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Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7ug6
Q-score: 0.533
Yelland JN, Bravo JPK, Black JJ, Taylor DW, Johnson AW
Nat Struct Mol Biol (2023) 30 pp. 91-98 [ DOI: doi:10.1038/s41594-022-00891-8 Pubmed: 36536102 ]
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l12-a (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l39 (6 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l5 (33 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ribosome assembly protein 4 (56 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ribosome biogenesis protein nsa2 (29 kDa, Protein from Saccharomyces cerevisiae S288C)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ribosome biogenesis protein alb1 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l11-a (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ribosome assembly factor mrt4 (27 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae S288C)
- Nucle(ol)ar intermediate of large ribosomal subunit biogenesis, immunopurified by nog2-3xflag (Complex from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Nucleolar gtp-binding protein 2 (59 kDa, Protein from Saccharomyces cerevisiae S288C)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Nucleolar gtp-binding protein 1 (74 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Bud site selection protein 20 (18 kDa, Protein from Saccharomyces cerevisiae S288C)
- Nuclear gtp-binding protein nug1 (57 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ribosome biogenesis protein rpf2 (39 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae S288C)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae S288C)
- Upf0642 protein ybl028c (12 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae S288C)
- Regulator of ribosome biosynthesis (23 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l34-a (13 kDa, Protein from Saccharomyces cerevisiae S288C)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall map
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 7u0h
Q-score: 0.592
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 ]
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Nuclear gtp-binding protein nug1 (57 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)
- Magnesium ion (24 Da, Ligand)
- Nucleolar gtp-binding protein 2 (1 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein nop53 (52 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein 15 (25 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 27s pre-rrna (guanosine(2922)-2'-o)-methyltransferase (96 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l25 (15 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)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae BY4741)
- Early nucleoplasmic 60s intermediate purified with tags on nop53 and spb1. (2 MDa, Complex from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l43-a (10 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Its2 rrna (27 kDa, RNA from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l2-a (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Proteasome-interacting protein cic1 (42 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l28 (16 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Pescadillo homolog (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome assembly factor mrt4 (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein nsa2 (29 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Upf0642 protein ybl028c (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae BY4741)
Cryo-EM structure of the human SAGA complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8h7g
Q-score: 0.273
Zhang Y, Yin C, Yin Y, Wei M, Jing W, Peng C, Chen Z, Huang J
Cell Discov (2022) 8 pp. 125-125 [ Pubmed: 36414614 DOI: doi:10.1038/s41421-022-00489-w ]
- Human saga transcriptional coactivator complex (1 MDa, Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from human)
- Staga complex 65 subunit gamma (50 kDa, Protein from Homo sapiens)
- Transformation/transcription domain-associated protein (438 kDa, Protein from human)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from human)
- Transcription factor spt20 homolog (85 kDa, Protein from human)
- Transcription initiation protein spt3 homolog (35 kDa, Protein from human)
- Transcriptional adapter 1 (41 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from human)
- Ataxin-7 (95 kDa, Protein from human)
- Taf5-like rna polymerase ii p300/cbp-associated factor-associated factor 65 kda subunit 5l (66 kDa, Protein from human)
- Splicing factor 3b subunit 3 (135 kDa, Protein from human)
- Splicing factor 3b subunit 5 (10 kDa, Protein from human)
- Taf6-like rna polymerase ii p300/cbp-associated factor-associated factor 65 kda subunit 6l (67 kDa, Protein from human)
- Unassigned sequence (1 kDa, Protein from human)
Structure of WTAP-VIRMA in the m6A writer complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7yg4
Q-score: 0.471
Yan X, Pei K, Guan Z, Liu F, Yan J, Jin X, Wang Q, Hou M, Tang C, Yin P
Cell Res (2022) 32 pp. 1124-1127 [ DOI: doi:10.1038/s41422-022-00741-8 Pubmed: 36357785 ]
- Protein virilizer homolog (123 kDa, Protein from Homo sapiens)
- Wtap-virma complex (Complex from Homo sapiens)
- Pre-mrna-splicing regulator wtap (34 kDa, Protein from Homo sapiens)
State E2 nucleolar 60S ribosomal biogenesis intermediate - Overall map
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 ]
- 60s ribosomal protein l31-a (12 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)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Noc2 isoform 1 (81 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 l34-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 25s rrna (cytosine(2870)-c(5))-methyltransferase (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 5.8s ribosomal rna gene and internal transcribed spacer 2 (27 kDa, RNA from Saccharomyces cerevisiae BY4741)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein 15 (25 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 27s pre-rrna (guanosine(2922)-2'-o)-methyltransferase (96 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosome subunit biogenesis protein nip7 (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l25 (15 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)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal subunit assembly/export protein loc1 (23 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Atp-dependent