The cryo-EM structure of human pre-C*-I complex
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7w59
Q-score: 0.268
Zhan X, Lu Y, Zhang X, Yan C, Shi Y
Mol Cell (2022) 82 pp. 2769-2778.e4 [ Pubmed: 35705093 DOI: doi:10.1016/j.molcel.2022.05.021 ]
- Pre-mrna-splicing factor spf27 (26 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Homo sapiens)
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
- Rna-binding protein 8a (19 kDa, Protein from Homo sapiens)
- Human pre-c*-i complex (Complex from Homo sapiens)
- Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
- Psme3-interacting protein (28 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Serine/arginine repetitive matrix protein 2 (300 kDa, Protein from Homo sapiens)
- U2 snrna (60 kDa, RNA from Homo sapiens)
- Rna helicase aquarius (171 kDa, Protein from Homo sapiens)
- Pre-mrna (14 kDa, RNA from unidentified adenovirus)
- Crooked neck-like protein 1 (100 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
- Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
- Eukaryotic initiation factor 4a-iii (46 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor syf2 (28 kDa, Protein from Homo sapiens)
- U5 snrna (37 kDa, RNA from Homo sapiens)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from Homo sapiens)
- Protein casc3 (76 kDa, Protein from Homo sapiens)
- Pre-mrna-processing factor 17 (65 kDa, Protein from Homo sapiens)
- Pleiotropic regulator 1 (57 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
- Protein mago nashi homolog (17 kDa, Protein from Homo sapiens)
- Pre-mrna-processing factor 19 (55 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- U6 snrna (34 kDa, RNA from Homo sapiens)
- Pre-mrna (55 kDa, RNA from unidentified adenovirus)
- Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Atp-dependent rna helicase dhx8 (139 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase e (33 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Homo sapiens)
- Snw domain-containing protein 1 (61 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
The cryo-EM structure of human pre-C*-II complex
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7w5a
Q-score: 0.269
Zhan X, Lu Y, Zhang X, Yan C, Shi Y
Mol Cell (2022) 82 pp. 2769-2778.e4 [ Pubmed: 35705093 DOI: doi:10.1016/j.molcel.2022.05.021 ]
- Pre-mrna-splicing factor spf27 (26 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Homo sapiens)
- Prkr-interacting protein 1 (21 kDa, Protein from Homo sapiens)
- Crooked neck-like protein 1 (100 kDa, Protein from Homo sapiens)
- Pre-mrna-processing factor 17 (65 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-processing factor 19 (55 kDa, Protein from Homo sapiens)
- Protein casc3 (76 kDa, Protein from Homo sapiens)
- U5 snrna (37 kDa, RNA from Homo sapiens)
- Pre-mrna (55 kDa, RNA from unidentified adenovirus)
- Human pre-c*-ii complex (Complex from Homo sapiens)
- U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Homo sapiens)
- U6 snrna (34 kDa, RNA from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Homo sapiens)
- Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Pre-mrna (14 kDa, RNA from unidentified adenovirus)
- Rna helicase aquarius (171 kDa, Protein from Homo sapiens)
- Serine/arginine repetitive matrix protein 2 (300 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from Homo sapiens)
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
- Protein mago nashi homolog (17 kDa, Protein from Homo sapiens)
- Pleiotropic regulator 1 (57 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase e (33 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from Homo sapiens)
- Cactin (88 kDa, Protein from Homo sapiens)
- Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
- Protein fam32a (13 kDa, Protein from Homo sapiens)
- U2 snrna (60 kDa, RNA from Homo sapiens)
- Rna-binding protein 8a (19 kDa, Protein from Homo sapiens)
- Psme3-interacting protein (28 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor slu7 (68 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor syf2 (28 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Eukaryotic initiation factor 4a-iii (46 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)
- Atp-dependent rna helicase dhx8 (139 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
- Snw domain-containing protein 1 (61 kDa, Protein from Homo sapiens)
Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme transcription open complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 6gh5
Q-score: 0.412
Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang X
Mol Cell (2018) 70 pp. 1111-1120.e3 [ DOI: doi:10.1016/j.molcel.2018.05.021 Pubmed: 29932903 ]
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli (strain K12))
