Electron Microscopy Data Bank

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sample_name:"60S ribosomal subunit assembly/export protein LOC1"

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EMD-43017

Download Map 3D View

60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)

Release date: May 1, 2024
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 8v83
Q-score: 0.53

Cruz VE, Weirich CS, Peddada N, Erzberger JP

Nat Commun (2024) 15 pp. 3296-3296 [ DOI: doi:10.1038/s41467-024-47616-7 Pubmed: 38632236 ]

Sample:

60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein ul13a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein el15a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
Saccharomyces cerevisiae s288c 25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosome subunit biogenesis protein nip7 (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosome biogenesis intermediate (Complex from Saccharomyces cerevisiae BY4741)
Pescadillo homolog (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
Zinc ion (65 Da, Ligand)
Saccharomyces cerevisiae its-2 (74 kDa, RNA 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 l36-a (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein nsa1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae BY4741)
Proteasome-interacting protein cic1 (42 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein el8a (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein ssf1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
Eukaryotic translation initiation factor 6 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein 15 (25 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar protein 16 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
Atp-dependent rna helicase has1 (56 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Saccharomyces cerevisiae s288c 5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae BY4741)
Protein mak16 (35 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein ul1a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar gtp-binding protein 1 (74 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp7 (36 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosomal rna-processing protein 1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosomal rna-processing protein 15 (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal subunit assembly/export protein loc1 (23 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome assembly factor mrt4 (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae BY4741)
Rrna-processing protein ebp2 (49 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein nsa2 (29 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein ul6a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosomal rna-processing protein 14 (50 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein el20a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein erb1 (91 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein brx1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
25s rrna (cytosine(2870)-c(5))-methyltransferase (69 kDa, Protein from Saccharomyces cerevisiae BY4741)

[Show more]

EMD-43021

Download Map 3D View

60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)

Release date: May 1, 2024
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8v84
Q-score: 0.461

Cruz VE, Weirich CS, Peddada N, Erzberger JP

Nat Commun (2024) 15 pp. 3296-3296 [ DOI: doi:10.1038/s41467-024-47616-7 Pubmed: 38632236 ]

Sample:

60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein ul13a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein el15a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosome subunit biogenesis protein nip7 (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosome biogenesis intermediate (Complex from Saccharomyces cerevisiae BY4741)
Pescadillo homolog (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
Atp-dependent rna helicase dbp10 (113 kDa, Protein from Saccharomyces cerevisiae BY4741)
Zinc ion (65 Da, Ligand)
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 l36-a (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein nsa1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae BY4741)
Proteasome-interacting protein cic1 (42 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein el8a (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein ssf1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
Eukaryotic translation initiation factor 6 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein ul3 (43 kDa, Protein from Saccharomyces cerevisiae BY4741-AV16)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein 15 (25 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar protein 16 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
Atp-dependent rna helicase has1 (56 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Protein mak16 (35 kDa, Protein from Saccharomyces cerevisiae BY4741)
Saccharomyces cerevisiae 25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein ul1a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar gtp-binding protein 1 (74 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp7 (36 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosomal rna-processing protein 1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosomal rna-processing protein 15 (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
Its2 rna (74 kDa, RNA from Saccharomyces cerevisiae BY4741)
60s ribosomal subunit assembly/export protein loc1 (23 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome assembly factor mrt4 (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
Rrna-processing protein ebp2 (49 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
Saccharomyces cerevisiae 5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae BY4741)
Magnesium ion (24 Da, Ligand)
Ribosome biogenesis protein nsa2 (29 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein ul6a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosomal rna-processing protein 14 (50 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein el20a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Guanosine-5'-diphosphate (443 Da, Ligand)
Ribosome biogenesis protein erb1 (91 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein brx1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
25s rrna (cytosine(2870)-c(5))-methyltransferase (69 kDa, Protein from Saccharomyces cerevisiae BY4741)

[Show more]

EMD-43027

Download Map 3D View

60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)

Release date: May 1, 2024
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8v87
Q-score: 0.519

Cruz VE, Weirich CS, Peddada N, Erzberger JP

Nat Commun (2024) 15 pp. 3296-3296 [ DOI: doi:10.1038/s41467-024-47616-7 Pubmed: 38632236 ]

Sample:

