Human NEXT dimer in complex with the nuclear RNA exosome
Gerlach P, Garland W, Lingaraju M, Salerno-Kochan A, Bonneau F, Basquin J, Jensen TH, Conti E
Mol Cell (2022) 82 pp. 2505-2518.e7 [ Pubmed: 35688157 DOI: doi:10.1016/j.molcel.2022.04.011 ]
- Exosome complex component rrp45 (Protein from Homo sapiens)
- Rna 5 prime hairpin u60 (Complex from synthetic construct)
- Human next dimer in complex with the nuclear rna exosome (Complex)
- Human next dimer in complex with the nuclear rna exosome (Complex from Homo sapiens)
- Exosome complex component rrp4 (Protein from Homo sapiens)
- Rna-binding protein 7 (Protein from Homo sapiens)
- M-phase phosphoprotein 6 (Protein from Homo sapiens)
- Rna 5 prime hairpin u60 (RNA from synthetic construct)
- Nuclear nucleic acid-binding protein c1d (Protein from Homo sapiens)
- Exosome complex exonuclease rrp44 (Protein from Homo sapiens)
- Exosome complex component rrp46 (Protein from Homo sapiens)
- Exosome rna helicase mtr4 (Protein from Homo sapiens)
- Exosome complex component rrp41 (Protein from Homo sapiens)
- Exosome complex component rrp40 (Protein from Homo sapiens)
- Zinc finger cchc domain-containing protein 8 (Protein from Homo sapiens)
- Exosome complex component mtr3 (Protein from Homo sapiens)
- Exosome component 10 (Protein from Homo sapiens)
- Exosome complex component csl4 (Protein from Homo sapiens)
- Exosome complex component rrp42 (Protein from Homo sapiens)
Structure of the plant mitochondrial ribosome
Resolution: 3.86 Å
EM Method: Single-particle
Fitted PDBs: 6xyw
Q-score: 0.359
Waltz F, Soufari H, Bochler A, Giege P, Hashem Y
Nat Plants (2020) 6 pp. 377-383 [ Pubmed: 32251374 DOI: doi:10.1038/s41477-020-0631-5 ]
- F10k1.8 protein (29 kDa, Protein from Arabidopsis thaliana)
- At4g22000 (15 kDa, Protein from Arabidopsis thaliana)
- At5g55140 (12 kDa, Protein from Arabidopsis thaliana)
- At5g49210/k21p3_8 (23 kDa, Protein from Arabidopsis thaliana)
- Adenylyl cyclase (43 kDa, Protein from Arabidopsis thaliana)
- Expressed protein (22 kDa, Protein from Arabidopsis thaliana)
- At1g64880 (60 kDa, Protein from Arabidopsis thaliana)
- Pentatricopeptide repeat-containing protein at3g02650, mitochondrial (63 kDa, Protein from Arabidopsis thaliana)
- At2g34520 (18 kDa, Protein from Arabidopsis thaliana)
- At1g24240/f3i6_17 (25 kDa, Protein from Arabidopsis thaliana)
- 50s ribosomal protein l3-2, mitochondrial (35 kDa, Protein from Arabidopsis thaliana)
- At3g06320 (6 kDa, Protein from Arabidopsis thaliana)
- Unk-2 (5 kDa, Protein from Arabidopsis thaliana)
- At1g01640 (23 kDa, Protein from Arabidopsis thaliana)
- 40s ribosomal protein s19, mitochondrial (23 kDa, Protein from Arabidopsis thaliana)
- At1g26740/t24p13_11 (14 kDa, Protein from Arabidopsis thaliana)
- At3g51010 (21 kDa, Protein from Arabidopsis thaliana)
- At5g26800 (12 kDa, Protein from Arabidopsis thaliana)
- At4g39880 (19 kDa, Protein from Arabidopsis thaliana)
- Probable ribosomal protein s11, mitochondrial (33 kDa, Protein from Arabidopsis thaliana)
- Ribosomal protein l9/rnase h1 (25 kDa, Protein from Arabidopsis thaliana)
- Pentatricopeptide repeat-containing protein pnm1, mitochondrial (59 kDa, Protein from Arabidopsis thaliana)
- Rppr* (24 kDa, Protein from Arabidopsis thaliana)
- 50s ribosomal protein l27 (16 kDa, Protein from Arabidopsis thaliana)
- At1g73940/f2p9_19 (17 kDa, Protein from Arabidopsis thaliana)
- Pentatricopeptide repeat-containing protein at1g60770 (55 kDa, Protein from Arabidopsis thaliana)
- Ms31/ms46 (8 kDa, Protein from Arabidopsis thaliana)
- Putative ribosomal protein l6 (11 kDa, Protein from Arabidopsis thaliana)
- Rppr* (47 kDa, Protein from Arabidopsis thaliana)
- 28s ribosomal s34 protein (15 kDa, Protein from Arabidopsis thaliana)
- At4g31460/f3l17_30 (24 kDa, Protein from Arabidopsis thaliana)
- Rna (118-mer) (37 kDa, RNA from Arabidopsis thaliana)
- 39s ribosomal protein (14 kDa, Protein from Arabidopsis thaliana)
- 37s ribosomal protein s27 (11 kDa, Protein from Arabidopsis thaliana)
- At1g15810/f7h2_23 (47 kDa, Protein from Arabidopsis thaliana)
- Ribosomal protein s7, mitochondrial (17 kDa, Protein from Arabidopsis thaliana)
- Unk-1 (4 kDa, Protein from Arabidopsis thaliana)
- At1g14620/t5e21_15 (27 kDa, Protein from Arabidopsis thaliana)
- At1g07830/f24b9_7 (16 kDa, Protein from Arabidopsis thaliana)
- At3g18240 protein (48 kDa, Protein from Arabidopsis thaliana)
- Ms38 (15 kDa, Protein from Arabidopsis thaliana)
- At5g40080 (10 kDa, Protein from Arabidopsis thaliana)
