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Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (DATASET1).

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

PDB: 7OF0
Type: protein + RNA
Length: 9,878 residues
Chains: 56
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 39S ribosomal protein L32, mitochondrial; 39S ribosomal protein L33, mitochondrial; 39S…
EC: 2.1.1.-, 3.1.26.-, 3.1.1.29
UniProt: Q9BYC8, O75394, Q9BQ48, Q9NZE8, Q9P0J6, Q9BZE1, Q96DV4, Q9NYK5, Q9NQ50, Q8IXM3, Q96CB9, Q5T653, P09001, Q9BYD3, Q7Z6M4, Q9BYD2, Q7Z7H8, Q9Y3B7, Q9BYD1, Q6P1L8, Q9P015, Q9NX20, Q9NRX2, Q9H0U6, P49406, Q9BYC9, Q7Z2W9, Q9NWU5, Q16540, Q96A35, Q9P0M9, Q13084, Q9HD33, Q8TCC3, Q9Y6G3, Q8N983, Q9H9J2, Q9BRJ2, Q9H2W6, Q96GC5, Q13405, Q8N5N7, Q4U2R6, Q86TS9, Q96EL3, Q7Z7F7, Q9BQC6, Q14197, Q8TAE8, Q9NVS2, Q9NP92, Q96EH3, L0R8F8, O14561
Ligands: MG, ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 56 distinct chains · 36% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	39S ribosomal protein L32, mitochondrial	protein	108	28% helix, 14% strand	Q9BYC8
1	39S ribosomal protein L33, mitochondrial	protein	52	0% helix, 60% strand	O75394
2	39S ribosomal protein L34, mitochondrial	protein	45	58% helix, 0% strand	Q9BQ48
3	39S ribosomal protein L35, mitochondrial	protein	95	33% helix, 8% strand	Q9NZE8
4	39S ribosomal protein L36, mitochondrial	protein	37	8% helix, 43% strand	Q9P0J6
5	39S ribosomal protein L37, mitochondrial	protein	392	27% helix, 26% strand	Q9BZE1
6	39S ribosomal protein L38, mitochondrial	protein	324	30% helix, 22% strand	Q96DV4
7	39S ribosomal protein L39, mitochondrial	protein	287	41% helix, 25% strand	Q9NYK5
8	39S ribosomal protein L40, mitochondrial	protein	77	65% helix, 1% strand	Q9NQ50
9	39S ribosomal protein L41, mitochondrial	protein	117	27% helix, 9% strand	Q8IXM3
A	16S ribosomal RNA	rna	1376	—	—
B	Mitochondrial trnaval	rna	56	—	—
C	5-methylcytosine rRNA methyltransferase NSUN4 (EC 2.1.1.-)	protein	327	43% helix, 18% strand	Q96CB9
D	39S ribosomal protein L2, mitochondrial	protein	240	8% helix, 28% strand	Q5T653
E	39S ribosomal protein L3, mitochondrial	protein	308	17% helix, 29% strand	P09001
F	39S ribosomal protein L4, mitochondrial	protein	250	30% helix, 15% strand	Q9BYD3
G	Transcription termination factor 4, mitochondrial	protein	238	71% helix, 0% strand	Q7Z6M4
H	39S ribosomal protein L9, mitochondrial	protein	95	29% helix, 29% strand	Q9BYD2
I	39S ribosomal protein L10, mitochondrial	protein	151	44% helix, 13% strand	Q7Z7H8
J	39S ribosomal protein L11, mitochondrial	protein	140	35% helix, 14% strand	Q9Y3B7
K	39S ribosomal protein L13, mitochondrial	protein	177	36% helix, 16% strand	Q9BYD1
L	39S ribosomal protein L14, mitochondrial	protein	115	11% helix, 33% strand	Q6P1L8
M	39S ribosomal protein L15, mitochondrial	protein	287	34% helix, 12% strand	Q9P015
N	39S ribosomal protein L16, mitochondrial	protein	183	34% helix, 21% strand	Q9NX20
O	39S ribosomal protein L17, mitochondrial	protein	152	51% helix, 11% strand	Q9NRX2
P	39S ribosomal protein L18, mitochondrial	protein	141	32% helix, 18% strand	Q9H0U6
Q	39S ribosomal protein L19, mitochondrial	protein	217	29% helix, 24% strand	P49406
R	39S ribosomal protein L20, mitochondrial	protein	116	78% helix, 0% strand	Q9BYC9
