Cryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail complex
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 8gtc
Q-score: 0.275
Huang Y, Sun H, Wei S, Cai L, Liu L, Jiang Y, Xin J, Chen Z, Que Y, Kong Z, Li T, Yu H, Zhang J, Gu Y, Zheng Q, Li S, Zhang R, Xia N
Nat Commun (2023) 14 pp. 3609-3609 [ Pubmed: 37330604 DOI: doi:10.1038/s41467-023-39220-y ]
- Dinoroseobacter phage vb_dshs-r4c (Virus from Dinoroseobacter phage vB DshS-R4C)
- Major tail protein (13 kDa, Protein from Dinoroseobacter phage vB DshS-R4C)
- Ribonuclease iii (22 kDa, Protein from Dinoroseobacter phage vB DshS-R4C)
- Distal tail protein (23 kDa, Protein from Dinoroseobacter phage vB DshS-R4C)
- Hub protein (31 kDa, Protein from Dinoroseobacter phage vB DshS-R4C)
- Megatron protein (154 kDa, Protein from Dinoroseobacter phage vB DshS-R4C)
The structure of the mitoribosome from Neurospora crassa in the P/E tRNA bound state
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 6ywe
Q-score: 0.575
Itoh Y, Naschberger A, Mortezaei N, Herrmann JM, Amunts A
Nat Commun (2020) 11 pp. 5187-5187 [ DOI: doi:10.1038/s41467-020-18830-w Pubmed: 33056988 ]
- Related to ribosomal protein s15 (mitochondrial) (35 kDa, Protein from Neurospora crassa)
- Bs1m (51 kDa, Protein from Neurospora crassa)
- Ribosomal protein s19/s15 (10 kDa, Protein from Neurospora crassa)
- Ms27 (44 kDa, Protein from Neurospora crassa)
- Bs16m (12 kDa, Protein from Neurospora crassa)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Mitochondrial ribosomal protein dap3 (51 kDa, Protein from Neurospora crassa)
- Ul17m (22 kDa, Protein from Neurospora crassa)
- Potassium ion (39 Da, Ligand)
- Ribosomal protein l15 (33 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein l30 (18 kDa, Protein from Neurospora crassa)
- Ul13m (20 kDa, Protein from Neurospora crassa)
- Ribosomal protein l14 (14 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein yml49, mitochondrial (23 kDa, Protein from Neurospora crassa)
- Mito ribosomal protein s2 (47 kDa, Protein from Neurospora crassa)
- 23s rrna (1 MDa, RNA from Neurospora crassa)
- Ml41 (11 kDa, Protein from Neurospora crassa)
- Ms46 (43 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein l34, mitochondrial (14 kDa, Protein from Neurospora crassa)
- Trna p/e state (23 kDa, RNA from Neurospora crassa)
- Related to ribosomal protein yml11, mitochondrial (37 kDa, Protein from Neurospora crassa)
- Mitochondrial 37s ribosomal protein mrp2 (13 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein yml20, mitochondrial (25 kDa, Protein from Neurospora crassa)
- Ml40 (41 kDa, Protein from Neurospora crassa)
- Bs21m (25 kDa, Protein from Neurospora crassa)
- Zinc ion (65 Da, Ligand)
- 54s ribosomal protein l4, mitochondrial (29 kDa, Protein from Neurospora crassa)
- Ml54 (23 kDa, Protein from Neurospora crassa)
- Spermine (202 Da, Ligand)
- 16s rrna (600 kDa, RNA from Neurospora crassa)
- Ribonuclease iii (48 kDa, Protein from Neurospora crassa)
- Kow domain-containing protein (45 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l2, mitochondrial (42 kDa, Protein from Neurospora crassa)
- Ribosomal_l9 domain-containing protein (33 kDa, Protein from Neurospora crassa)
- Related to 60s ribosomal protein l2 (mitochondrial) (49 kDa, Protein from Neurospora crassa)
- Ribosomal protein s5 (58 kDa, Protein from Neurospora crassa)
- Duf1713 domain-containing protein (38 kDa, Protein from Neurospora crassa)
- L51_s25_ci-b8 domain-containing protein (15 kDa, Protein from Neurospora crassa)
- Protein fyv4, mitochondrial (26 kDa, Protein from Neurospora crassa)
- Ribosomal protein s18 (28 kDa, Protein from Neurospora crassa)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Mrp-l46 domain-containing protein (41 kDa, Protein from Neurospora crassa)
- Ms33 (12 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein l5, mitochondrial (39 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l4, variant (36 kDa, Protein from Neurospora crassa)
- Pebp-like protein (50 kDa, Protein from Neurospora crassa)
- L51_s25_ci-b8 domain-containing protein (22 kDa, Protein from Neurospora crassa)
- Ml67 (32 kDa, Protein from Neurospora crassa)
- Us9m (35 kDa, Protein from Neurospora crassa)
- Mitochondrial large ribosomal subunit (41 kDa, Protein from Neurospora crassa)
- Ml50 (49 kDa, Protein from Neurospora crassa)