60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar complex-associated protein 3 (75 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein ul13a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein el15a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
5.8s ribosomal rna (50 kDa, RNA from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosome subunit biogenesis protein nip7 (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosome biogenesis intermediate (Complex from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae BY4741)
Pescadillo homolog (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
Atp-dependent rna helicase dbp10 (113 kDa, Protein from Saccharomyces cerevisiae BY4741)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae BY4741)
Upf0642 protein ybl028c (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ytm1 isoform 1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae BY4741)
Proteasome-interacting protein cic1 (42 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein el8a (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
Eukaryotic translation initiation factor 6 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein 15 (25 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar protein 16 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
Atp-dependent rna helicase has1 (56 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar gtp-binding protein 1 (74 kDa, Protein from Saccharomyces cerevisiae BY4741)
Potassium ion (39 Da, Ligand)
Large ribosomal subunit protein ul1a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp7 (36 kDa, Protein from Saccharomyces cerevisiae BY4741)
27s pre-rrna (guanosine(2922)-2'-o)-methyltransferase (96 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
Its2 rna (74 kDa, RNA from Saccharomyces cerevisiae BY4741)
60s ribosomal subunit assembly/export protein loc1 (23 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome assembly factor mrt4 (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nuclear gtp-binding protein nug1 (57 kDa, Protein from Saccharomyces cerevisiae BY4741)
Rrna-processing protein ebp2 (49 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
25s ribosomal rna (1 MDa, RNA from Saccharomyces cerevisiae BY4741)
Nucleolar complex protein 2 (81 kDa, Protein from Saccharomyces cerevisiae BY4741)
Adenosine-5'-diphosphate (427 Da, Ligand)
Magnesium ion (24 Da, Ligand)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein nsa2 (29 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein ul6a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
Large ribosomal subunit protein el20a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Guanosine-5'-diphosphate (443 Da, Ligand)
Ribosome biogenesis protein erb1 (91 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein brx1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
25s rrna (cytosine(2870)-c(5))-methyltransferase (69 kDa, Protein from Saccharomyces cerevisiae BY4741)

[Show more]

EMD-24269

Download Map 3D View

State E2 nucleolar 60S ribosomal biogenesis intermediate - Overall map

Release date: Nov. 9, 2022
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 7nac
Q-score: 0.549

Cruz VE, Sekulski K, Peddada N, Sailer C, Balasubramanian S, Weirich CS, Stengel F, Erzberger JP

Nat Struct Mol Biol (2022) 29 pp. 1228-1238 [ Pubmed: 36482249 DOI: doi:10.1038/s41594-022-00874-9 ]

Sample:

60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar complex-associated protein 3 (75 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar 60s intermediate purified with tags on ytm1 and spb4. (3 MDa, Complex from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosome subunit biogenesis protein nip7 (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Pescadillo homolog (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
Upf0642 protein ybl028c (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
5.8s ribosomal rna gene and internal transcribed spacer 2 (27 kDa, RNA from Saccharomyces cerevisiae BY4741)
Ytm1 isoform 1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
Proteasome-interacting protein cic1 (42 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein 15 (25 kDa, Protein from Saccharomyces cerevisiae BY4741)
Eukaryotic translation initiation factor 6 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar protein 16 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
25s rrna (1 MDa, RNA from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
Noc2 isoform 1 (81 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar gtp-binding protein 1 (74 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
Atp-dependent rna helicase has1 (56 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp7 (36 kDa, Protein from Saccharomyces cerevisiae BY4741)
27s pre-rrna (guanosine(2922)-2'-o)-methyltransferase (96 kDa, Protein from Saccharomyces cerevisiae BY4741)
Atp-dependent rrna helicase spb4 (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosomal protein (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
S-adenosyl-l-homocysteine (384 Da, Ligand)
60s ribosomal subunit assembly/export protein loc1 (23 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome assembly factor mrt4 (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein erb1 (91 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nuclear gtp-binding protein nug1 (57 kDa, Protein from Saccharomyces cerevisiae BY4741)
Rrna-processing protein ebp2 (49 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein nsa2 (29 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
Rrp17 isoform 1 (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein brx1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae BY4741)
25s rrna (cytosine(2870)-c(5))-methyltransferase (69 kDa, Protein from Saccharomyces cerevisiae BY4741)

[Show more]

EMD-24280

Download Map 3D View

State E2 nucleolar 60S ribosomal intermediate - Local Map for Noc2/Noc3 region

Release date: Nov. 9, 2022
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 7r6k
Q-score: 0.495

Cruz VE, Sekulski K, Peddada N, Sailer C, Balasubramanian S, Weirich CS, Stengel F, Erzberger JP

Nat Struct Mol Biol (2022) 29 pp. 1228-1238 [ Pubmed: 36482249 DOI: doi:10.1038/s41594-022-00874-9 ]

