate of the human mitochondrial ribosome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OOL
Type: protein + RNA
Length: 9,723 residues
Chains: 56
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.06
Source: Homo sapiens
Molecule: 16S ribosomal RNA; mitochondrial tRNAVal; 39S ribosomal protein L2, mitochondrial; 39S…
EC: 3.1.26.-, 3.1.1.29
UniProt: Q5T653, P09001, Q9BYD3, Q9BYD2, Q7Z7H8, Q9Y3B7, Q9BYD1, Q6P1L8, Q9P015, Q9NX20, Q9NRX2, Q9H0U6, P49406, Q9BYC9, Q7Z2W9, Q9NWU5, Q16540, Q96A35, Q9P0M9, Q13084, Q9HD33, Q8TCC3, Q9BYC8, O75394, Q9BQ48, Q9NZE8, Q9P0J6, Q9BZE1, Q96DV4, Q9NYK5, Q9NQ50, Q8IXM3, Q9Y6G3, Q8N983, Q9H9J2, Q9BRJ2, Q9H2W6, Q96GC5, Q13405, Q8N5N7, Q4U2R6, Q86TS9, Q96EL3, Q6P161, Q7Z7F7, Q9BQC6, Q14197, Q8TAE8, Q9NVS2, Q9NP92, Q96EH3, L0R8F8, O14561
Ligands: PNS, MG, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 3.06 · 56 distinct chains · 31% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	16S ribosomal RNA	rna	1441	—	—
B	mitochondrial tRNAVal	rna	56	—	—
D	39S ribosomal protein L2, mitochondrial	protein	236	5% helix, 31% strand	Q5T653
E	39S ribosomal protein L3, mitochondrial	protein	304	14% helix, 29% strand	P09001
F	39S ribosomal protein L4, mitochondrial	protein	250	28% helix, 13% strand	Q9BYD3
H	39S ribosomal protein L9, mitochondrial	protein	95	21% helix, 25% strand	Q9BYD2
I	39S ribosomal protein L10, mitochondrial	protein	158	42% helix, 9% strand	Q7Z7H8
J	39S ribosomal protein L11, mitochondrial	protein	140	32% helix, 13% strand	Q9Y3B7
K	39S ribosomal protein L13, mitochondrial	protein	177	34% helix, 18% strand	Q9BYD1
L	39S ribosomal protein L14, mitochondrial	protein	115	3% helix, 29% strand	Q6P1L8
M	39S ribosomal protein L15, mitochondrial	protein	287	25% helix, 11% strand	Q9P015
N	39S ribosomal protein L16, mitochondrial	protein	205	26% helix, 21% strand	Q9NX20
O	39S ribosomal protein L17, mitochondrial	protein	152	47% helix, 10% strand	Q9NRX2
P	39S ribosomal protein L18, mitochondrial	protein	141	30% helix, 18% strand	Q9H0U6
Q	39S ribosomal protein L19, mitochondrial	protein	217	26% helix, 22% strand	P49406
R	39S ribosomal protein L20, mitochondrial	protein	140	64% helix, 1% strand	Q9BYC9
S	39S ribosomal protein L21, mitochondrial	protein	156	13% helix, 42% strand	Q7Z2W9
T	39S ribosomal protein L22, mitochondrial	protein	166	33% helix, 23% strand	Q9NWU5
U	39S ribosomal protein L23, mitochondrial	protein	139	15% helix, 19% strand	Q16540
V	39S ribosomal protein L24, mitochondrial	protein	192	13% helix, 24% strand	Q96A35
W	39S ribosomal protein L27, mitochondrial	protein	109	6% helix, 40% strand	Q9P0M9
X	39S ribosomal protein L28, mitochondrial	protein	243	44% helix, 16% strand	Q13084
Y	39S ribosomal protein L47, mitochondrial	protein	176	58% helix, 7% strand	Q9HD33
Z	39S ribosomal protein L30, mitochondrial	protein	120	23% helix, 15% strand	Q8TCC3
0	39S ribosomal protein L32, mitochondrial	protein	108	28% helix, 13% strand	Q9BYC8
1	39S ribosomal protein L33, mitochondrial	protein	52	0% helix, 63% strand	O75394
2	39S ribosomal protein L34, mitochondrial	protein	45	56% helix, 0% strand	Q9BQ48
3	39S ribosomal protein L35, mitochondrial	protein	95	29% helix, 11% strand	Q9NZE8
4	39S ribosomal protein L36, mitochondrial	protein	37	8% helix, 35% strand	Q9P0J6
