Cryo-EM structure of the TnpB-omegaRNA-target DNA ternary complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8h1j
Q-score: 0.453
Nakagawa R, Hirano H, Omura SN, Nety S, Kannan S, Altae-Tran H, Yao X, Sakaguchi Y, Ohira T, Wu WY, Nakayama H, Shuto Y, Tanaka T, Sano FK, Kusakizako T, Kise Y, Itoh Y, Dohmae N, van der Oost J, Suzuki T, Zhang F, Nureki O
Nature (2023) 616 pp. 390-397 [ DOI: doi:10.1038/s41586-023-05933-9 Pubmed: 37020030 ]
- Rna-guided dna endonuclease tnpb (46 kDa, Protein from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Zinc ion (65 Da, Ligand)
- Non-target strand (10 kDa, DNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Tnpb-omegarna-target dna ternary complex (Complex from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Omegarna (130-mer) (79 kDa, RNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Target strand (10 kDa, DNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 7pnt
Q-score: 0.516
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Mus musculus)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (77 kDa, Protein from Mus musculus)
- 28s ribosomal protein s31, mitochondrial (43 kDa, Protein from Mus musculus)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Mus musculus)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18b, mitochondrial (28 kDa, Protein from Mus musculus)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Mus musculus)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Mus musculus)
- 12s mitochondrial rrna (306 kDa, RNA from Mus musculus)
- 28s ribosomal protein s14, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Mus musculus)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Mus musculus)
- 28s ribosomal protein s24, mitochondrial (18 kDa, Protein from Mus musculus)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Mus musculus)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Mus musculus)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s9, mitochondrial (44 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18c, mitochondrial (16 kDa, Protein from Mus musculus)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s2, mitochondrial (32 kDa, Protein from Mus musculus)
- Dimethyladenosine transferase 1, mitochondrial (39 kDa, Protein from Mus musculus)
- 28s ribosomal protein s29, mitochondrial (44 kDa, Protein from Mus musculus)
- Water (18 Da, Ligand)
- Putative ribosome-binding factor a, mitochondrial (39 kDa, Protein from Mus musculus)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s25, mitochondrial (19 kDa, Protein from Mus musculus)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (13 kDa, Protein from Mus musculus)
- 28s ribosomal protein s10, mitochondrial (18 kDa, Protein from Mus musculus)
- Aurora kinase a-interacting protein (23 kDa, Protein from Mus musculus)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Mus musculus)
- 28s ribosomal protein s23, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s26, mitochondrial (23 kDa, Protein from Mus musculus)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 7pnu
Q-score: 0.552
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Mus musculus)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (77 kDa, Protein from Mus musculus)
- 28s ribosomal protein s31, mitochondrial (43 kDa, Protein from Mus musculus)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Mus musculus)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18b, mitochondrial (28 kDa, Protein from Mus musculus)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Mus musculus)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Mus musculus)
- 12s mitochondrial rrna (306 kDa, RNA from Mus musculus)
- 28s ribosomal protein s14, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Mus musculus)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Mus musculus)
- 28s ribosomal protein s24, mitochondrial (18 kDa, Protein from Mus musculus)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Mus musculus)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Mus musculus)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s9, mitochondrial (44 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18c, mitochondrial (16 kDa, Protein from Mus musculus)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s2, mitochondrial (32 kDa, Protein from Mus musculus)
- 28s ribosomal protein s29, mitochondrial (44 kDa, Protein from Mus musculus)
- Water (18 Da, Ligand)
- Putative ribosome-binding factor a, mitochondrial (39 kDa, Protein from Mus musculus)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s25, mitochondrial (19 kDa, Protein from Mus musculus)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (13 kDa, Protein from Mus musculus)
- 28s ribosomal protein s10, mitochondrial (18 kDa, Protein from Mus musculus)
- Aurora kinase a-interacting protein (23 kDa, Protein from Mus musculus)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Mus musculus)
- 28s ribosomal protein s23, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s26, mitochondrial (23 kDa, Protein from Mus musculus)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 7pnv
Q-score: 0.544
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Mus musculus)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (77 kDa, Protein from Mus musculus)
- 28s ribosomal protein s31, mitochondrial (43 kDa, Protein from Mus musculus)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Mus musculus)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 12s mitochondrial rrna (306 kDa, RNA from Mus musculus)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18b, mitochondrial (28 kDa, Protein from Mus musculus)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Mus musculus)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s14, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Mus musculus)
- 12s rrna n4-methylcytidine methyltransferase (45 kDa, Protein from Mus musculus)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Mus musculus)