S	39S ribosomal protein L21, mitochondrial	protein	156	13% helix, 44% strand	Q7Z2W9
T	39S ribosomal protein L22, mitochondrial	protein	166	36% helix, 25% strand	Q9NWU5
U	39S ribosomal protein L23, mitochondrial	protein	139	17% helix, 22% strand	Q16540
V	39S ribosomal protein L24, mitochondrial	protein	47	30% helix, 9% strand	Q96A35
W	39S ribosomal protein L27, mitochondrial	protein	100	8% helix, 43% strand	Q9P0M9
X	39S ribosomal protein L28, mitochondrial	protein	243	47% helix, 16% strand	Q13084
Y	39S ribosomal protein L47, mitochondrial	protein	176	62% helix, 7% strand	Q9HD33
Z	39S ribosomal protein L30, mitochondrial	protein	115	26% helix, 19% strand	Q8TCC3
a	39S ribosomal protein L42, mitochondrial	protein	71	35% helix, 15% 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	60% helix, 9% strand	Q9H9J2
d	39S ribosomal protein L45, mitochondrial	protein	199	22% helix, 28% strand	Q9BRJ2
e	39S ribosomal protein L46, mitochondrial	protein	197	27% helix, 22% strand	Q9H2W6
f	39S ribosomal protein L48, mitochondrial	protein	108	31% helix, 20% strand	Q96GC5
g	39S ribosomal protein L49, mitochondrial	protein	129	24% helix, 25% strand	Q13405
h	39S ribosomal protein L50, mitochondrial	protein	105	46% helix, 7% strand	Q8N5N7
i	39S ribosomal protein L51, mitochondrial	protein	97	52% helix, 1% strand	Q4U2R6
j	39S ribosomal protein L52, mitochondrial	protein	85	64% helix, 5% strand	Q86TS9
k	39S ribosomal protein L53, mitochondrial	protein	80	33% helix, 26% strand	Q96EL3
m	39S ribosomal protein L55, mitochondrial	protein	29	0% helix, 45% strand	Q7Z7F7
o	Ribosomal protein 63, mitochondrial	protein	80	65% helix, 1% strand	Q9BQC6
p	Peptidyl-tRNA hydrolase ICT1, mitochondrial (EC 3.1.1.29)	protein	127	43% helix, 18% strand	Q14197
q	Growth arrest and DNA damage-inducible proteins-interacting protein 1	protein	128	72% helix, 1% strand	Q8TAE8
r	39S ribosomal protein S18A, mitochondrial	protein	146	29% helix, 12% strand	Q9NVS2
s	39S ribosomal protein S30, mitochondrial	protein	370	35% helix, 23% strand	Q9NP92
u	Mitochondrial assembly of ribosomal large subunit protein 1	protein	111	37% helix, 22% strand	Q96EH3
v	MIEF1 upstream open reading frame protein	protein	69	62% helix, 3% strand	L0R8F8
w	Acyl carrier protein, mitochondrial	protein	79	56% helix, 0% strand	O14561

Ligands and binding sites

MG · Magnesium ion · metal · 61 copies · chains A, F, i, Q, M, O, 2, U, E, T, g
ZN · Zinc ion · metal · 3 copies · chains 0, 4, I, r

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	885	0.87	0.90	95	MG
2	1012	0.86	0.88	97	empty
3	911	0.86	0.88	89	empty
4	677	0.85	0.90	71	MG
5	479	0.85	0.93	65	empty

Interfaces

204 interfaces between chains.

A–E · 5121 Å² buried · 106 hydrogen bonds · protein-nucleic
A–D · 4401 Å² buried · 122 hydrogen bonds · protein-nucleic
A–M · 4162 Å² buried · 115 hydrogen bonds · protein-nucleic
A–F · 3561 Å² buried · 66 hydrogen bonds · protein-nucleic
A–R · 3173 Å² buried · 89 hydrogen bonds · protein-nucleic

Compared structures

7OF0 · Structure of a human mitochondrial ribosome large subunit assembly intermediate in… · the same entry in another collection · chain 9 against 9, TM-score 1.00

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