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tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)

Analyse tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GZ5
Type: protein + RNA
Length: 18,458 residues
Chains: 86
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.5
Source: Enterobacteria phage SP6; Oryctolagus cuniculus; Saccharomyces cerevisiae
Molecule: 28S ribosomal RNA; P/P-site-tRNA; mRNA; E/E-site-tRNA; 18S ribosomal RNA; ribosomal…
Ligands: GNP, MG, ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 3.5 · 86 distinct chains · 30% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A2	28S ribosomal RNA	rna	3612	—	—
Bv	P/P-site-tRNA	rna	76	—	—
Bx	mRNA	rna	11	—	—
Bw	E/E-site-tRNA	rna	76	—	—
B1	18S ribosomal RNA	rna	1708	—	—
BD	ribosomal protein uS3	protein	220	33% helix, 26% strand	—
BF	ribosomal protein uS7	protein	190	45% helix, 4% strand	—
BK	ribosomal protein eS10	protein	98	36% helix, 13% strand	—
BM	ribosomal protein eS12	protein	120	44% helix, 13% strand	—
BP	ribosomal protein uS19	protein	120	29% helix, 12% strand	—
BQ	ribosomal protein uS9	protein	139	29% helix, 16% strand	—
BR	ribosomal protein eS17	protein	125	52% helix, 1% strand	—
BS	ribosomal protein uS13	protein	139	37% helix, 4% strand	—
BT	ribosomal protein eS19	protein	143	52% helix, 7% strand	—
BU	ribosomal protein uS10	protein	97	24% helix, 26% strand	—
BZ	ribosomal protein eS25	protein	86	36% helix, 9% strand	—
Bc	ribosomal protein eS28	protein	62	0% helix, 34% strand	—
Bd	ribosomal protein uS14	protein	51	18% helix, 2% strand	—
Bf	ribosomal protein eS31	protein	73	0% helix, 8% strand	—
Bg	ribosomal protein RACK 1	protein	314	0% helix, 50% strand	—
BA	ribosomal protein uS2	protein	215	36% helix, 13% strand	—
BB	ribosomal protein eS1	protein	212	26% helix, 31% strand	—
BC	ribosomal protein uS5	protein	222	32% helix, 27% strand	—
BE	ribosomal protein eS4	protein	257	18% helix, 30% strand	—
BG	ribosomal protein eS6	protein	232	28% helix, 23% strand	—
BH	ribosomal protein eS7	protein	183	32% helix, 18% strand	—
BI	ribosomal protein eS8	protein	207	25% helix, 23% strand	—
BJ	ribosomal protein uS4	protein	179	49% helix, 1% strand	—
BL	ribosomal protein uS17	protein	153	0% helix, 25% strand	—
BN	ribosomal protein uS15	protein	149	56% helix, 0% strand	—
BO	ribosomal protein uS11	protein	136	21% helix, 24% strand	—
BV	ribosomal protein eS21	protein	81	23% helix, 27% strand	—
BW	ribosomal protein uS8	protein	129	33% helix, 27% strand	—
BX	ribosomal protein uS12	protein	141	18% helix, 28% strand	—
BY	ribosomal protein eS24	protein	125	34% helix, 26% strand	—
Ba	ribosomal protein eS26	protein	97	13% helix, 22% strand	—
Bb	ribosomal protein eS27	protein	80	8% helix, 18% strand	—
Be	ribosomal protein eS30	protein	55	29% helix, 0% strand	—
A3	5.8S ribosomal RNA	rna	157	—	—
A4	5S ribosomal RNA	rna	119	—	—
AA	ribosomal protein uL2	protein	252	10% helix, 24% strand	—
AB	ribosomal protein uL3	protein	394	16% helix, 25% strand	—
AC	ribosomal protein uL4	protein	363	36% helix, 10% strand	—
AD	ribosomal protein uL18	protein	294	39% helix, 11% strand	—
AE	ribosomal protein eL6	protein	194	14% helix, 15% strand	—
AF	ribosomal protein uL30	protein	234	53% helix, 10% strand	—
AG	ribosomal protein eL8	protein	234	47% helix, 7% strand	—
AH	ribosomal protein uL6	protein	191	20% helix, 37% strand	—
