Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8kde
Q-score: 0.548
Li A, You T, Pang X, Wang Y, Tian L, Li X, Liu Z
Nat Commun (2024) 15 pp. 5211-5211 [ Pubmed: 38890314 DOI: doi:10.1038/s41467-024-49532-2 ]
- Photosystem ii reaction center protein i (4 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii cp43 reaction center protein (50 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein h (9 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii repair factor 2 (prf2) (12 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chlamydomonas reinhardtii)
- Thylakoid enriched factor 14 (tef14) (20 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chlamydomonas reinhardtii)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Chlamydomonas reinhardtii)
- Rrr-alpha-tocopherylquinone (446 Da, Ligand)
- Uncharacterized protein (9 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii d2 protein (39 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein k (5 kDa, Protein from Chlamydomonas reinhardtii)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Cryo-em structure of an intermediate-state complex during the process of photosystem ii repair (Complex from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii repair factor 1 (prf1) (13 kDa, Protein from Chlamydomonas reinhardtii)
- Beta-carotene (536 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii protein d1 (39 kDa, Protein from Chlamydomonas reinhardtii)
The closed state of the ASFV apo-RNA polymerase
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 8q3b
Q-score: 0.54
Pilotto S, Sykora M, Cackett G, Dulson C, Werner F
Nat Commun (2024) 15 pp. 1606-1606 [ DOI: doi:10.1038/s41467-024-45842-7 Pubmed: 38383525 ]
- Dna-directed rna polymerase rpb10 homolog (9 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb7 homolog (38 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb5 homolog (23 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb6 homolog (16 kDa, Protein from African swine fever virus BA71V)
- Apo-form of the 8-subunit rna polymerase from african swine fever virus (450 kDa, Complex from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb1 homolog (163 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb3-11 homolog (41 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb2 homolog (140 kDa, Protein from African swine fever virus BA71V)
- Magnesium ion (24 Da, Ligand)
- Uncharacterized protein c122r (11 kDa, Protein from African swine fever virus BA71V)
- Zinc ion (65 Da, Ligand)
The open state of the ASFV apo-RNA polymerase
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 8q3k
Q-score: 0.531
Pilotto S, Sykora M, Cackett G, Dulson C, Werner F
Nat Commun (2024) 15 pp. 1606-1606 [ DOI: doi:10.1038/s41467-024-45842-7 Pubmed: 38383525 ]
- Dna-directed rna polymerase rpb10 homolog (9 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb7 homolog (38 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb5 homolog (23 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb6 homolog (16 kDa, Protein from African swine fever virus BA71V)
- Apo-form of the 8-subunit rna polymerase from african swine fever virus (450 kDa, Complex from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb1 homolog (163 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb3-11 homolog (41 kDa, Protein from African swine fever virus BA71V)
- Dna-directed rna polymerase rpb2 homolog (140 kDa, Protein from African swine fever virus BA71V)
- Magnesium ion (24 Da, Ligand)
- Uncharacterized protein c122r (11 kDa, Protein from African swine fever virus BA71V)
- Zinc ion (65 Da, Ligand)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7qhm
Q-score: 0.567
Kao WC, Ortmann de Percin Northumberland C, Cheng TC, Ortiz J, Durand A, von Loeffelholz O, Schilling O, Biniossek ML, Klaholz BP, Hunte C
Nat Commun (2022) 13 pp. 545-545 [ Pubmed: 35087070 DOI: doi:10.1038/s41467-022-28179-x ]
- Copper (ii) ion (63 Da, Ligand)
- Hypothetical membrane protein (12 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase subunit 2 (36 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Heme c (618 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- Heme-as (920 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Hypothetical membrane protein (6 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- [(2~{r})-3-[[(1~{s},2~{r},3~{s},4~{s},5~{r},6~{r})-2-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-[[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-[[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{r},3~{s},4~{s},5~{s},6~{r})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{r})-10-methyldodecanoate (1 kDa, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Uncharacterized protein cgl2664/cg2949 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome bcc-aa3 supercomplex (Complex from Corynebacterium glutamicum ATCC 13032)
- Lycopene (536 Da, Ligand)
- Stigmatellin a (514 Da, Ligand)
- Cytochrome c oxidase subunit 1 (66 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Actinobacterial supercomplex, subunit c (ascc) (8 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- Dinuclear copper ion (127 Da, Ligand)
- Oxygen molecule (31 Da, Ligand)
- Uncharacterized membrane protein cgl2017/cg2211 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- [(2~{r})-3-[[(1~{s},2~{r},3~{r},4~{s},5~{s},6~{r})-2-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{s})-10-methylhenicosanoate (1 kDa, Ligand)