- Ribosomal protein l31 (8 kDa, Protein from Arabidopsis thaliana)
- 50s ribosomal protein l20 (14 kDa, Protein from Arabidopsis thaliana)
- At4g05400 (27 kDa, Protein from Arabidopsis thaliana)
- Ribosomal protein s4, mitochondrial (43 kDa, Protein from Arabidopsis thaliana)
- 3-hydroxyisobutyryl-coa hydrolase-like protein 2, mitochondrial (45 kDa, Protein from Arabidopsis thaliana)
- Ribosomal protein l25/gln-trna synthetase, anti-codon-binding domain-containing protein (27 kDa, Protein from Arabidopsis thaliana)
- At4g35490 (16 kDa, Protein from Arabidopsis thaliana)
- Small ribosomal subunit protein s13, mitochondrial (17 kDa, Protein from Arabidopsis thaliana)
- Rna (1743-mer) (564 kDa, RNA from Arabidopsis thaliana)
- Ribosomal protein l35 (20 kDa, Protein from Arabidopsis thaliana)
- At1g52370 protein (30 kDa, Protein from Arabidopsis thaliana)
- Unk-6 (2 kDa, Protein from Arabidopsis thaliana)
- Rna (2842-mer) (918 kDa, RNA from Arabidopsis thaliana)
- Translation elongation factor ef1b/ribosomal protein s6 family protein (15 kDa, Protein from Arabidopsis thaliana)
- Ribosomal protein s12, mitochondrial (14 kDa, Protein from Arabidopsis thaliana)
- 50s ribosomal protein l4 (33 kDa, Protein from Arabidopsis thaliana)
- 50s ribosomal protein l10 (19 kDa, Protein from Arabidopsis thaliana)
- Ribosomal protein (11 kDa, Protein from Arabidopsis thaliana)
- 40s ribosomal protein s15a-5 (14 kDa, Protein from Arabidopsis thaliana)
- Mitochondrial 28s ribosomal protein s29-like protein (53 kDa, Protein from Arabidopsis thaliana)
- 60s ribosomal protein l16, mitochondrial (20 kDa, Protein from Arabidopsis thaliana)
- 50s ribosomal protein l21, mitochondrial (30 kDa, Protein from Arabidopsis thaliana)
- Uncharacterized protein at1g27435/f17l21.30 (8 kDa, Protein from Arabidopsis thaliana)
- Cx9c domain-containing protein (10 kDa, Protein from Arabidopsis thaliana)
- The large mitoribosomal subunit of the plant mitoribosome (Complex from Arabidopsis thaliana)
- Uncharacterized protein (22 kDa, Protein from Arabidopsis thaliana)
- 30s ribosomal protein s9, mitochondrial (48 kDa, Protein from Arabidopsis thaliana)
- Rppr* (22 kDa, Protein from Arabidopsis thaliana)
- Ribosomal protein s2, mitochondrial (24 kDa, Protein from Arabidopsis thaliana)
- 60s ribosomal protein l5, mitochondrial (21 kDa, Protein from Arabidopsis thaliana)
- Ribosomal protein s21 family protein (11 kDa, Protein from Arabidopsis thaliana)
- 50s ribosomal protein hlp, mitochondrial (18 kDa, Protein from Arabidopsis thaliana)
- 30s ribosomal protein s16-2, chloroplastic/mitochondrial (15 kDa, Protein from Arabidopsis thaliana)
- Unk-5 (6 kDa, Protein from Arabidopsis thaliana)
- Rppr* (18 kDa, Protein from Arabidopsis thaliana)
- 30s ribosomal protein s31, mitochondrial (10 kDa, Protein from Arabidopsis thaliana)
- 50s ribosomal protein l24 (17 kDa, Protein from Arabidopsis thaliana)
- At5g09770 (18 kDa, Protein from Arabidopsis thaliana)
- Gb|aac32909.1 (48 kDa, Protein from Arabidopsis thaliana)
- Unk-3 (4 kDa, Protein from Arabidopsis thaliana)
- Mitochondrial ribosomal protein l51/s25/ci-b8 family protein (16 kDa, Protein from Arabidopsis thaliana)
- 60s ribosomal protein l2, mitochondrial (37 kDa, Protein from Arabidopsis thaliana)
- At5g27820 (12 kDa, Protein from Arabidopsis thaliana)
- 40s ribosomal protein s10, mitochondrial (27 kDa, Protein from Arabidopsis thaliana)
- Ribosomal protein l18e/l15 superfamily protein (31 kDa, Protein from Arabidopsis thaliana)
- Nucleic acid-binding, ob-fold-like protein (12 kDa, Protein from Arabidopsis thaliana)
- Ribosomal protein s3, mitochondrial (64 kDa, Protein from Arabidopsis thaliana)
- Unk-4 (2 kDa, Protein from Arabidopsis thaliana)
RNA Polymerase I Closed Conformation 2 (CC2)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6rql
Q-score: 0.355
Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R, Weis F, Muller CW
Nat Commun (2019) 10 pp. 5543-5543 [ Pubmed: 31804486 DOI: doi:10.1038/s41467-019-13510-w ]
- Nontemplate strand (21 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa49 (46 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn6 (102 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa34 (26 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i and iii subunit rpac1 (37 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn3 (72 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn7 (60 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i closed complex conformation 2 (cc2) (Complex)
