MolNFT v2 · #173730 · protein + RNA

Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis

6ZJ3 · 18S rRNA: “Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis”. Electron microscopy at 3.15, 1 ligand (ZN), 20 pockets (best druggability 0.90). MolNFT v2 #173730 on GenesisL1: 3D structure, binding…

PDB: 6ZJ3
Type: protein + RNA
Length: 17,647 residues
Chains: 98
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.15
Source: Euglena gracilis
Molecule: 18S rRNA; A-tRNA; P-tRNA; E-tRNA; A-site tRNA; Ribosomal protein eS1; Ribosomal protein…
UniProt: Q4VH13, Q39724
Ligands: ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 3.15 · 98 distinct chains · 32% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
S1	18S rRNA	rna	2024	—	—
S2	A-tRNA	rna	76	—	—
S3	P-tRNA	rna	76	—	—
S4	E-tRNA	rna	76	—	—
S5	A-site tRNA	rna	12	—	—
SA	Ribosomal protein eS1	protein	221	30% helix, 32% strand	—
SB	Ribosomal protein uS2	protein	207	34% helix, 13% strand	—
SC	Ribosomal protein uS3	protein	212	36% helix, 27% strand	—
SD	Ribosomal protein uS4	protein	177	47% helix, 7% strand	—
SE	Ribosomal protein eS4	protein	265	14% helix, 29% strand	—
SF	Ribosomal protein uS5	protein	221	31% helix, 26% strand	—
SG	Ribosomal protein eS6	protein	248	34% helix, 21% strand	—
SH	Ribosomal protein uS7	protein	182	51% helix, 6% strand	—
SI	Ribosomal protein eS7	protein	187	33% helix, 21% strand	—
SJ	Ribosomal protein uS8	protein	129	33% helix, 26% strand	—
SK	Ribosomal protein eS8	protein	199	25% helix, 21% strand	—
SL	Ribosomal protein uS9	protein	143	41% helix, 19% strand	—
SM	Ribosomal protein uS10	protein	101	26% helix, 48% strand	—
SN	Ribosomal protein eS10	protein	92	41% helix, 20% strand	—
SO	Ribosomal protein uS11	protein	135	24% helix, 25% strand	—
SP	Ribosomal protein uS12	protein	141	23% helix, 29% strand	—
SQ	Ribosomal protein eS12	protein	122	40% helix, 11% strand	—
SR	Ribosomal protein uS13	protein	146	41% helix, 8% strand	—
SS	Ribosomal protein uS14	protein	52	21% helix, 10% strand	—
ST	Ribosomal protein uS15	protein	148	53% helix, 1% strand	—
SU	Ribosomal protein uS17	protein	148	3% helix, 30% strand	—
SV	Ribosomal protein eS17	protein	125	58% helix, 0% strand	—
SW	Ribosomal protein uS19	protein	125	34% helix, 13% strand	—
SX	Ribosomal protein eS19	protein	143	39% helix, 7% strand	—
SY	Ribosomal protein eS21	protein	82	21% helix, 22% strand	—
SZ	Ribosomal protein eS24	protein	127	35% helix, 26% strand	—
Sa	Ribosomal protein eS25	protein	78	42% helix, 17% strand	—
Sb	Ribosomal protein eS26	protein	97	18% helix, 20% strand	—
Sc	Ribosomal protein eS27	protein	84	7% helix, 21% strand	—
Sd	Ribosomal protein eS28	protein	63	0% helix, 48% strand	—
Se	Ribosomal protein eS30	protein	64	33% helix, 0% strand	—
Sf	Ribosomal protein eS31	protein	64	8% helix, 23% strand	—
Sg	Ribosomal protein eSEug1	protein	199	36% helix, 15% strand	—
Sh	RACK1	protein	311	0% helix, 44% strand	—
LA	5.8S rRNA	rna	160	—	—
LB	LSU rRNA chain 1	rna	133	—	—
LC	LSU rRNA chain 2	rna	350	—	—
LD	LSU rRNA chain 3	rna	110	—	—
LE	LSU rRNA chain 4	rna	652	—	—
LF	LSU rRNA chain 5	rna	456	—	—
LG	LSU rRNA chain 6	rna	207	—	—
LH	LSU rRNA chain 7	rna	559	—	—
LI	LSU rRNA chain 8	rna	573	—	—
LJ	LSU rRNA chain 9	rna	163	—	—
LK	LSU rRNA chain 10	rna	61	—	—
LL	LSU rRNA chain 11	rna	92	—	—
LM	LSU rRNA chain 12	rna	54	—	—
LN	LSU rRNA chain 13	rna	79	—	—
LO	5S rRNA	rna	120	—	—
LP	Ribosomal protein uL2	protein	249	8% helix, 27% strand	—
LQ	Ribosomal protein uL3	protein	392	18% helix, 27% strand	—
LR	Ribosomal protein uL4	protein	365	39% helix, 8% strand	—