- Thiamine biosynthesis protein x (17 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Diacyl glycerol (625 Da, Ligand)
- Water (18 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Azide ion (42 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (45 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Calcium ion (40 Da, Ligand)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7qho
Q-score: 0.516
Kao W-C, Ortmann de Percin Northumberland C, Cheng TC, Ortiz J, Durand A, von Loeffelholz O, Schilling O, Biniossek ML, Klaholz BP, Hunte C
Nat Commun (2022) 13 pp. 545- [ DOI: doi:10.1038/s41467-022-28179-x Pubmed: 35087070 ]
- Cytochrome bcc-aa3 supercomplex (Complex from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Thiamine biosynthesis protein x (17 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Uncharacterized protein cgl2664/cg2949 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome bc1 complex rieske iron-sulfur subunit (45 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Hypothetical membrane protein (6 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 1 (66 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- 1,2-diacyl-glycerol-3-sn-phosphate (704 Da, Ligand)
- [(2~{r})-3-[[(1~{s},2~{r},3~{r},4~{s},5~{s},6~{r})-2-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{s})-10-methylhenicosanoate (1 kDa, Ligand)
- Palmitic acid (256 Da, Ligand)
- Cytochrome c oxidase subunit 2 (36 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Calcium ion (40 Da, Ligand)
- Uncharacterized membrane protein cgl2017/cg2211 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Dinuclear copper ion (127 Da, Ligand)
- Heme c (618 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- (2r)-2-(hexadecanoyloxy)-3-{[(s)-hydroxy{[(1r,2r,3r,4r,5r,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9s)-9-methyloctadecanoate (853 Da, Ligand)
- Water (18 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Actinobacterial supercomplex, subunit c (ascc) (8 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Diacyl glycerol (625 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Hypothetical membrane protein (12 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme-as (920 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- [(2~{r})-3-[[(1~{s},2~{r},3~{s},4~{s},5~{r},6~{r})-2-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-[[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-[[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{r},3~{s},4~{s},5~{s},6~{r})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{r})-10-methyldodecanoate (1 kDa, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Capsid of empty GTA particle computed with C5 symmetry
Resolution: 3.42 Å
EM Method: Single-particle
Fitted PDBs: 6tsu
Q-score: 0.532
Bardy P, Fuzik T, Hrebik D, Pantucek R, Thomas Beatty J, Plevka P
Nat Commun (2020) 11 pp. 3034-3034 [ DOI: doi:10.1038/s41467-020-16669-9 Pubmed: 32541663 ]
- Rhodobacter capsulatus de442 gene transfer agent capsid (80 kDa, Complex from Rhodobacter capsulatus DE442)
- Uncharacterized protein (32 kDa, Protein from Rhodobacter capsulatus DE442)
- Head spike (Complex from Rhodobacter capsulatus DE442)
- Major capsid protein rcc01687 (40 kDa, Protein from Rhodobacter capsulatus DE442)
- Uncharacterized protein (9 kDa, Protein from Rhodobacter capsulatus DE442)
Cryo-EM structure of the ribosome from Encephalitozoon cuniculi
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7qep
Q-score: 0.577
Nicholson D, Salamina M, Panek J, Helena-Bueno K, Brown CR, Hirt RP, Ranson NA, Melnikov SV
Nat Commun (2022) 13 pp. 591- [ DOI: doi:10.1038/s41467-022-28281-0 ]
- 60s ribosomal protein l34 (12 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s10 (11 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l37a (l43) (9 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s20 (14 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s8 (19 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l21 (18 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l6 (19 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Ribosome from encephalitozoon cuniculi (Complex from Encephalitozoon cuniculi)
- 60s ribosomal protein l23 (16 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l7 (27 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s23 (15 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s12 (14 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l36 (10 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s4 (30 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s18 (17 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l35a (l33) (12 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l20 (21 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l44 (12 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Ecu06_1135 protein (9 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s28 (7 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s3 (24 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l13 (18 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l31 (13 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s0 (27 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Small subunit (Complex from Encephalitozoon cuniculi)
- 18s ribosomal rna (422 kDa, RNA from Encephalitozoon cuniculi GB-M1)