5	39S ribosomal protein L37, mitochondrial	protein	387	25% helix, 24% strand	Q9BZE1
6	39S ribosomal protein L38, mitochondrial	protein	324	29% helix, 20% strand	Q96DV4
7	39S ribosomal protein L39, mitochondrial	protein	287	37% helix, 24% strand	Q9NYK5
8	39S ribosomal protein L40, mitochondrial	protein	99	46% helix, 1% strand	Q9NQ50
9	39S ribosomal protein L41, mitochondrial	protein	117	21% helix, 10% strand	Q8IXM3
a	39S ribosomal protein L42, mitochondrial	protein	82	27% helix, 16% strand	Q9Y6G3
b	39S ribosomal protein L43, mitochondrial	protein	148	24% helix, 19% strand	Q8N983
c	39S ribosomal protein L44, mitochondrial (EC 3.1.26.-)	protein	275	57% helix, 9% strand	Q9H9J2
d	39S ribosomal protein L45, mitochondrial	protein	211	26% helix, 22% strand	Q9BRJ2
e	39S ribosomal protein L46, mitochondrial	protein	217	29% helix, 20% strand	Q9H2W6
f	39S ribosomal protein L48, mitochondrial	protein	116	28% helix, 19% strand	Q96GC5
g	39S ribosomal protein L49, mitochondrial	protein	129	21% helix, 22% strand	Q13405
h	39S ribosomal protein L50, mitochondrial	protein	100	42% helix, 5% strand	Q8N5N7
i	39S ribosomal protein L51, mitochondrial	protein	97	44% helix, 1% strand	Q4U2R6
j	39S ribosomal protein L52, mitochondrial	protein	85	62% helix, 5% strand	Q86TS9
k	39S ribosomal protein L53, mitochondrial	protein	80	28% helix, 25% strand	Q96EL3
l	39S ribosomal protein L54, mitochondrial	protein	23	78% helix, 0% strand	Q6P161
m	39S ribosomal protein L55, mitochondrial	protein	45	0% helix, 31% strand	Q7Z7F7
o	Ribosomal protein 63, mitochondrial	protein	91	51% helix, 1% strand	Q9BQC6
p	Peptidyl-tRNA hydrolase ICT1, mitochondrial (EC 3.1.1.29)	protein	127	38% helix, 14% strand	Q14197
q	Growth arrest and DNA damage-inducible proteins-interacting protein 1	protein	128	67% helix, 1% strand	Q8TAE8
r	39S ribosomal protein S18a, mitochondrial	protein	146	25% helix, 12% strand	Q9NVS2
s	39S ribosomal protein S30, mitochondrial	protein	370	29% helix, 19% strand	Q9NP92
t	Unknown protein or protein extension	protein	28	86% helix, 0% strand	—
u	Mitochondrial assembly of ribosomal large subunit protein 1	protein	111	36% helix, 21% strand	Q96EH3
v	MIEF1 upstream open reading frame protein	protein	69	61% helix, 1% strand	L0R8F8
w	Acyl carrier protein, mitochondrial	protein	79	52% helix, 0% strand	O14561

Ligands and binding sites

PNS · 4'-phosphopantetheine · ligand · chains v, w
MG · Magnesium ion · metal · 92 copies · chains A, F, Q, M, W, 2, U, E, T, R, o, D, g
ZN · Zinc ion · metal · 3 copies · chains I, r, 0, 4

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	1129	0.88	0.90	103	MG
2	930	0.88	0.90	98	MG
3	891	0.87	0.90	93	empty
4	800	0.87	0.91	85	MG
5	871	0.87	0.90	91	MG

Interfaces

208 interfaces between chains.

A–E · 5168 Å² buried · 92 hydrogen bonds · protein-nucleic
A–D · 4929 Å² buried · 122 hydrogen bonds · protein-nucleic
A–M · 4228 Å² buried · 102 hydrogen bonds · protein-nucleic
A–F · 3629 Å² buried · 65 hydrogen bonds · protein-nucleic
A–R · 3327 Å² buried · 63 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 cofactor (phosphopantetheinylation).

Compared structures

5OOL · Structure of a native assembly intermediate of the human mitochondrial ribosome with… · the same entry in another collection · chain A against A, TM-score 1.00

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