- 30s ribosomal protein s10, mitochondrial (30 kDa, Protein from Neurospora crassa)
- Ms26 (35 kDa, Protein from Neurospora crassa)
- Ribosomal protein (13 kDa, Protein from Neurospora crassa)
- 37s ribosomal protein s24, mitochondrial (44 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l1, mitochondrial (33 kDa, Protein from Neurospora crassa)
- Probable ribosomal protein yml44, mitochondrial (11 kDa, Protein from Neurospora crassa)
- Translational machinery component (42 kDa, Protein from Neurospora crassa)
- Bl19m (28 kDa, Protein from Neurospora crassa)
- Ml49 (18 kDa, Protein from Neurospora crassa)
- Ms45 (39 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein yml36, mitochondrial (23 kDa, Protein from Neurospora crassa)
- 54s ribosomal protein l31, mitochondrial (13 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein yml32 (mitochondrial),mitochondrial ribosomal protein subunit l32 (14 kDa, Protein from Neurospora crassa)
- 3-hydroxyisobutyryl-coa hydrolase, mitochondrial (56 kDa, Protein from Neurospora crassa)
- Manganese and iron superoxide dismutase (34 kDa, Protein from Neurospora crassa)
- Bl33m (7 kDa, Protein from Neurospora crassa)
- Rnase iii domain-containing protein (29 kDa, Protein from Neurospora crassa)
- 37s ribosomal protein mrp10, mitochondrial (9 kDa, Protein from Neurospora crassa)
- Ul11m (16 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein s5 (mitochondrial) (53 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein l16, mitochondrial (27 kDa, Protein from Neurospora crassa)
- Mitoc_ml59 domain-containing protein (18 kDa, Protein from Neurospora crassa)
- Ribosomal_s7 domain-containing protein (33 kDa, Protein from Neurospora crassa)
- S4 rna-binding domain-containing protein (51 kDa, Protein from Neurospora crassa)
- Ribosomal protein s12 (18 kDa, Protein from Neurospora crassa)
- Mrna (3 kDa, RNA from Neurospora crassa)
- 37s ribosomal protein s25, mitochondrial (29 kDa, Protein from Neurospora crassa)
- Us8m (17 kDa, Protein from Neurospora crassa)
- Bl28m (31 kDa, Protein from Neurospora crassa)
- Ul23m (26 kDa, Protein from Neurospora crassa)
- Ribosomal protein s6 (13 kDa, Protein from Neurospora crassa)
- Mitoribosome of neurospora crassa in the p/e state (Complex from Neurospora crassa)
- Related to ribosomal protein l3, mitochondrial (41 kDa, Protein from Neurospora crassa)
- Us17m (18 kDa, Protein from Neurospora crassa)
- If1 (10 kDa, Protein from Neurospora crassa)
- Magnesium ion (24 Da, Ligand)
- Probable ribosomal protein s13 (13 kDa, Protein from Neurospora crassa)
- Ul6m (28 kDa, Protein from Neurospora crassa)
The structure of the mitoribosome from Neurospora crassa with bound tRNA at the P-site
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 6ywy
Q-score: 0.56
Itoh Y, Naschberger A, Mortezaei N, Herrmann JM, Amunts A
Nat Commun (2020) 11 pp. 5187-5187 [ DOI: doi:10.1038/s41467-020-18830-w Pubmed: 33056988 ]
- Related to ribosomal protein s15 (mitochondrial) (35 kDa, Protein from Neurospora crassa)
- Bs1m (51 kDa, Protein from Neurospora crassa)
- Ribosomal protein s19/s15 (10 kDa, Protein from Neurospora crassa)
- Ms27 (44 kDa, Protein from Neurospora crassa)
- Bs16m (12 kDa, Protein from Neurospora crassa)
- P-site-trna (23 kDa, RNA from Neurospora crassa)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Mitochondrial ribosomal protein dap3 (51 kDa, Protein from Neurospora crassa)
- Ul17m (22 kDa, Protein from Neurospora crassa)
- Potassium ion (39 Da, Ligand)
- Poly-peptide (515 Da, Protein from Neurospora crassa)
- Ribosomal protein l15 (33 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein l30 (18 kDa, Protein from Neurospora crassa)
- Ul13m (20 kDa, Protein from Neurospora crassa)
- Ribosomal protein l14 (14 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein yml49, mitochondrial (23 kDa, Protein from Neurospora crassa)
- Mito ribosomal protein s2 (47 kDa, Protein from Neurospora crassa)
- 23s rrna (1 MDa, RNA from Neurospora crassa)
- Ml41 (11 kDa, Protein from Neurospora crassa)
- Ms46 (43 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein l34, mitochondrial (14 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein yml11, mitochondrial (37 kDa, Protein from Neurospora crassa)
- Mitochondrial 37s ribosomal protein mrp2 (13 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein yml20, mitochondrial (25 kDa, Protein from Neurospora crassa)