- 5s ribosomal rna (38 kDa, RNA from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s7 (19 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l30 (11 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l8 (25 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l13a (l16) (22 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s24 (15 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Ecu11_0225 protein (7 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s16 (16 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Ribosomal protein l15 (23 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s29 (7 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l22 (12 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s5 (20 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Similarity to monoubiquitin/carboxy-extension protein fusion (17 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Uncharacterized protein ecu01_0250 (19 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s1 (26 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Guanine nucleotide binding protein beta subunit (36 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l5 (32 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Ribosomal protein s15 (16 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l35-1 (14 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Similarity to 60s ribosomal protein l24 (11 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s27 (9 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s26 (11 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l37 (10 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s14 (14 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Ubiquitin/ l40 ribosomal protein fusion (14 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s17 (14 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s2 (26 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l32 (16 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l23a (11 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l3 (42 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s13 (16 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s19 (15 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Ecu06_1215 protein (12 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l18 (22 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l1 (24 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l39 (6 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l27a (17 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Adenosine monophosphate (347 Da, Ligand)
- 40s ribosomal protein s11 (17 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l4 (37 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 5.8s-23s ribosomal rna (807 kDa, RNA from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l10 (25 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s9 (20 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l11 (19 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l9 (20 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s25 (12 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l29 (6 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l19 (20 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l26 (16 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s6 (25 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l17 (20 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l7a (23 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 60s ribosomal protein l27 (14 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- 40s ribosomal protein s15a (s22 in yeast) (14 kDa, Protein from Encephalitozoon cuniculi GB-M1)
- Large subunit (Complex from Encephalitozoon cuniculi)
The structure of the large subunit of the mitoribosome from Neurospora crassa
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 6yws
Q-score: 0.601
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 ]
- Ribosomal protein (13 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l6 (28 kDa, Protein from Neurospora crassa OR74A)
- Potassium ion (39 Da, Ligand)
- 60s ribosomal protein l2 (42 kDa, Protein from Neurospora crassa OR74A)
- Ribosomal_l9 domain-containing protein (33 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (49 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l14 (14 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (37 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l20 (25 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal subunit l30 (41 kDa, Protein from Neurospora crassa OR74A)
- Magnesium ion (24 Da, Ligand)
- Uncharacterized protein (32 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (49 kDa, Protein from Neurospora crassa OR74A)
- 54s ribosomal protein l4, mitochondrial (29 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (41 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l4, variant (36 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l5 (39 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial ribosomal protein subunit l32 (14 kDa, Protein from Neurospora crassa OR74A)
- Aconitate hydratase (23 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l30 (18 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial ribosomal protein l43 (15 kDa, Protein from Neurospora crassa OR74A)
- Ribosomal protein l13 (20 kDa, Protein from Neurospora crassa OR74A)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Mitochondrial ribosomal protein l44 (11 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l24 (31 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l16 (27 kDa, Protein from Neurospora crassa OR74A)