Sample:

Nucleolar complex-associated protein 3 (75 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar complex protein 2 (81 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
25s rrna (cytosine(2870)-c(5))-methyltransferase (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
Rrp17 isoform 1 (1 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosome subunit biogenesis protein nip7 (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein nsa2 (29 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar 60s intermediate purified with tags on ytm1 and spb4 (3 MDa, Complex from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
27s pre-rrna (guanosine(2922)-2'-o)-methyltransferase (96 kDa, Protein from Saccharomyces cerevisiae BY4741)
25s rrna (49 kDa, RNA from Saccharomyces cerevisiae BY4741)
60s ribosomal subunit assembly/export protein loc1 (23 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein erb1 (91 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein brx1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
Rrna-processing protein ebp2 (49 kDa, Protein from Saccharomyces cerevisiae BY4741)

[Show more]

EMD-24296

Download Map 3D View

State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model

Release date: Nov. 9, 2022
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 7r7a
Q-score: 0.527

Cruz VE, Sekulski K, Peddada N, Sailer C, Balasubramanian S, Weirich CS, Stengel F, Erzberger JP

Nat Struct Mol Biol (2022) 29 pp. 1228-1238 [ Pubmed: 36482249 DOI: doi:10.1038/s41594-022-00874-9 ]

Sample:

60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar complex-associated protein 3 (75 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar 60s intermediate purified with tags on ytm1 and spb4. (3 MDa, Complex from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosome subunit biogenesis protein nip7 (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Pescadillo homolog (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
Zinc ion (65 Da, Ligand)
60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l6-a (19 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
Upf0642 protein ybl028c (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
5.8s ribosomal rna gene and internal transcribed spacer 2 (27 kDa, RNA from Saccharomyces cerevisiae BY4741)
Ytm1 isoform 1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
Proteasome-interacting protein cic1 (42 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
Eukaryotic translation initiation factor 6 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar protein 16 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein 15 (25 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar gtp-binding protein 1 (74 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
Atp-dependent rna helicase has1 (56 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein rlp7 (36 kDa, Protein from Saccharomyces cerevisiae BY4741)
27s pre-rrna (guanosine(2922)-2'-o)-methyltransferase (96 kDa, Protein from Saccharomyces cerevisiae BY4741)
Atp-dependent rrna helicase spb4 (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosomal protein (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal subunit assembly/export protein loc1 (23 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome assembly factor mrt4 (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein erb1 (91 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nuclear gtp-binding protein nug1 (57 kDa, Protein from Saccharomyces cerevisiae BY4741)
Rrna-processing protein ebp2 (49 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar complex protein 2 (81 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein nsa2 (29 kDa, Protein from Saccharomyces cerevisiae BY4741)
25s rrna (1 MDa, RNA from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein brx1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae BY4741)
25s rrna (cytosine(2870)-c(5))-methyltransferase (69 kDa, Protein from Saccharomyces cerevisiae BY4741)

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EMD-24297

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State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local map

Release date: Nov. 9, 2022
Resolution: 3.71 Å
EM Method: Single-particle
Fitted PDBs: 7r7c
Q-score: 0.401

Cruz VE, Sekulski K, Peddada N, Sailer C, Balasubramanian S, Weirich CS, Stengel F, Erzberger JP

Nat Struct Mol Biol (2022) 29 pp. 1228-1238 [ Pubmed: 36482249 DOI: doi:10.1038/s41594-022-00874-9 ]

Sample:

Ribosome biogenesis protein nsa2 homolog (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
27s pre-rrna (guanosine(2922)-2'-o)-methyltransferase (1 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosomal protein l1-a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
25s rrna (72 kDa, RNA from Saccharomyces cerevisiae BY4741)
Nucleolar gtp-binding protein 1 (6 kDa, Protein from Saccharomyces cerevisiae BY4741)
60s ribosome subunit biogenesis protein nip7 (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein erb1 (6 kDa, Protein from Saccharomyces cerevisiae BY4741)
Nucleolar 60s intermediate purified with tags on ytm1 and spb4 (3 MDa, Complex from Saccharomyces cerevisiae BY4741)
60s ribosomal subunit assembly/export protein loc1 (23 kDa, Protein from Saccharomyces cerevisiae BY4741)
Rrna-processing protein ebp2 (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
Ribosome biogenesis protein brx1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
25s rrna (cytosine(2870)-c(5))-methyltransferase (69 kDa, Protein from Saccharomyces cerevisiae BY4741)

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