- Ml40 (41 kDa, Protein from Neurospora crassa)
- Bs21m (25 kDa, Protein from Neurospora crassa)
- Zinc ion (65 Da, Ligand)
- 54s ribosomal protein l4, mitochondrial (29 kDa, Protein from Neurospora crassa)
- Ml54 (23 kDa, Protein from Neurospora crassa)
- Spermine (202 Da, Ligand)
- 16s rrna (600 kDa, RNA from Neurospora crassa)
- Ribonuclease iii (48 kDa, Protein from Neurospora crassa)
- Ml46 (41 kDa, Protein from Neurospora crassa)
- Kow domain-containing protein (45 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l2, mitochondrial (42 kDa, Protein from Neurospora crassa)
- Mrna (3 kDa, RNA from Neurospora crassa)
- Ribosomal_l9 domain-containing protein (33 kDa, Protein from Neurospora crassa)
- Related to 60s ribosomal protein l2 (mitochondrial) (49 kDa, Protein from Neurospora crassa)
- Ribosomal protein s5 (58 kDa, Protein from Neurospora crassa)
- Duf1713 domain-containing protein (38 kDa, Protein from Neurospora crassa)
- L51_s25_ci-b8 domain-containing protein (15 kDa, Protein from Neurospora crassa)
- Protein fyv4, mitochondrial (26 kDa, Protein from Neurospora crassa)
- Ribosomal protein s18 (28 kDa, Protein from Neurospora crassa)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Ms33 (12 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein l5, mitochondrial (39 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l4, variant (36 kDa, Protein from Neurospora crassa)
- Pebp-like protein (50 kDa, Protein from Neurospora crassa)
- L51_s25_ci-b8 domain-containing protein (22 kDa, Protein from Neurospora crassa)
- Ml67 (32 kDa, Protein from Neurospora crassa)
- Us9m (35 kDa, Protein from Neurospora crassa)
- Mitochondrial large ribosomal subunit (41 kDa, Protein from Neurospora crassa)
- Ml50 (49 kDa, Protein from Neurospora crassa)
- 30s ribosomal protein s10, mitochondrial (30 kDa, Protein from Neurospora crassa)
- Ms26 (35 kDa, Protein from Neurospora crassa)
- Ribosomal protein (13 kDa, Protein from Neurospora crassa)
- 37s ribosomal protein s24, mitochondrial (44 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l1, mitochondrial (33 kDa, Protein from Neurospora crassa)
- Probable ribosomal protein yml44, mitochondrial (11 kDa, Protein from Neurospora crassa)
- Translational machinery component (42 kDa, Protein from Neurospora crassa)
- Bl19m (28 kDa, Protein from Neurospora crassa)
- Ml49 (18 kDa, Protein from Neurospora crassa)
- Ms45 (39 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein yml36, mitochondrial (23 kDa, Protein from Neurospora crassa)
- 54s ribosomal protein l31, mitochondrial (13 kDa, Protein from Neurospora crassa)
- 3-hydroxyisobutyryl-coa hydrolase, mitochondrial (56 kDa, Protein from Neurospora crassa)
- Manganese and iron superoxide dismutase (34 kDa, Protein from Neurospora crassa)
- Bl33m (7 kDa, Protein from Neurospora crassa)
- Rnase iii domain-containing protein (29 kDa, Protein from Neurospora crassa)
- 37s ribosomal protein mrp10, mitochondrial (9 kDa, Protein from Neurospora crassa)
- Ul11m (16 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein yml32 (mitochondrial) (14 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein s5 (mitochondrial) (53 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein l16, mitochondrial (27 kDa, Protein from Neurospora crassa)
- Mitoc_ml59 domain-containing protein (18 kDa, Protein from Neurospora crassa)
- Ribosomal_s7 domain-containing protein (33 kDa, Protein from Neurospora crassa)
- S4 rna-binding domain-containing protein (51 kDa, Protein from Neurospora crassa)
- Ribosomal protein s12 (18 kDa, Protein from Neurospora crassa)
- Mitoribosome of neurospora crassa in the trna bound state (p-site). (Complex from Neurospora crassa)
- 37s ribosomal protein s25, mitochondrial (29 kDa, Protein from Neurospora crassa)
- Us8m (17 kDa, Protein from Neurospora crassa)
- Bl28m (31 kDa, Protein from Neurospora crassa)
- Ul23m (26 kDa, Protein from Neurospora crassa)
- Ribosomal protein s6 (13 kDa, Protein from Neurospora crassa)
- Related to ribosomal protein l3, mitochondrial (41 kDa, Protein from Neurospora crassa)
- Us17m (18 kDa, Protein from Neurospora crassa)
- If1 (10 kDa, Protein from Neurospora crassa)
- Magnesium ion (24 Da, Ligand)
- Probable ribosomal protein s13 (13 kDa, Protein from Neurospora crassa)
- Ul6m (28 kDa, Protein from Neurospora crassa)