- Mitoc_ml59 domain-containing protein (18 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (23 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial ribosomal protein subunit l23 (26 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l3 (48 kDa, Protein from Neurospora crassa OR74A)
- Kow domain-containing protein (45 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (7 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (18 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (23 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l1 (33 kDa, Protein from Neurospora crassa OR74A)
- L51_s25_ci-b8 domain-containing protein (22 kDa, Protein from Neurospora crassa OR74A)
- Spermine (202 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Mitochondrial ribosomal protein (28 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (11 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial large ribosomal subunit (41 kDa, Protein from Neurospora crassa OR74A)
- Ribosomal protein l15 (33 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l19 (16 kDa, Protein from Neurospora crassa OR74A)
- Rnase iii domain-containing protein (29 kDa, Protein from Neurospora crassa OR74A)
- Mitoribosome of neurospora crassa (Complex from Neurospora crassa OR74A)
- 50s ribosomal protein l17 (22 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial large ribosomal subunit yml35 (50 kDa, Protein from Neurospora crassa OR74A)
- Rna (2820-mer) (1 MDa, RNA from Neurospora crassa OR74A)
- 54s ribosomal protein l31, mitochondrial (13 kDa, Protein from Neurospora crassa OR74A)
- Related to ribosomal protein l34, mitochondrial (14 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l3 (41 kDa, Protein from Neurospora crassa OR74A)
The structure of the Atp25 bound assembly intermediate of the mitoribosome from Neurospora crassa
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 6ywv
Q-score: 0.544
Itoh Y, Naschberger A, Mortezaei N, Herrmann JM, Amunts A
Nat Commun (2020) 11 pp. 5187-5187 [ Pubmed: 33056988 DOI: doi:10.1038/s41467-020-18830-w ]
- Mitochondrial ribosomal protein l43 (15 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial ribosomal protein subunit l32 (14 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (49 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial ribosomal protein subunit l23 (26 kDa, Protein from Neurospora crassa OR74A)
- Assembly intermediate of the mitoribosome of neurospora crassa (Complex from Neurospora crassa OR74A)
- 60s ribosomal protein l6 (28 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (14 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (11 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l17 (22 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (23 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l20 (25 kDa, Protein from Neurospora crassa OR74A)
- Rnase iii domain-containing protein (29 kDa, Protein from Neurospora crassa OR74A)
- 54s ribosomal protein l4, mitochondrial (29 kDa, Protein from Neurospora crassa OR74A)
- 23 s rrna (1 MDa, RNA from Neurospora crassa OR74A)
- Ribosomal protein (13 kDa, Protein from Neurospora crassa OR74A)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- 50s ribosomal subunit protein l15 (33 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l30 (18 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (37 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial large ribosomal subunit yml35 (50 kDa, Protein from Neurospora crassa OR74A)
- Spermine (202 Da, Ligand)
- Uncharacterized protein (18 kDa, Protein from Neurospora crassa OR74A)
- Kow domain-containing protein (45 kDa, Protein from Neurospora crassa OR74A)
- Potassium ion (39 Da, Ligand)
- Uncharacterized protein (7 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l24 (31 kDa, Protein from Neurospora crassa OR74A)
- Zinc ion (65 Da, Ligand)
- 60s ribosomal protein l16 (27 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l3 (41 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial ribosomal protein (28 kDa, Protein from Neurospora crassa OR74A)
- Atpase synthesis protein 25, mitochondrial (77 kDa, Protein from Neurospora crassa OR74A)
- Aconitate hydratase (23 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (41 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial large ribosomal subunit (41 kDa, Protein from Neurospora crassa OR74A)
- 54s ribosomal protein l31, mitochondrial (13 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (23 kDa, Protein from Neurospora crassa OR74A)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l5 (39 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l2 (42 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal subunit l30 (41 kDa, Protein from Neurospora crassa OR74A)
- 50s ribosomal protein l14 (14 kDa, Protein from Neurospora crassa OR74A)
- Ribosomal protein l13 (20 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l4, variant (36 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l19 (16 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial ribosomal protein l44 (11 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (32 kDa, Protein from Neurospora crassa OR74A)
- Uncharacterized protein (49 kDa, Protein from Neurospora crassa OR74A)
- 60s ribosomal protein l3 (48 kDa, Protein from Neurospora crassa OR74A)
- Mitochondrial 60s ribosomal protein l25 (18 kDa, Protein from Neurospora crassa OR74A)