rna helicase has1 (56 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Nucleolar protein 16 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Rrp17 isoform 1 (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Proteasome-interacting protein cic1 (42 kDa, Protein from Saccharomyces cerevisiae BY4741)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein brx1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Atp-dependent rrna helicase spb4 (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Rrna-processing protein ebp2 (49 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Nucleolar complex-associated protein 3 (75 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Pescadillo homolog (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ytm1 isoform 1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome assembly factor mrt4 (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein nsa2 (29 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosomal protein (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Upf0642 protein ybl028c (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae BY4741)
State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 7nad
Q-score: 0.547
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 ]
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Noc2 isoform 1 (81 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Rpl38 isoform 1 (8 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Pescadillo homolog (12 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 l34-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Rlp7 isoform 1 (36 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein erb1 (48 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l25 (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Nucleolar gtp-binding protein 1 (74 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Rpl8a isoform 1 (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Spb1 isoform 1 (96 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Rrp17 isoform 1 (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l23-a (4 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 25s rrna (225 kDa, RNA from Saccharomyces cerevisiae BY4741)
- 5.8s rrna (23 kDa, RNA from Saccharomyces cerevisiae BY4741)
- Ytm1 isoform 1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Noc3 isoform 1 (75 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Spb4 isoform 1 (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 locally refined map
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 7r72
Q-score: 0.519
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 ]
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Pescadillo homolog (12 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 l34-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Nucleolar complex protein 2 (81 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein ytm1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein erb1 (48 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 27s pre-rrna (guanosine(2922)-2'-o)-methyltransferase (96 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l25 (15 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)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 25s rrna (207 kDa, RNA from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Zinc ion (65 Da, Ligand)
- 5.8s rrna (23 kDa, RNA from Saccharomyces cerevisiae BY4741)
- Atp-dependent rrna helicase spb4 (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Nucleolar complex-associated protein 3 (75 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model
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 ]
- 60s ribosomal protein l31-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein erb1 (91 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Nuclear gtp-binding protein nug1 (57 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 l34-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 25s rrna (cytosine(2870)-c(5))-methyltransferase (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 5.8s ribosomal rna gene and internal transcribed spacer 2 (27 kDa, RNA from Saccharomyces cerevisiae BY4741)
- Nucleolar complex protein 2 (81 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l6-a (19 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l30 (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein 15 (25 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l23-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein rlp24 (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 27s pre-rrna (guanosine(2922)-2'-o)-methyltransferase (96 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosome subunit biogenesis protein nip7 (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l25 (15 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)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l22-a (13 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l21-a (18 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal subunit assembly/export protein loc1 (23 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Atp-dependent rna helicase has1 (56 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Nucleolar protein 16 (26 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Proteasome-interacting protein cic1 (42 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l38 (8 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein brx1 (33 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l19-a (21 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Atp-dependent rrna helicase spb4 (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Rrna-processing protein ebp2 (49 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Nucleolar complex-associated protein 3 (75 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Pescadillo homolog (69 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ytm1 isoform 1 (51 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome assembly factor mrt4 (27 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosome biogenesis protein nsa2 (29 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Ribosomal protein (24 kDa, Protein from Saccharomyces cerevisiae BY4741)
- Upf0642 protein ybl028c (12 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l27-a (15 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae BY4741)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae BY4741)
