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High-resolution cryo-EM structure of pyrococcus abyssi 30S ribosomal subunit bound to mRNA and initiator tRNA anticodon stem-loop

Analyse High-resolution cryo-EM structure of pyrococcus abyssi 30S ribosomal subunit… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ZHG
Type: protein + RNA
Length: 5,134 residues
Chains: 31
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RRNA 16S; 30S ribosomal protein S3AE; 30S ribosomal protein S2; Zn-ribbon RNA-binding…
UniProt: Q9V2K7, Q9V191, G8ZFK7, P61992, Q9V1U8, Q9V1V5, Q9UYS3, Q9V109, Q9V1V0, Q9UZL4, Q9V195, Q9V0V6, P62010, P61994, Q9V1A0, P62012, Q9V2K9, Q9V1U5, Q9V0G0, Q9V1T9, Q9V0G8, Q9UY20, Q9UXZ3, P61029, P61238, Q9V1U1, Q8U232, P62008
Ligands: MG, ZN
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 31 distinct chains · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	RRNA 16S	rna	1497	—	—
A	30S ribosomal protein S3AE	protein	188	35% helix, 39% strand	Q9V2K7
B	30S ribosomal protein S2	protein	196	39% helix, 15% strand	Q9V191
C	Zn-ribbon RNA-binding protein involved in translation	protein	57	11% helix, 21% strand	G8ZFK7
D	30S ribosomal protein S4	protein	173	53% helix, 6% strand	P61992
E	30S ribosomal protein S4E	protein	242	14% helix, 37% strand	Q9V1U8
F	30S ribosomal protein S5	protein	229	36% helix, 28% strand	Q9V1V5
G	30S ribosomal protein S6E	protein	124	11% helix, 40% strand	Q9UYS3
H	30S ribosomal protein S7	protein	214	47% helix, 14% strand	Q9V109
I	30S ribosomal protein S8	protein	129	32% helix, 27% strand	Q9V1V0
J	30S ribosomal protein S8E	protein	125	9% helix, 42% strand	Q9UZL4
K	30S ribosomal protein S9	protein	135	41% helix, 21% strand	Q9V195
L	30S ribosomal protein S10	protein	100	24% helix, 48% strand	Q9V0V6
M	30S ribosomal protein S11	protein	127	26% helix, 27% strand	P62010
N	30S ribosomal protein S12	protein	146	26% helix, 28% strand	P61994
O	30S ribosomal protein S13	protein	141	43% helix, 9% strand	Q9V1A0
P	30S ribosomal protein S14 type Z	protein	55	36% helix, 9% strand	P62012
Q	30S ribosomal protein S15	protein	151	50% helix, 1% strand	Q9V2K9
R	30S ribosomal protein S17	protein	107	0% helix, 43% strand	Q9V1U5
S	30S ribosomal protein S17E	protein	64	72% helix, 2% strand	Q9V0G0
T	30S ribosomal protein S19	protein	124	34% helix, 12% strand	Q9V1T9
U	30S ribosomal protein S19E	protein	149	50% helix, 13% strand	Q9V0G8
V	30S ribosomal protein S24E	protein	96	29% helix, 38% strand	Q9UY20
W	30S ribosomal protein S27E	protein	61	0% helix, 39% strand	Q9UXZ3
X	30S ribosomal protein S28E	protein	65	0% helix, 48% strand	P61029
Y	30S ribosomal protein S27AE	protein	49	0% helix, 8% strand	P61238
Z	30S ribosomal protein S3	protein	196	38% helix, 29% strand	Q9V1U1
0	50S ribosomal protein L41E	protein	36	67% helix, 0% strand	Q8U232
3	50S ribosomal protein L7AE	protein	122	36% helix, 11% strand	P62008
5	MRNA	rna	17	—	—
4	Met-trnaimet	rna	19	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 90 copies · chains 2, K, 5, U, D, F, Q, E, M, 4
ZN · Zinc ion · metal · 6 copies · chains C, F, P, R, W

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	949	0.86	0.89	90	MG
2	695	0.86	0.91	68	MG
3	1112	0.85	0.87	84	MG
4	907	0.85	0.87	93	MG
5	1094	0.84	0.86	94	MG

Interfaces

71 interfaces between chains.

2–E · 3977 Å² buried · 69 hydrogen bonds · protein-nucleic
2–N · 3559 Å² buried · 62 hydrogen bonds · protein-nucleic
2–J · 3295 Å² buried · 68 hydrogen bonds · protein-nucleic
2–Q · 3212 Å² buried · 62 hydrogen bonds · protein-nucleic
2–U · 3142 Å² buried · 70 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 69 modified (nucleotide modification).

Compared structures

7ZHG · High-resolution cryo-EM structure of Pyrococcus abyssi 30S ribosomal subunit bound to… · the same entry in another collection · chain I against I, 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 Q9V2K7
Every structure of UniProt Q9V191
Every structure of UniProt G8ZFK7
Every structure of UniProt P61992
Every structure of UniProt Q9V1U8
Every structure of UniProt Q9V1V5
Every structure of UniProt Q9UYS3
Every structure of UniProt Q9V109
Every structure of UniProt Q9V1V0
Every structure of UniProt Q9UZL4
Every structure of UniProt Q9V195
Every structure of UniProt Q9V0V6
Every structure of UniProt P62010
Every structure of UniProt P61994
Every structure of UniProt Q9V1A0
Every structure of UniProt P62012
Every structure of UniProt Q9V2K9
Every structure of UniProt Q9V1U5
Every structure of UniProt Q9V0G0
Every structure of UniProt Q9V1T9
Every structure of UniProt Q9V0G8
Every structure of UniProt Q9UY20
Every structure of UniProt Q9UXZ3
Every structure of UniProt P61029
Every structure of UniProt P61238
Every structure of UniProt Q9V1U1
Every structure of UniProt Q8U232
Every structure of UniProt P62008
Elsewhere: RCSB PDB 7ZHG · PDBe 7ZHG · UniProt Q9V2K7 · UniProt Q9V191 · UniProt G8ZFK7 · UniProt P61992 · UniProt Q9V1U8 · UniProt Q9V1V5 · UniProt Q9UYS3 · UniProt Q9V109 · UniProt Q9V1V0 · UniProt Q9UZL4 · UniProt Q9V195 · UniProt Q9V0V6 · UniProt P62010 · UniProt P61994 · UniProt Q9V1A0 · UniProt P62012 · UniProt Q9V2K9 · UniProt Q9V1U5 · UniProt Q9V0G0 · UniProt Q9V1T9 · UniProt Q9V0G8 · UniProt Q9UY20 · UniProt Q9UXZ3 · UniProt P61029 · UniProt P61238 · UniProt Q9V1U1 · UniProt Q8U232 · UniProt P62008

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