- Dna (Complex from Klebsiella pneumoniae)
- Nifh promoter template dna (19 kDa, DNA from Klebsiella pneumoniae)
- Nifh promoter non-template dna (19 kDa, DNA from Klebsiella pneumoniae)
- Cryo-em structure of bacterial rna polymerase-sigma54 holoenzyme transcription open complex (490 kDa, Complex)
- Dna-directed rna polymerase (Complex from Escherichia coli K-12)
- Rna polymerase sigma-54 factor (Complex from Klebsiella pneumoniae)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli (strain K12))
- Rna polymerase sigma-54 factor,rna polymerase sigma-54 factor,rna polymerase sigma-54 factor,rna polymerase sigma-54 factor,rna polymerase sigma-54 factor (54 kDa, Protein from Klebsiella pneumoniae)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli (strain K12))
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli (strain K12))
Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme initial transcribing complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6gfw
Q-score: 0.372
Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang X
Mol Cell (2018) 70 pp. 1111-1120.e3 [ DOI: doi:10.1016/j.molcel.2018.05.021 Pubmed: 29932903 ]
- Cryo-em structure of bacterial rna polymerase-sigma54 holoenzyme initial transcribing complex (490 kDa, Complex)
- De novo dna (Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Nifh promoter template dna (19 kDa, DNA from Klebsiella pneumoniae)
- Promoter dna (Complex from Klebsiella pneumoniae)
- Rna polymerase sigma-54 factor (54 kDa, Protein from Klebsiella pneumoniae)
- De novo synthesized rna (1 kDa, RNA from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase (Complex from Escherichia coli K-12)
- Nifh promoter non-template dna (19 kDa, DNA from Klebsiella pneumoniae)
- Rna polymerase sigma-54 factor (Complex from Klebsiella pneumoniae)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 6cg0
Q-score: 0.452
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W
Mol Cell (2018) 70 pp. 358-370.e4 [ DOI: doi:10.1016/j.molcel.2018.03.008 Pubmed: 29628308 ]
- Dna (46-mer) (14 kDa, DNA from Escherichia coli K-12)
- V(d)j recombination-activating protein 2 (58 kDa, Protein from Mus musculus)
- Calcium ion (40 Da, Ligand)
- Dna (5'-d(p*cp*tp*gp*gp*ap*tp*cp*tp*gp*gp*cp*cp*tp*gp*tp*cp*tp*tp*a)-3') (5 kDa, DNA from Escherichia coli K-12)
- Dna (5'-d(*gp*ap*tp*cp*tp*gp*gp*cp*cp*tp*gp*tp*cp*tp*tp*a)-3') (4 kDa, DNA from Homo sapiens)
- Dna (60-mer) (18 kDa, DNA from Escherichia coli K-12)
- High mobility group protein b1 (14 kDa, Protein from Homo sapiens)
- Rag1/2 in complex with nicked dnas (Complex from Mus musculus)
- V(d)j recombination-activating protein 1 (88 kDa, Protein from Mus musculus)
- Dna (41-mer) (12 kDa, DNA from Escherichia coli K-12)
- Dna (30-mer) (9 kDa, DNA from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6cij
Q-score: 0.409
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W
Mol Cell (2018) 70 pp. 358-370.e4 [ DOI: doi:10.1016/j.molcel.2018.03.008 Pubmed: 29628308 ]
- Dna (30-mer) (9 kDa, DNA from Homo sapiens)
- High mobility group protein b1 (18 kDa, Protein from Homo sapiens)
- V(d)j recombination-activating protein 1 (88 kDa, Protein from Mus musculus)
- Dna (5'-d(p*cp*tp*gp*gp*ap*tp*cp*tp*gp*gp*cp*cp*tp*gp*tp*cp*tp*tp*a)-3') (6 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rag1/2 in complex with nicked dnas (Complex from Mus musculus)
- V(d)j recombination-activating protein 2 (58 kDa, Protein from Mus musculus)
- Dna (5'-d(*gp*ap*tp*cp*tp*gp*gp*cp*cp*tp*gp*tp*cp*tp*tp*a)-3') (4 kDa, DNA from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Dna (46-mer) (14 kDa, DNA from Homo sapiens)
- Dna (41-mer) (12 kDa, DNA from Homo sapiens)
- Dna (60-mer) (18 kDa, DNA from Homo sapiens)
Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 5nsr
Q-score: 0.289
Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang X
Mol Cell (2017) 67 pp. 106-116.e4 [ Pubmed: 28579332 DOI: doi:10.1016/j.molcel.2017.05.010 ]
- Sigma-54 transcription initiation factor (Complex from Klebsiella pneumoniae)
- Sigma-54 promoter dna (Complex from Klebsiella pneumoniae)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Escherichia coli core rna polymerase (Complex from Escherichia coli K-12)
- Non-template promoter dna (19 kDa, DNA from Klebsiella pneumoniae)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma-54 factor,rna polymerase sigma-54 factor,rna polymerase sigma-54 factor,rna polymerase sigma-54 factor,rna polymerase sigma-54 factor,rna polymerase sigma-54 factor,rna polymerase sigma-54 factor (62 kDa, Protein from Klebsiella pneumoniae)
- Cryo-em structure of rna polymerase-sigma54 holo enzyme with promoter dna closed complex (Complex)
- Template dna promoter (19 kDa, DNA from Klebsiella pneumoniae)