MolNFT v1 · #123148 · protein + RNA

Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-remote conformation

5JB3 · 16S ribosomal RNA: “Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-remote conformation”. Electron microscopy, 4 ligands (MET, GNP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #123148…

PDB: 5JB3
Type: protein + RNA
Length: 6,159 residues
Chains: 36
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S ribosomal RNA; 30S ribosomal protein S11; 30S ribosomal protein S12; 30S ribosomal…
UniProt: P62010, P61994, Q9V2K9, Q9V1U5, Q9V2K7, Q9V191, Q9UY20, Q9UXZ3, Q9V1U1, P61992, Q9V1U8, Q9V1V5, Q9UYS3, Q9V1V0, Q9UZL4, P62008, Q9V0V6, Q9V1A0, P62012, Q9V0G0, Q9V1T9, Q9V0G8, P61029, P61238, Q9V109, Q9V195, Q9V138
Ligands: MET, GNP, MG, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 36 distinct chains · 28% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	16S ribosomal RNA	rna	1495	—	—
M	30S ribosomal protein S11	protein	133	20% helix, 24% strand	P62010
N	30S ribosomal protein S12	protein	145	21% helix, 25% strand	P61994
Q	30S ribosomal protein S15	protein	158	56% helix, 0% strand	Q9V2K9
R	30S ribosomal protein S17P	protein	113	0% helix, 40% strand	Q9V1U5
A	30S ribosomal protein S3AE	protein	190	27% helix, 34% strand	Q9V2K7
B	30S ribosomal protein S2	protein	202	34% helix, 10% strand	Q9V191
V	30S ribosomal protein S24E	protein	99	22% helix, 30% strand	Q9UY20
W	30S ribosomal protein S27E	protein	63	0% helix, 35% strand	Q9UXZ3
Z	30S ribosomal protein S3	protein	186	38% helix, 28% strand	Q9V1U1
D	30S ribosomal protein S4	protein	172	51% helix, 3% strand	P61992
E	30S ribosomal protein S4E	protein	241	7% helix, 32% strand	Q9V1U8
F	30S ribosomal protein S5	protein	217	30% helix, 24% strand	Q9V1V5
G	30S ribosomal protein S6E	protein	125	2% helix, 30% strand	Q9UYS3
I	30S ribosomal protein S8	protein	129	33% helix, 24% strand	Q9V1V0
J	30S ribosomal protein S8E	protein	127	6% helix, 28% strand	Q9UZL4
C	30S ribosomal protein sx	protein	57	28% helix, 11% strand	—
3	50S ribosomal protein L7AE	protein	123	37% helix, 9% strand	P62008
L	30S ribosomal protein S10	protein	102	21% helix, 47% strand	Q9V0V6
O	30S ribosomal protein S13	protein	148	34% helix, 8% strand	Q9V1A0
P	30S ribosomal protein S14 type Z	protein	56	20% helix, 2% strand	P62012
S	30S ribosomal protein S17E	protein	67	70% helix, 0% strand	Q9V0G0
T	30S ribosomal protein S19	protein	111	24% helix, 13% strand	Q9V1T9
U	30S ribosomal protein S19E	protein	144	53% helix, 6% strand	Q9V0G8
X	30S ribosomal protein S28E	protein	71	0% helix, 38% strand	P61029
Y	30S ribosomal protein S27AE	protein	50	0% helix, 30% strand	P61238
H	30S ribosomal protein S7	protein	214	43% helix, 7% strand	Q9V109
K	30S ribosomal protein S9	protein	135	39% helix, 22% strand	Q9V195
0	30S ribosomal protein EL41	protein	22	91% helix, 0% strand	—
4	Initiator met-tRNA fmet from E. COLI (A1U72 variant)	rna	76	—	—
5	MRNA	rna	18	—	—
1	Protein translation factor SUI1 homolog	protein	83	27% helix, 27% strand	—
6	Translation initiation factor 1A	protein	95	16% helix, 36% strand	Q9V138
7	Translation initiation factor 2 subunit gamma	protein	409	17% helix, 34% strand	—
8	Translation initiation factor 2 subunit beta	protein	129	33% helix, 17% strand	—
9	Translation initiation factor 2 subunit alpha	protein	254	31% helix, 22% strand	—

Ligands and binding sites

MET · Methionine · ligand · chains 4, 7
GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains 7, 8
MG · Magnesium ion · metal · chains 7
ZN · Zinc ion · metal · chains 8

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	1039	0.88	0.90	81	empty
2	998	0.86	0.88	96	empty
3	922	0.85	0.88	79	empty
4	1018	0.85	0.87	87	empty
5	856	0.85	0.88	105	empty

Interfaces

81 interfaces between chains.

2–E · 4460 Å² buried · 67 hydrogen bonds · protein-nucleic
2–N · 3560 Å² buried · 69 hydrogen bonds · protein-nucleic
2–K · 3499 Å² buried · 72 hydrogen bonds · protein-nucleic
2–J · 3431 Å² buried · 67 hydrogen bonds · protein-nucleic
2–Q · 3308 Å² buried · 81 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 modified, 1 disulfide (nucleotide modification, disulfide).

Compared structures

5JB3 · Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the… · the same entry in another collection · chain Y against Y, 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 P62010
Every structure of UniProt P61994
Every structure of UniProt Q9V2K9
Every structure of UniProt Q9V1U5
Every structure of UniProt Q9V2K7
Every structure of UniProt Q9V191
Every structure of UniProt Q9UY20
Every structure of UniProt Q9UXZ3
Every structure of UniProt Q9V1U1
Every structure of UniProt P61992
Every structure of UniProt Q9V1U8
Every structure of UniProt Q9V1V5
Every structure of UniProt Q9UYS3
Every structure of UniProt Q9V1V0
Every structure of UniProt Q9UZL4
Every structure of UniProt P62008
Every structure of UniProt Q9V0V6
Every structure of UniProt Q9V1A0
Every structure of UniProt P62012
Every structure of UniProt Q9V0G0
Every structure of UniProt Q9V1T9
Every structure of UniProt Q9V0G8
Every structure of UniProt P61029
Every structure of UniProt P61238
Every structure of UniProt Q9V109
Every structure of UniProt Q9V195
Every structure of UniProt Q9V138
Elsewhere: RCSB PDB 5JB3 · PDBe 5JB3 · UniProt P62010 · UniProt P61994 · UniProt Q9V2K9 · UniProt Q9V1U5 · UniProt Q9V2K7 · UniProt Q9V191 · UniProt Q9UY20 · UniProt Q9UXZ3 · UniProt Q9V1U1 · UniProt P61992 · UniProt Q9V1U8 · UniProt Q9V1V5 · UniProt Q9UYS3 · UniProt Q9V1V0 · UniProt Q9UZL4 · UniProt P62008 · UniProt Q9V0V6 · UniProt Q9V1A0 · UniProt P62012 · UniProt Q9V0G0 · UniProt Q9V1T9 · UniProt Q9V0G8 · UniProt P61029 · UniProt P61238 · UniProt Q9V109 · UniProt Q9V195 · UniProt Q9V138

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