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tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-2 (TI-POST-2)

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: 6GZ4
Type: protein + RNA
Length: 18,458 residues
Chains: 86
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.6
Source: Oryctolagus cuniculus
Molecule: ribosomal protein uL2; ribosomal protein uS2; ribosomal protein uL3; ribosomal protein…
Ligands: GNP, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 3.6 · 86 distinct chains · 30% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
AA	ribosomal protein uL2	protein	252	10% helix, 25% strand	—
BA	ribosomal protein uS2	protein	215	36% helix, 13% strand	—
AB	ribosomal protein uL3	protein	394	15% helix, 24% strand	—
BB	ribosomal protein eS1	protein	212	27% helix, 28% strand	—
AC	ribosomal protein uL4	protein	363	36% helix, 10% strand	—
BC	ribosomal protein eS28	protein	222	32% helix, 27% strand	—
A2	28S ribosomal RNA	rna	3612	—	—
Bv	ap/P-site tRNA	rna	76	—	—
Bx	mRNA	rna	11	—	—
Bw	pe/E-site-tRNA	rna	76	—	—
B1	18S ribosomal RNA	rna	1708	—	—
BD	ribosomal protein uS3	protein	220	30% helix, 28% strand	—
BF	ribosomal protein uS7	protein	190	47% helix, 5% strand	—
BK	ribosomal protein eS10	protein	98	37% helix, 13% strand	—
BM	ribosomal protein eS12	protein	120	44% helix, 15% strand	—
BP	ribosomal protein uS19	protein	120	29% helix, 12% strand	—
BQ	ribosomal protein uS9	protein	139	32% helix, 17% strand	—
BR	ribosomal protein eS17	protein	125	50% helix, 2% strand	—
BS	ribosomal protein uS13	protein	139	34% helix, 4% strand	—
BT	ribosomal protein eS19	protein	143	52% helix, 12% strand	—
BU	ribosomal protein uS10	protein	97	24% helix, 30% strand	—
BZ	ribosomal protein uS10	protein	86	38% helix, 10% strand	—
Bc	ribosomal protein eS28	protein	62	0% helix, 39% strand	—
Bd	ribosomal protein uS14	protein	51	24% helix, 2% strand	—
Bf	ribosomal protein eS31	protein	73	0% helix, 25% strand	—
Bg	ribosomal protein RACK 1	protein	314	0% helix, 50% strand	—
BE	ribosomal protein eS4	protein	257	18% helix, 30% strand	—
BG	ribosomal protein eS6	protein	232	28% helix, 22% strand	—
BH	ribosomal protein eS7	protein	183	33% helix, 20% strand	—
BI	ribosomal protein eS8	protein	207	25% helix, 24% strand	—
BJ	ribosomal protein uS4	protein	179	48% helix, 2% strand	—
BL	ribosomal protein uS17	protein	153	0% helix, 27% 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	22% helix, 25% strand	—
BW	ribosomal protein uS8	protein	129	33% helix, 25% strand	—
BX	ribosomal protein uS12	protein	141	19% helix, 26% strand	—
BY	ribosomal protein eS24	protein	125	34% helix, 27% strand	—
Ba	ribosomal protein eS26	protein	97	9% helix, 24% strand	—
Bb	ribosomal protein eS27	protein	80	8% helix, 23% strand	—
Be	ribosomal protein eS30	protein	55	29% helix, 0% strand	—
A3	5.8S ribosomal RNA	rna	157	—	—
A4	5S ribosomal RNA	rna	119	—	—
AD	ribosomal protein uL18	protein	294	40% helix, 11% strand	—
AE	ribosomal protein eL6	protein	194	14% helix, 15% strand	—
AF	ribosomal protein uL30	protein	234	50% helix, 11% strand	—
AG	ribosomal protein eL8	protein	234	48% helix, 9% strand	—
AH	ribosomal protein uL6	protein	191	20% helix, 36% strand	—
AI	ribosomal protein uL16	protein	208	21% helix, 25% strand	—
AJ	ribosomal protein uL5	protein	169	27% helix, 19% strand	—
AL	ribosomal protein eL13	protein	205	35% helix, 7% strand	—
AM	ribosomal protein eL14	protein	139	45% helix, 22% 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	29% helix, 11% strand	—
AR	ribosomal protein eL19	protein	181	71% helix, 0% strand	—
AS	ribosomal protein eL20	protein	175	20% helix, 30% strand	—
AT	ribosomal protein eL21	protein	157	16% helix, 20% strand	—
AU	ribosomal protein eL22	protein	99	30% helix, 23% strand	—
AV	ribosomal protein uL14	protein	129	9% helix, 39% strand	—
AW	ribosomal protein eL24	protein	121	40% helix, 10% strand	—
AX	ribosomal protein uL23	protein	117	26% helix, 22% strand	—
AY	ribosomal protein uL24	protein	127	31% helix, 27% strand	—
AZ	ribosomal protein eL27	protein	134	23% helix, 27% strand	—
Aa	ribosomal protein uL15	protein	147	20% helix, 13% strand	—
Ab	ribosomal protein eL29	protein	68	53% helix, 0% strand	—
Ac	ribosomal protein eL30	protein	103	50% helix, 17% strand	—
Ad	ribosomal protein eL31	protein	106	28% helix, 25% strand	—
Ae	ribosomal protein eL32	protein	129	22% helix, 9% strand	—
Af	ribosomal protein eL33	protein	109	0% helix, 45% strand	—
Ag	ribosomal protein eL34	protein	114	26% helix, 7% strand	—
Ah	ribosomal protein uL29	protein	122	61% helix, 3% strand	—
Ai	ribosomal protein eL36	protein	97	61% helix, 0% strand	—
Aj	ribosomal protein eL37	protein	84	21% helix, 6% strand	—
Ak	ribosomal protein eL38	protein	69	26% helix, 33% 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	26% helix, 8% strand	—
AK	ribosomal protein uL10	protein	202	28% helix, 14% strand	—
Ct	eukaryotic elongation factor 2 (eEF2)	protein	853	31% helix, 18% strand	—

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains Ct
MG · Magnesium ion · metal · 327 copies · chains AA, A2, AR, Af, AL, Aa, Al, AO, B1, BI, Ag, AN, AP, AB, Aj, AD, AC, Ai, AQ, Ab, Ct, A3, A4, AF, Ae, Bx, BU, BQ, BN, BD, Bd, BS, BX, 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	775	0.89	0.93	102	MG
2	975	0.89	0.91	106	empty
3	749	0.89	0.93	110	empty
4	1039	0.89	0.91	90	MG
5	1114	0.88	0.91	99	MG

Interfaces

278 interfaces between chains.

AB–A2 · 9688 Å² buried · 183 hydrogen bonds · protein-nucleic
AC–A2 · 9048 Å² buried · 165 hydrogen bonds · protein-nucleic
AA–A2 · 7863 Å² buried · 170 hydrogen bonds · protein-nucleic
A2–AN · 7314 Å² buried · 138 hydrogen bonds · protein-nucleic
A2–Aa · 5492 Å² buried · 129 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 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 6GZ4 · PDBe 6GZ4

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