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Barcelona

Tissue biology and disease modelling

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Structural biology

Hamburg

Structural biology

Heidelberg

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Hinxton

EMBL-EBI: European Bioinformatics Institute

Rome

Epigenetics and neurobiology

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sample_name:"Translocon-associated protein subunit alpha" AND microscope_name:"FEI TITAN KRIOS"

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EMD-19197

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Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1

Release date: Jan. 24, 2024
Resolution: 2.90061 Å
EM Method: Single-particle
Fitted PDBs: 8rjc
Q-score: 0.568

Lewis AJO, Zhong F, Keenan RJ, Hegde RS

eLife (2024) 13 [ Pubmed: 38896445 DOI: doi:10.7554/eLife.95814 ]

Sample:

60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
Calnexin (67 kDa, Protein from Canis lupus familiaris)
60s ribosomal protein l13 (24 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l36a-like (12 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
Zinc ion (65 Da, Ligand)
5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
Translocon-associated protein subunit delta (18 kDa, Protein from Canis lupus familiaris)
Ribosomal protein l26 (17 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
Translocon-associated protein subunit alpha (32 kDa, Protein from Canis lupus familiaris)
60s ribosomal protein l37a (10 kDa, Protein from Oryctolagus)
Translocon-associated protein subunit beta (20 kDa, Protein from Canis lupus familiaris)
60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
El40 (11 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l18 (21 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
60s ribosomal protein l29 (24 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l35 (14 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l8 (28 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l21 (18 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l32 (15 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l35a (12 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l13 (23 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
Translocon-associated protein subunit gamma (21 kDa, Protein from Canis lupus familiaris)
60s ribosomal protein l39-like (6 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein ul30 (29 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l30 (12 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
Stress-associated endoplasmic reticulum protein (7 kDa, Protein from Canis lupus familiaris)
Protein transport protein sec61 subunit gamma (7 kDa, Protein from Canis lupus familiaris)
P-site trna (24 kDa, RNA from Sus scrofa)
Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l22 (14 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
Nascent chain (23 kDa, Protein from Bos taurus)
Ribosomal_l23en domain-containing protein (17 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Canis lupus familiaris)
Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l7a (36 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l28 (15 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l38 (8 kDa, Protein from Oryctolagus cuniculus)
5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
Magnesium ion (24 Da, Ligand)
80s ribosome translating a stalled, two-tmd nascent chain (derived from rhodopsin), and bound to sec61, the trap complex, and ramp4 (Complex from Canis lupus familiaris)
Large ribosomal subunit protein ul4 (47 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l31 (14 kDa, Protein from Oryctolagus cuniculus)
Protein transport protein sec61 subunit beta (9 kDa, Protein from Canis lupus familiaris)

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EMD-19198

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Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2

Release date: Jan. 24, 2024
Resolution: 2.78574 Å
EM Method: Single-particle
Fitted PDBs: 8rjd
Q-score: 0.573

Lewis AJO, Zhong F, Keenan RJ, Hegde RS

eLife (2024) 13 [ Pubmed: 38896445 DOI: doi:10.7554/eLife.95814 ]

Sample:

60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
Large ribosomal subunit protein el22 (14 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l18 (21 kDa, Protein from Oryctolagus cuniculus)
5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
Large ribosomal subunit protein el38 (8 kDa, Protein from Oryctolagus)
80s ribosome translating a stalled, two-tmd nascent chain (derived from rhodopsin), and bound to sec61, the trap complex, and ramp4 (Complex from Canis lupus familiaris)
5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
60s ribosomal protein l13a (23 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l7a (36 kDa, Protein from Oryctolagus cuniculus)
Protein transport protein sec61 subunit gamma (7 kDa, Protein from Canis lupus familiaris)
Large ribosomal subunit protein ul23 n-terminal domain-containing protein (17 kDa, Protein from Oryctolagus)
60s ribosomal protein l39-like (6 kDa, Protein from Oryctolagus cuniculus)
P-site trna (24 kDa, RNA from Sus scrofa)
Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l29 (24 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
Translocon-associated protein subunit beta (20 kDa, Protein from Canis lupus familiaris)
60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
Translocon-associated protein subunit delta (18 kDa, Protein from Canis lupus familiaris)
Ribosomal protein l8 (28 kDa, Protein from Oryctolagus cuniculus)
Nascent chain (23 kDa, Protein from Bos taurus)
60s ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
Large ribosomal subunit protein el30 (12 kDa, Protein from Oryctolagus)
Translocon-associated protein subunit alpha (32 kDa, Protein from Canis lupus familiaris)
Ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
60s ribosomal protein l35 (14 kDa, Protein from Oryctolagus cuniculus)
El40 (11 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
Large ribosomal subunit protein ul4 (47 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
Translocon-associated protein subunit gamma (21 kDa, Protein from Canis lupus familiaris)
Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l28 (15 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l32 (15 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l35a (12 kDa, Protein from Oryctolagus cuniculus)
Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Canis lupus familiaris)
60s ribosomal protein l13 (24 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein ul30 (29 kDa, Protein from Oryctolagus cuniculus)
Protein transport protein sec61 subunit beta (9 kDa, Protein from Canis lupus familiaris)
Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
Zinc ion (65 Da, Ligand)
Stress-associated endoplasmic reticulum protein (7 kDa, Protein from Canis lupus familiaris)
Calnexin (67 kDa, Protein from Canis lupus familiaris)
60s ribosomal protein l21 (18 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l31 (14 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l36a-like (12 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l37a (10 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l26 (17 kDa, Protein from Oryctolagus)
60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)

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EMD-16017

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Molecular view of ER membrane remodeling by the Sec61/TRAP translocon.

Release date: Nov. 1, 2023
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 8bf9
Q-score: 0.552

Karki S, Javanainen M, Rehan S, Tranter D, Kellosalo J, Huiskonen JT, Happonen L, Paavilainen V

EMBO Rep (2023) 24 pp. e57910-e57910 [ Pubmed: 37983950 DOI: doi:10.15252/embr.202357910 ]

Sample:

Sec61a (52 kDa, Protein from Ovis aries)
Ribosomal protein l23/l25 n-terminal domain-containing protein (17 kDa, Protein from Ovis aries)
Rl26 protein (fragment) (15 kDa, Protein from Ovis aries)
Rna (1766) (1 MDa, RNA from Ovis aries)
Ribosomal protein l37 (11 kDa, Protein from Ovis aries)
Translocon-associated protein subunit alpha (39 kDa, Protein from Ovis aries)
Rna (156-mer) (50 kDa, RNA from Ovis aries)
Large ribosomal subunit protein ul22 (21 kDa, Protein from Ovis aries)
Large ribosomal subunit protein el31 (14 kDa, Protein from Ovis aries)
Mammlian ribosome sec61 trap complex (3 MDa, Complex from Ovis aries)
Large ribosomal subunit protein el38 (8 kDa, Protein from Ovis aries)
Translocon-associated protein subunit beta (20 kDa, Protein from Ovis aries)
Translocon-associated protein subunit delta (18 kDa, Protein from Ovis aries)
60s ribosomal protein l39 (6 kDa, Protein from Ovis aries)
Rl22 protein (fragment) (14 kDa, Protein from Ovis aries)
Sec61b (2 kDa, Protein from Ovis aries)
Protein transport protein sec61 subunit gamma (9 kDa, Protein from Ovis aries)
Large ribosomal subunit protein ul29 (14 kDa, Protein from Ovis aries)
Translocon-associated protein subunit gamma (21 kDa, Protein from Ovis aries)
Ribosomal protein l19 (23 kDa, Protein from Ovis aries)

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EMD-16232

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Structure of the TRAP complex with the Sec translocon and a translating ribosome

Release date: May 24, 2023
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8btk
Q-score: 0.362

Jaskolowski M, Jomaa A, Gamerdinger M, Shrestha S, Leibundgut M, Deuerling E, Ban N

Nat Struct Mol Biol (2023) 30 pp. 770-777 [ DOI: doi:10.1038/s41594-023-00990-0 Pubmed: 37170030 ]

Sample:

Ribosomal large subunit (60s) (Complex from Oryctolagus cuniculus)
60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
Us15 (17 kDa, Protein from Oryctolagus cuniculus)
Sec61 translocon (Complex from canis lupus familiaris)
P-site trna (24 kDa, RNA from Oryctolagus cuniculus)
P-site trna (Complex from Oryctolagus cuniculus)
Ribosomal protein s9 (predicted) (22 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s19 (16 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein ul1 (24 kDa, Protein from Oryctolagus cuniculus)
Translocon-associated protein subunit delta (18 kDa, Protein from Canis lupus familiaris)
El43 (10 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s11 (18 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l28 (15 kDa, Protein from Oryctolagus cuniculus)
El39 (6 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l22 (14 kDa, Protein from Oryctolagus cuniculus)
El32 (15 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l35 (14 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l21 (18 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
Rack1 (35 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s3a (30 kDa, Protein from Oryctolagus cuniculus)
Ribosomal_l23en domain-containing protein (17 kDa, Protein from Oryctolagus cuniculus)
Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Canis lupus familiaris)
60s ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s8 (24 kDa, Protein from Oryctolagus cuniculus)
Us9 (19 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein es17 (15 kDa, Protein from Oryctolagus cuniculus)
Spermidine (145 Da, Ligand)
Ul30,60s ribosomal protein l7 (29 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
Trap complex (Complex from canis lupus familiaris)
Zinc ion (65 Da, Ligand)
El42 (12 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s4 (29 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
Spermine (202 Da, Ligand)
40s ribosomal protein s21 (9 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l13a (23 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein us10 (13 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l8 (28 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s7 (47 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
El18 (21 kDa, Protein from Oryctolagus cuniculus)
L13 (24 kDa, Protein from Oryctolagus cuniculus)
Ribosomal small subunit (ssu) (Complex from Oryctolagus cuniculus)
Ubiquitin (14 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l12 (17 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein us19 (17 kDa, Protein from Oryctolagus cuniculus)
Structure of the trap complex with the sec translocon and a translating ribosome (Complex from Oryctolagus cuniculus)
Ribosomal protein l31 (14 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s12 (14 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein s27a (18 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l7a (30 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
Guanosine-5'-triphosphate (523 Da, Ligand)
5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
Signal sequence receptor subunit 3 (21 kDa, Protein from Canis lupus familiaris)
Ribosomal protein l26 (17 kDa, Protein from Oryctolagus cuniculus)
Nascent chain (2 kDa, Protein from Saccharomyces cerevisiae)
Acetylamino-acetic acid (117 Da, Ligand)
40s ribosomal protein s18 (17 kDa, Protein from Oryctolagus cuniculus)
28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
40s ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s14 (16 kDa, Protein from Oryctolagus cuniculus)
El30 (12 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l35a (12 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
Protein transport protein sec61 subunit gamma (7 kDa, Protein from Canis lupus familiaris)
Ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
Protein transport protein sec61 subunit beta (9 kDa, Protein from Canis lupus familiaris)
18s rrna (603 kDa, RNA from Oryctolagus cuniculus)
Ribosomal_s5_c domain-containing protein,40s ribosomal protein s2 (31 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s6 (28 kDa, Protein from Oryctolagus cuniculus)
Us14 (6 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
Es26 (13 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
Mrna (1 kDa, RNA from Oryctolagus cuniculus)
40s ribosomal protein sa (32 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein s5 (22 kDa, Protein from Oryctolagus cuniculus)
Translocon-associated protein subunit alpha (32 kDa, Protein from Canis lupus familiaris)
Translocon-associated protein subunit beta (20 kDa, Protein from Canis lupus familiaris)
El38 (8 kDa, Protein from Oryctolagus cuniculus)
Ribosomal protein es10 (18 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s30 (14 kDa, Protein from Oryctolagus cuniculus)
60s acidic ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
40s ribosomal protein s3 (31 kDa, Protein from Oryctolagus cuniculus)
60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
Magnesium ion (24 Da, Ligand)
5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
40s ribosomal protein s25 (13 kDa, Protein from Oryctolagus cuniculus)

[Show more]

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Showing 1 - 4 of 4. Page 1 of 1

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EMDB [4]

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