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

Analyse Cryo-EM structure of a full archaeal ribosomal translation initiation complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JBH
Type: protein + RNA
Length: 6,155 residues
Chains: 36
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S ribosomal RNA; 30S ribosomal protein US3; 50S ribosomal protein UL30; 30S ribosomal…
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	—	—
Z	30S ribosomal protein US3	protein	186	38% helix, 28% strand	—
3	50S ribosomal protein UL30	protein	123	37% helix, 9% strand	—
L	30S ribosomal protein US10	protein	102	21% helix, 47% strand	—
O	30S ribosomal protein US13	protein	148	34% helix, 8% strand	—
P	30S ribosomal protein US14	protein	56	20% helix, 2% strand	—
S	30S ribosomal protein ES17	protein	67	70% helix, 0% strand	—
T	30S ribosomal protein US19	protein	111	24% helix, 13% strand	—
U	30S ribosomal protein ES19	protein	144	53% helix, 6% strand	—
X	30S ribosomal protein ES28	protein	71	0% helix, 38% strand	—
Y	30S ribosomal protein ES27	protein	50	0% helix, 30% strand	—
H	30S ribosomal protein US7	protein	214	43% helix, 7% strand	—
K	30S ribosomal protein US9	protein	135	39% helix, 22% strand	—
M	30S ribosomal protein US11	protein	133	20% helix, 24% strand	—
N	30S ribosomal protein US12	protein	145	21% helix, 25% strand	—
Q	30S ribosomal protein US15	protein	158	56% helix, 0% strand	—
R	30S ribosomal protein US17	protein	113	0% helix, 40% strand	—
A	30S ribosomal protein US3	protein	190	27% helix, 34% strand	—
B	30S ribosomal protein US2	protein	202	34% helix, 10% strand	—
V	30S ribosomal protein ES24	protein	99	22% helix, 30% strand	—
W	30S ribosomal protein ES27	protein	63	0% helix, 35% strand	—
D	30S ribosomal protein US4	protein	172	51% helix, 3% strand	—
E	30S ribosomal protein ES4	protein	241	7% helix, 32% strand	—
F	30S ribosomal protein US5	protein	217	30% helix, 24% strand	—
G	30S ribosomal protein ES6	protein	125	2% helix, 30% strand	—
I	30S ribosomal protein US8	protein	129	33% helix, 24% strand	—
J	30S ribosomal protein ES8	protein	127	6% helix, 28% strand	—
C	30S ribosomal protein sx	protein	57	28% helix, 11% strand	—
0	30S ribosomal protein EL41	protein	22	91% helix, 0% strand	—
5	MRNA	rna	18	—	—
1	AIF1	protein	80	31% helix, 28% strand	—
4	Initiator met-tRNA fmet from E. COLI (A1U72 variant)	rna	76	—	—
6	AIF1A	protein	95	19% helix, 36% strand	—
7	AIF2-gamma	protein	409	16% helix, 34% strand	—
8	AIF2-beta	protein	129	34% helix, 19% strand	—
9	AIF2-alpha	protein	253	36% helix, 24% strand	—

Ligands and binding sites

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

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	886	0.88	0.91	79	empty
2	823	0.87	0.91	87	empty
3	861	0.86	0.89	97	empty
4	995	0.86	0.88	69	empty
5	418	0.84	0.93	42	empty

Interfaces

86 interfaces between chains.

2–E · 4469 Å² buried · 67 hydrogen bonds · protein-nucleic
2–N · 3557 Å² buried · 69 hydrogen bonds · protein-nucleic
2–K · 3497 Å² buried · 72 hydrogen bonds · protein-nucleic
2–J · 3429 Å² buried · 67 hydrogen bonds · protein-nucleic
2–Q · 3305 Å² buried · 81 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 modified, 1 disulfide, 1 isopeptide (nucleotide modification, disulfide, isopeptide).

Compared structures

5JBH · Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-IN… · the same entry in another collection · chain O against O, 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
Elsewhere: RCSB PDB 5JBH · PDBe 5JBH

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