AI	ribosomal protein uL16	protein	208	22% helix, 25% strand	—
AJ	ribosomal protein uL5	protein	169	27% helix, 20% strand	—
AL	ribosomal protein eL13	protein	205	40% helix, 7% strand	—
AM	ribosomal protein eL14	protein	139	45% helix, 20% strand	—
AN	ribosomal protein eL15	protein	203	36% helix, 18% strand	—
AO	ribosomal protein uL13	protein	195	55% helix, 11% strand	—
AP	ribosomal protein uL22	protein	153	34% helix, 27% strand	—
AQ	ribosomal protein eL18	protein	187	28% helix, 12% strand	—
AR	ribosomal protein eL19	protein	181	69% helix, 0% strand	—
AS	ribosomal protein eL20	protein	175	21% helix, 30% strand	—
AT	ribosomal protein eL21	protein	157	17% helix, 21% strand	—
AU	ribosomal protein eL22	protein	99	31% helix, 26% strand	—
AV	ribosomal protein uL14	protein	129	9% helix, 35% strand	—
AW	ribosomal protein eL24	protein	121	40% helix, 10% strand	—
AX	ribosomal protein uL23	protein	117	28% helix, 22% strand	—
AY	ribosomal protein uL24	protein	127	31% helix, 25% strand	—
AZ	ribosomal protein eL27	protein	134	23% helix, 27% strand	—
Aa	ribosomal protein uL15	protein	147	22% helix, 12% strand	—
Ab	ribosomal protein eL29	protein	68	50% helix, 0% strand	—
Ac	ribosomal protein eL30	protein	103	50% helix, 17% strand	—
Ad	ribosomal protein eL31	protein	106	29% helix, 27% strand	—
Ae	ribosomal protein eL32	protein	129	22% helix, 9% strand	—
Af	ribosomal protein eL33	protein	109	0% helix, 47% strand	—
Ag	ribosomal protein eL34	protein	114	26% helix, 11% strand	—
Ah	ribosomal protein uL29	protein	122	64% helix, 3% strand	—
Ai	ribosomal protein eL36	protein	97	61% helix, 0% strand	—
Aj	ribosomal protein eL37	protein	84	21% helix, 7% strand	—
Ak	ribosomal protein eL38	protein	69	26% helix, 35% strand	—
Al	ribosomal protein eL39	protein	50	26% helix, 0% strand	—
Am	ribosomal protein eL40	protein	50	22% helix, 14% strand	—
An	ribosomal protein eL41	protein	25	84% helix, 0% strand	—
Ao	ribosomal protein eL42	protein	105	10% helix, 30% strand	—
Ap	ribosomal protein eL43	protein	91	41% helix, 12% strand	—
At	ribosomal protein eL28	protein	122	29% helix, 16% strand	—
Au	ribosomal protein uL1	protein	217	34% helix, 18% strand	—
Aq	ribosomal protein uL11	protein	151	27% helix, 9% strand	—
AK	ribosomal protein uL10	protein	202	27% helix, 17% strand	—
Ct	eukaryotic elongation factor 2 (eEF2)	protein	853	31% helix, 17% strand	—

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A2, Ct
MG · Magnesium ion · metal · 327 copies · chains A2, AR, Aa, AN, BI, AI, Ag, AP, AB, Aj, AD, AC, AO, AA, Ai, AL, AQ, Ab, AF, Ct, A3, A4, Ae, Bx, B1, BU, BQ, BC, BX, BD, Ba, AY, An
ZN · Zinc ion · metal · 5 copies · chains Bd, Ba, Aj, Ao, Ap

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	1009	0.90	0.93	137	MG
2	959	0.89	0.91	95	empty
3	827	0.89	0.93	79	MG
4	980	0.88	0.91	94	empty
5	1044	0.88	0.91	88	MG

Interfaces

278 interfaces between chains.

A2–AB · 9698 Å² buried · 183 hydrogen bonds · protein-nucleic
A2–AC · 9059 Å² buried · 160 hydrogen bonds · protein-nucleic
A2–AA · 7815 Å² buried · 164 hydrogen bonds · protein-nucleic
A2–AN · 7365 Å² buried · 142 hydrogen bonds · protein-nucleic
A2–Aa · 5506 Å² buried · 121 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 disulfide, 1 modified (disulfide, nonstandard).

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6GZ5 · PDBe 6GZ5

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