- Dna-directed rna polymerase i subunit rpa135 (135 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa43 (36 kDa, Protein from Saccharomyces cerevisiae)
- Nucleic acid (Complex from synthetic construct)
- Dna-directed rna polymerases i and iii subunit rpac2 (16 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor (Complex from Saccharomyces cerevisiae)
- Rna polymerase i-specific transcription initiation factor rrn11 (59 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa14 (14 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase i subunit rpa190 (186 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase i (Complex from Saccharomyces cerevisiae)
- Template strand (21 kDa, DNA from synthetic construct)
S. cerevisiae CMG-Pol epsilon-DNA
Resolution: 4.98 Å
EM Method: Single-particle
Fitted PDBs: 6hv9
Q-score: 0.231
Goswami P, Abid Ali F, Douglas ME, Locke J, Purkiss A, Janska A, Eickhoff P, Early A, Nans A, Cheung AMC, Diffley JFX, Costa A
Nat Commun (2018) 9 pp. 5061-5061 [ Pubmed: 30498216 DOI: doi:10.1038/s41467-018-07417-1 ]
- Dna polymerase epsilon subunit b (78 kDa, Protein from Saccharomyces cerevisiae)
- Nucleic acid (Complex from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm4 (105 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm6 (113 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication complex gins protein sld5 (33 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm5 (86 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm7 (95 kDa, Protein from Saccharomyces cerevisiae)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Cmg-pol epsilon (Complex from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*ap*ap*ap*ap*cp*gp*gp*cp*cp*ap*gp*cp*gp*tp*gp*gp*cp*tp*gp*c)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Dna (5'-d(p*tp*tp*tp*tp*tp*tp*t)-3') (2 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf3 (21 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm3 (107 kDa, Protein from Saccharomyces cerevisiae)
- Cmg-pol epsilon-dna (Complex)
- Dna replication complex gins protein psf1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Cell division control protein 45 (74 kDa, Protein from Saccharomyces cerevisiae)
- Dna polymerase epsilon catalytic subunit (104 kDa, Protein from Saccharomyces cerevisiae)
- Dna (5'-d(*gp*cp*ap*gp*cp*cp*ap*cp*gp*cp*tp*gp*gp*cp*cp*gp*tp*tp*tp*tp*a)-3') (6 kDa, DNA from Saccharomyces cerevisiae)
- Dna replication complex gins protein psf2 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna replication licensing factor mcm2 (98 kDa, Protein from Saccharomyces cerevisiae)
RNA Polymerase III open pre-initiation complex (OC-PIC)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6eu0
Q-score: 0.313
Abascal-Palacios G, Ramsay EP, Beuron F, Morris E, Vannini A
Nature (2018) 553 pp. 301-306 [ Pubmed: 29345637 DOI: doi:10.1038/nature25441 ]
- Dna-directed rna polymerase iii subunit rpc7 (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Template (21 kDa, DNA from Saccharomyces cerevisiae S288c)
- Transcription factors (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase iii subunit rpc10 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase iii (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase iii subunit rpc2 (129 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase iii open pre-initiation complex (Complex)
- Dna-directed rna polymerases i and iii subunit rpac2 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase iii subunit rpc5 (32 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase iii subunit rpc1 (162 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase iii subunit rpc3 (74 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription factor iiib 70 kda subunit (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription factor tfiiib component b'' (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Tata-box-binding protein (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i and iii subunit rpac1 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Non-template (21 kDa, DNA from Saccharomyces cerevisiae S288c)
- Nucleic acid (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase iii subunit rpc8 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase iii subunit rpc9 (18 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase iii subunit rpc4 (46 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna-directed rna polymerase iii subunit rpc6 (36 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))