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proteasome* AND xref_links:"pfam" AND software_ft:"CTFFIND" AND film_detector_model:"GATAN K2 SUMMIT (4K X 4K)"

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EMD-31765

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CryoEM structure of DDB1-VprBP complex in ARM-up conformation

Release date: Aug. 31, 2022
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7v7b
Q-score: 0.262

Wang D, Xu J, Liu Q, Xiang Y

To Be Published

Sample:

Cryoem structure of ddb1-vprbp complex in "arm-up" conformation (Complex from Homo sapiens)
Ddb1- and cul4-associated factor 1 (169 kDa, Protein from Homo sapiens)
Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)

EMD-11807

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Cryo-EM structure of the 90S-exosome super-complex (state Pre-A1-exosome)

Release date: Dec. 30, 2020
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 7ajt
Q-score: 0.308

Lau B, Cheng J, Flemming D, La Venuta G, Berninghausen O, Beckmann R, Hurt E

Mol Cell (2021) 81 pp. 293- [ DOI: doi:10.1016/j.molcel.2020.11.009 Pubmed: 33326748 ]

Sample:

Atp-dependent rna helicase dob1 (122 kDa, Protein from Baker's yeast)
Exosome complex component rrp43 (44 kDa, Protein from Baker's yeast)
Nucleolar complex protein 4 (63 kDa, Protein from Baker's yeast)
40s ribosomal protein s11-a (17 kDa, Protein from Baker's yeast)
Rrna biogenesis protein rrp5 (193 kDa, Protein from Baker's yeast)
40s ribosomal protein s18-a (17 kDa, Protein from Baker's yeast)
Protein bfr2 (61 kDa, Protein from Baker's yeast)
Exosome complex component mtr3 (27 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 18 (66 kDa, Protein from Baker's yeast)
Rrna-processing protein fcf2 (25 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 8 (80 kDa, Protein from Baker's yeast)
40s ribosomal protein s16-a (15 kDa, Protein from Baker's yeast)
Rna cytidine acetyltransferase (119 kDa, Protein from Baker's yeast)
Guanosine-5'-triphosphate (523 Da, Ligand)
U3 small nucleolar rna-associated protein 12 (106 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 4 (87 kDa, Protein from Baker's yeast)
40s ribosomal protein s27-a (8 kDa, Protein from Baker's yeast)
Protein sof1 (56 kDa, Protein from Baker's yeast)
40s ribosomal protein s23-a (16 kDa, Protein from Baker's yeast)
Pre-rrna-processing protein pno1 (30 kDa, Protein from Baker's yeast)
Net1-associated nuclear protein 1 (101 kDa, Protein from Baker's yeast)
40s ribosomal protein s22-a (14 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 13 (91 kDa, Protein from Baker's yeast)
40s ribosomal protein s9-a (22 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 11 (29 kDa, Protein from Baker's yeast)
Ribosomal rna-processing protein 9 (65 kDa, Protein from Baker's yeast)
U3 small nucleolar ribonucleoprotein protein imp3 (21 kDa, Protein from Baker's yeast)
Exosome complex component rrp45 (34 kDa, Protein from Baker's yeast)
Exosome complex component rrp46 (24 kDa, Protein from Baker's yeast)
40s ribosomal protein s13 (17 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 7 (62 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 21 (104 kDa, Protein from Baker's yeast)
18s rrna (582 kDa, RNA from Saccharomyces cerevisiae S288C)
Ribosome biogenesis protein enp2 (81 kDa, Protein from Baker's yeast)
Ribosome biogenesis protein utp30 (31 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 14 (103 kDa, Protein from Baker's yeast)
Exosome complex component rrp40 (26 kDa, Protein from Baker's yeast)