LS	Ribosomal protein uL5	protein	178	32% helix, 26% strand	—
LT	Ribosomal protein uL6	protein	190	21% helix, 38% strand	—
LU	Ribosomal protein eL6	protein	194	28% helix, 15% strand	—
LV	60S ribosomal protein L7a	protein	238	50% helix, 6% strand	Q4VH13
LW	Ribosomal protein uL13	protein	208	53% helix, 9% strand	—
LX	Ribosomal protein eL13	protein	219	39% helix, 8% strand	—
LY	Ribosomal protein uL14	protein	134	9% helix, 27% strand	—
LZ	Ribosomal protein eL14	protein	217	40% helix, 14% strand	—
La	Ribosomal protein uL15	protein	151	29% helix, 14% strand	—
Lb	Ribosomal protein eL15	protein	203	42% helix, 18% strand	—
Lc	60S ribosomal protein L10	protein	203	24% helix, 24% strand	Q39724
Ld	Ribosomal protein uL18	protein	260	38% helix, 10% strand	—
Le	Ribosomal protein eL18	protein	192	27% helix, 14% strand	—
Lf	Ribosomal protein eL19	protein	170	65% helix, 4% strand	—
Lg	Ribosomal protein eL20	protein	181	21% helix, 30% strand	—
Lh	Ribosomal protein eL21	protein	158	19% helix, 23% strand	—
Li	Ribosomal protein uL22	protein	155	35% helix, 25% strand	—
Lj	Ribosomal protein eL22	protein	101	32% helix, 32% strand	—
Lk	Ribosomal protein uL23	protein	131	28% helix, 20% strand	—
Ll	Ribosomal protein uL24	protein	124	31% helix, 24% strand	—
Lm	Ribosomal protein eL24	protein	66	26% helix, 17% strand	—
Ln	Ribosomal protein eL27	protein	133	29% helix, 28% strand	—
Lo	Ribosomal protein eLEgr1	protein	58	47% helix, 3% strand	—
Lp	Ribosomal protein uL29	protein	121	63% helix, 2% strand	—
Lq	Ribosomal protein eL29	protein	91	62% helix, 1% strand	—
Lr	Ribosomal protein uL30	protein	218	52% helix, 15% strand	—
Ls	Ribosomal protein eL30	protein	97	41% helix, 19% strand	—
Lt	Ribosomal protein eL31	protein	111	27% helix, 25% strand	—
Lu	Ribosomal protein eL32	protein	128	24% helix, 9% strand	—
Lv	Ribosomal protein eL33	protein	114	6% helix, 54% strand	—
Lw	Ribosomal protein eL34	protein	114	32% helix, 9% strand	—
Lx	Ribosomal protein eL36	protein	102	62% helix, 1% strand	—
Ly	Ribosomal protein eL37	protein	106	30% helix, 6% strand	—
Lz	Ribosomal protein eL38	protein	70	23% helix, 34% strand	—
L1	Ribosomal protein eL39	protein	50	32% helix, 0% strand	—
L2	Ribosomal protein eL40	protein	51	22% helix, 16% strand	—
L3	Ribosomal protein eL41	protein	33	67% helix, 0% strand	—
L5	Ribosomal protein eL42	protein	90	38% helix, 18% strand	—
L4	Ribosomal protein eL43	protein	97	10% helix, 31% strand	—
L6	Ribosomal protein eLEgr2	protein	59	58% helix, 0% strand	—
L7	Ribosomal protein eLEgr3	protein	54	91% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains Sb, Ly, L2, L5, L4

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	932	0.90	0.93	117	empty
2	1171	0.89	0.91	134	empty
3	779	0.89	0.93	78	empty
4	1033	0.88	0.91	94	empty
5	745	0.88	0.92	95	empty

Interfaces

459 interfaces between chains.

LH–LI · 9982 Å² buried · 483 hydrogen bonds · nucleic-nucleic
S1–SG · 6002 Å² buried · 136 hydrogen bonds · protein-nucleic
LE–LF · 5610 Å² buried · 258 hydrogen bonds · nucleic-nucleic
LF–LH · 5411 Å² buried · 237 hydrogen bonds · nucleic-nucleic
S1–SE · 4829 Å² buried · 79 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 317 modified, 1 disulfide (nucleotide modification, disulfide).

Compared structures

Q39724 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L10 (Q39724) · a predicted model of the same protein · chain Lc against A, TM-score 0.95

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 Q4VH13
Every structure of UniProt Q39724
Elsewhere: RCSB PDB 6ZJ3 · PDBe 6ZJ3 · UniProt Q4VH13 · UniProt Q39724

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