- 28s ribosomal protein s24, mitochondrial (18 kDa, Protein from Mus musculus)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Mus musculus)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Mus musculus)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s9, mitochondrial (44 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18c, mitochondrial (16 kDa, Protein from Mus musculus)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s2, mitochondrial (32 kDa, Protein from Mus musculus)
- 28s ribosomal protein s29, mitochondrial (44 kDa, Protein from Mus musculus)
- Water (18 Da, Ligand)
- Putative ribosome-binding factor a, mitochondrial (39 kDa, Protein from Mus musculus)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s25, mitochondrial (19 kDa, Protein from Mus musculus)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (13 kDa, Protein from Mus musculus)
- 28s ribosomal protein s10, mitochondrial (18 kDa, Protein from Mus musculus)
- Aurora kinase a-interacting protein (23 kDa, Protein from Mus musculus)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Mus musculus)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Mus musculus)
- 28s ribosomal protein s23, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s26, mitochondrial (23 kDa, Protein from Mus musculus)
Mouse mitochondrial ribosome small subunit lacking m5U modification
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7pnw
Q-score: 0.565
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Mus musculus)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (77 kDa, Protein from Mus musculus)
- 28s ribosomal protein s31, mitochondrial (43 kDa, Protein from Mus musculus)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Mus musculus)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 12s mitochondrial rrna (306 kDa, RNA from Mus musculus)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18b, mitochondrial (28 kDa, Protein from Mus musculus)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Mus musculus)
- 28s ribosomal protein s14, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Mus musculus)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Mus musculus)
- 28s ribosomal protein s24, mitochondrial (18 kDa, Protein from Mus musculus)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Mus musculus)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Mus musculus)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Mus musculus)
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s9, mitochondrial (44 kDa, Protein from Mus musculus)
- 28s ribosomal protein s18c, mitochondrial (16 kDa, Protein from Mus musculus)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 (13 kDa, Protein from Mus musculus)
- 28s ribosomal protein s2, mitochondrial (32 kDa, Protein from Mus musculus)
- 28s ribosomal protein s29, mitochondrial (44 kDa, Protein from Mus musculus)
- Water (18 Da, Ligand)
- Small subunit of human mitochondrial ribosome (Complex from Mus musculus)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s25, mitochondrial (19 kDa, Protein from Mus musculus)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Mus musculus)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (13 kDa, Protein from Mus musculus)
- 28s ribosomal protein s10, mitochondrial (18 kDa, Protein from Mus musculus)
- Aurora kinase a-interacting protein (23 kDa, Protein from Mus musculus)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Mus musculus)
- 28s ribosomal protein s23, mitochondrial (20 kDa, Protein from Mus musculus)
- 28s ribosomal protein s26, mitochondrial (23 kDa, Protein from Mus musculus)
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 7pnx
Q-score: 0.603
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- 12s rrna n4-methylcytidine (m4c) methyltransferase (46 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- Putative ribosome-binding factor a, mitochondrial (38 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Homo sapiens)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 7pny
Q-score: 0.539
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- 12s rrna n4-methylcytidine (m4c) methyltransferase (46 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- Putative ribosome-binding factor a, mitochondrial (38 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Homo sapiens)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7pnz
Q-score: 0.533
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- 12s rrna n4-methylcytidine (m4c) methyltransferase (46 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- Putative ribosome-binding factor a, mitochondrial (38 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Homo sapiens)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7po0
Q-score: 0.587
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- Mitochondrial translational initiation factor 3, isoform cra_a (31 kDa, Protein from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- Putative ribosome-binding factor a, mitochondrial (38 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- Assembly intermediate of small subunit of human mitochondrial ribosome (Complex from Homo sapiens)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)
Initiation complex of human mitochondrial ribosome small subunit with IF3
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 7po1
Q-score: 0.578
Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A
Nature (2022) 606 pp. 603-608 [ Pubmed: 35676484 DOI: doi:10.1038/s41586-022-04795-x ]
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- Mitochondrial translational initiation factor 3, isoform cra_a (31 kDa, Protein from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- Small subunit of human mitochondrial ribosome in complex with initiation factor 3 (Complex from Homo sapiens)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 (13 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)