Regulator of rdna transcription protein 14 (23 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein mpp10 (67 kDa, Protein from Baker's yeast)
Exosome complex component rrp42 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Ribosomal rna-processing protein 7 (34 kDa, Protein from Baker's yeast)
Something about silencing protein 10 (70 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 22 (140 kDa, Protein from Baker's yeast)
Nucleolar protein 56 (56 kDa, Protein from Baker's yeast)
40s ribosomal protein s4-a (29 kDa, Protein from Baker's yeast)
40s ribosomal protein s1-a (28 kDa, Protein from Baker's yeast)
Ribosome biogenesis protein bms1 (135 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 20 (287 kDa, Protein from Baker's yeast)
Bud site selection protein 21 (24 kDa, Protein from Baker's yeast)
Exosome complex component ski6 (27 kDa, Protein from Baker's yeast)
Zinc ion (65 Da, Ligand)
U3 small nucleolar rna-associated protein 9 (65 kDa, Protein from Baker's yeast)
40s ribosomal protein s14-a (14 kDa, Protein from Baker's yeast)
Nucleolar protein 58 (57 kDa, Protein from Baker's yeast)
Ribosomal rna small subunit methyltransferase nep1 (27 kDa, Protein from Baker's yeast)
U3 small nucleolar ribonucleoprotein protein imp4 (33 kDa, Protein from Baker's yeast)
40s ribosomal protein s28-a (7 kDa, Protein from Baker's yeast)
Rrna-processing protein fcf1 (21 kDa, Protein from Baker's yeast)
Rna 3'-terminal phosphate cyclase-like protein (40 kDa, Protein from Baker's yeast)
40s ribosomal protein s6-a (27 kDa, Protein from Baker's yeast)
13 kda ribonucleoprotein-associated protein (13 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 10 (200 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 5 (72 kDa, Protein from Baker's yeast)
Protein faf1 (38 kDa, Protein from Baker's yeast)
5'ets rna (225 kDa, RNA from Saccharomyces cerevisiae S288C)
U3 small nucleolar rna-associated protein 6 (52 kDa, Protein from Baker's yeast)
40s ribosomal protein s24-a (15 kDa, Protein from Baker's yeast)
90s-exosome super-complex in state pre-a1-exosome (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
40s ribosomal protein s5 (25 kDa, Protein from Baker's yeast)
40s ribosomal protein s8-a (22 kDa, Protein from Baker's yeast)
U3 small nucleolar rna-associated protein 15 (57 kDa, Protein from Baker's yeast)
Exosome complex component csl4 (31 kDa, Protein from Baker's yeast)
Rna (6 kDa, RNA from Saccharomyces cerevisiae S288C)
Rrna 2'-o-methyltransferase fibrillarin (34 kDa, Protein from Baker's yeast)
Krr1 small subunit processome component (37 kDa, Protein from Baker's yeast)
Nucleolar complex protein 14 (94 kDa, Protein from Baker's yeast)
Exosome complex exonuclease dis3 (113 kDa, Protein from Baker's yeast)
40s ribosomal protein s7-a (21 kDa, Protein from Baker's yeast)
Exosome complex component rrp4 (39 kDa, Protein from Baker's yeast)
Essential nuclear protein 1 (55 kDa, Protein from Baker's yeast)
Magnesium ion (24 Da, Ligand)
Periodic tryptophan protein 2 (104 kDa, Protein from Baker's yeast)
U3 snorna (106 kDa, RNA from Saccharomyces cerevisiae S288C)

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EMD-9045

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Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state)

Release date: Oct. 17, 2018
Resolution: 4.17 Å
EM Method: Single-particle
Fitted PDBs: 6ef3
Q-score: 0.46

de la Pena AH, Goodall EA, Gates SN, Lander GC, Martin A

Science (2018) 362 [ Pubmed: 30309908 DOI: doi:10.1126/science.aav0725 ]

Sample:

Proteasome subunit alpha type-4 (28 kDa, Protein from Saccharomyces cerevisiae S288c)
26s proteasome regulatory subunit 7 homolog (52 kDa, Protein from Saccharomyces cerevisiae S288c)
Proteasome subunit alpha type-1 (28 kDa, Protein from Saccharomyces cerevisiae S288c)
Proteasome subunit beta type-7 (1 kDa, Protein from Saccharomyces cerevisiae S288c)
Proteasome subunit beta type-1 (23 kDa, Protein from Saccharomyces cerevisiae S288c)
Proteasome subunit beta type-2 (28 kDa, Protein from Saccharomyces cerevisiae S288c)
Proteasome subunit beta type-4 (22 kDa, Protein from Saccharomyces cerevisiae S288c)
Proteasome subunit beta type-5 (31 kDa, Protein from Saccharomyces cerevisiae S288c)
26s proteasome regulatory subunit 4 homolog (48 kDa, Protein from Saccharomyces cerevisiae S288c)
Proteasome subunit alpha type-3 (28 kDa, Protein from Saccharomyces cerevisiae S288c)
26s proteasome regulatory subunit 8 homolog (45 kDa, Protein from Saccharomyces cerevisiae S288c)
Proteasome subunit beta type-6 (26 kDa, Protein from Saccharomyces cerevisiae S288c)
Probable proteasome subunit alpha type-7 (31 kDa, Protein from Saccharomyces cerevisiae S288c)
Proteasome subunit beta type-3 (22 kDa, Protein from Saccharomyces cerevisiae S288c)
Model substrate polypeptide (4 kDa, Protein from Homo sapiens)
Proteasome (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Ubiquitin carboxyl-terminal hydrolase rpn11 (34 kDa, Protein from Saccharomyces cerevisiae S288c)
Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Saccharomyces cerevisiae S288c)
Proteasome subunit alpha type-6 (25 kDa, Protein from Saccharomyces cerevisiae S288c)
26s proteasome regulatory subunit 6b homolog (47 kDa, Protein from Saccharomyces cerevisiae S288c)
26s proteasome subunit rpt4 (49 kDa, Protein from Saccharomyces cerevisiae S288c)
26s proteasome regulatory subunit 6a (48 kDa, Protein from Saccharomyces cerevisiae S288c)
Substrate-engaged 26s proteasome in the 4d state (Complex)
Adenosine-5'-diphosphate (427 Da, Ligand)
Proteasome subunit beta type-7 (29 kDa, Protein from Saccharomyces cerevisiae S288c)
Adenosine-5'-triphosphate (507 Da, Ligand)
Substrate (Complex from Homo sapiens)
Proteasome subunit alpha type-5 (28 kDa, Protein from Saccharomyces cerevisiae S288c)
Proteasome subunit alpha type-2 (27 kDa, Protein from Saccharomyces cerevisiae S288c)

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EMD-7324

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Yeast nucleolar pre-60S ribosomal subunit (state 2)

Release date: March 14, 2018
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6c0f
Q-score: 0.339

Sanghai ZA, Miller L, Molloy KR, Barandun J, Hunziker M, Chaker-Margot M, Wang J, Chait BT, Klinge S

Nature (2018) 556 pp. 126-129 [ Pubmed: 29512650 DOI: doi:10.1038/nature26156 ]

Sample:

Atp-dependent rna helicase has1 (56 kDa, Protein from Saccharomyces cerevisiae BY4741)
Protein mak16 (35 kDa, Protein from Saccharomyces cerevisiae BY4741)
Saccharomyces cerevisiae s288c 35s pre-ribosomal rna miscrna (1 MDa, RNA from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp7 (36 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome production factor 1 (35 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
Pescadillo homolog (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Brx1-associated peptide (2 kDa, Protein from Saccharomyces cerevisiae BY4741)
Protein mak11 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein 15 (25 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein ssf1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosomal rna-processing protein 14 (50 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein nsa1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Rrna-processing protein ebp2 (6 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein erb1 (89 kDa, Protein from Saccharomyces cerevisiae BY4741)
Eukaryotic translation initiation factor 6 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein brx1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
Zinc ion (65 Da, Ligand)
Ribosomal rna-processing protein 1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar gtp-binding protein 1 (74 kDa, Protein from Saccharomyces cerevisiae BY4741)
Yeast large subunit processome (Complex from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Its2 (74 kDa, RNA from Saccharomyces cerevisiae BY4741)
Nucleolar protein 16 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosomal rna-processing protein 15 (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
Proteasome-interacting protein cic1 (42 kDa, Protein from Saccharomyces cerevisiae BY4741)

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Showing 1 - 4 of 4. Page 1 of 1

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EMDB [4]

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