Yeast RNA polymerase II transcription pre-initiation complex with core Mediator
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8cen
Q-score: 0.269
Schilbach S, Wang H, Dienemann C, Cramer P
PNAS (2023) 120 pp. e2220542120-e2220542120 [ Pubmed: 37014863 DOI: doi:10.1073/pnas.2220542120 ]
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 20 (22 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 8 (25 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 31 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with core mediator (2 MDa, Complex)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 4 (32 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 6 (32 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 1 (64 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (32 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factors and mediator of rna polymerase ii transcription subunits (Complex from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 14 (84 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase subunits (Complex from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (209-mer) (64 kDa, DNA from synthetic construct)
- Dna (Complex from Synthetic construct)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factors, and rna polymerase ii transcription factor b subunit 3 (Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 19 (24 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 22 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 10 (17 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Tata-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Template dna (209-mer) (64 kDa, DNA from synthetic construct)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8ceo
Q-score: 0.222
Schilbach S, Wang H, Dienemann C, Cramer P
PNAS (2023) 120 pp. e2220542120-e2220542120 [ Pubmed: 37014863 DOI: doi:10.1073/pnas.2220542120 ]
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 18 (34 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 20 (22 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 8 (25 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with core mediator and the +1 nucleosome (2 MDa, Complex from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 9 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 31 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia subunit 2 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Template dna (209-mer) (64 kDa, DNA from synthetic construct)
- Mediator of rna polymerase ii transcription subunit 21 (16 kDa, Protein from Saccharomyces cerevisiae)
- Toa1 isoform 1 (32 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 4 (32 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Mediator of rna polymerase ii transcription subunit 6 (32 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 7 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 1 (64 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 14 (123 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 19 (24 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 22 (13 kDa, Protein from Saccharomyces cerevisiae)
- Mediator of rna polymerase ii transcription subunit 10 (17 kDa, Protein from Saccharomyces cerevisiae)
- Tfb1 isoform 1 (72 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih (52 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Nontemplate dna (209-mer) (64 kDa, DNA from synthetic construct)
- Mediator of rna polymerase ii transcription subunit 17 (78 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Rna polymerase ii transcription factor b subunit 2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Tata-binding protein (27 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b (13 kDa, Protein from Saccharomyces cerevisiae)
In situ double-PBS-PSII-PSI-LHCs megacomplex from Porphyridium purpureum.
You X, Zhang X, Cheng J, Xiao Y, Ma J, Sun S, Zhang X, Wang HW, Sui SF
Nature (2023) 616 pp. 199-206 [ Pubmed: 36922595 DOI: doi:10.1038/s41586-023-05831-0 ]
- B-phycoerythrin beta chain (18 kDa, Protein from Porphyridium purpureum)
- In situ double-pbs-psii-psi-lhcs megacomplex from porphyridium purpureum. (Cell from Porphyridium purpureum)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Phycobilisome rod-core linker polypeptide (26 kDa, Protein from Porphyridium purpureum)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Carsp2 (15 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein of lhcii type iii, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i subunit o (9 kDa, Protein from Porphyridium purpureum)
- Ferredoxin (10 kDa, Protein from Porphyridium purpureum)
- Carsp1 (24 kDa, Protein from Porphyridium purpureum)
- Cytochrome c6 (8 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit iv (6 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (39 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein t (3 kDa, Protein from Porphyridium purpureum)
- Lrc5 (30 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit psak (6 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin beta subunit (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i iron-sulfur center (8 kDa, Protein from Porphyridium purpureum)
- Photosystem ii protein d1 (39 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (29 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein l (4 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Redcap (19 kDa, Protein from Porphyridium purpureum)
- Phycocyanobilin (588 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- 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)
- Phycourobilin (590 Da, Ligand)
- (2s)-2,3-dihydroxypropyl octadecanoate (358 Da, Ligand)
- Photosystem i reaction center subunit viii (3 kDa, Protein from Porphyridium purpureum)
- Photosystem ii cp43 reaction center protein (52 kDa, Protein from Porphyridium purpureum)
- Lpp2 (17 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center x protein (4 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Oxygen-evolving enhancer protein (30 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Porphyridium purpureum)
- Phycobiliprotein apce (99 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit iii (17 kDa, Protein from Porphyridium purpureum)
- Fucoxanthin-chlorophyll a-c binding protein, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit xi (14 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta 18 subunit (19 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (36 kDa, Protein from Porphyridium purpureum)
- Phycoerythrin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- (1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Psii_pbs31 domain-containing protein (22 kDa, Protein from Porphyridium purpureum)
- Fe (iii) ion (55 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Lr6 (46 kDa, Protein from Porphyridium purpureum)
- Psar (12 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Porphyridium purpureum)
- Lrh (20 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Porphyridium purpureum)
- Linker4 (11 kDa, Protein from Porphyridium purpureum)
- Psbm (10 kDa, Protein from Porphyridium purpureum)
- Beta-carotene (536 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (37 kDa, Protein from Porphyridium purpureum)
- Psb34 (2 kDa, Protein from Porphyridium purpureum)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Glycerol (92 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Porphyridium purpureum)
- Photosystem ii protein y (3 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein k (5 kDa, Protein from Porphyridium purpureum)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Phycoerythrobilin (588 Da, Ligand)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (10 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (31 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit ii (14 kDa, Protein from Porphyridium purpureum)
- Water (18 Da, Ligand)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod (53 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin gamma subunit (18 kDa, Protein from Porphyridium purpureum)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (26 kDa, Protein from Porphyridium purpureum)
- Psbw (3 kDa, Protein from Porphyridium purpureum)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lpp1 (10 kDa, Protein from Porphyridium purpureum)
- Ps ii complex 12 kda extrinsic protein (16 kDa, Protein from Porphyridium purpureum)
- Cytochrome c550 (17 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein h (7 kDa, Protein from Porphyridium purpureum)
- Lrc4 (16 kDa, Protein from Porphyridium purpureum)
- Lps1 (5 kDa, Protein from Porphyridium purpureum)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (34 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (55 kDa, Protein from Porphyridium purpureum)
- Beta-d-glucopyranose (180 Da, Ligand)
- Photosystem i p700 chlorophyll a apoprotein a1 (82 kDa, Protein from Porphyridium purpureum)
- Photosystem ii d2 protein (39 kDa, Protein from Porphyridium purpureum)
- Cnt (10 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein j (3 kDa, Protein from Porphyridium purpureum)
- Psbq' (22 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (27 kDa, Protein from Porphyridium purpureum)
- Cytochrome b559 subunit beta (5 kDa, Protein from Porphyridium purpureum)
- Psab (82 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta subunit (17 kDa, Protein from Porphyridium purpureum)
In situ single-PBS-PSII-PSI-LHCs megacomplex.
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7y5e
Q-score: 0.318
You X, Zhang X, Cheng J, Xiao Y, Ma J, Sun S, Zhang X, Wang HW, Sui SF
Nature (2023) 616 pp. 199-206 [ Pubmed: 36922595 DOI: doi:10.1038/s41586-023-05831-0 ]
- B-phycoerythrin beta chain (18 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (46 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Phycobilisome rod-core linker polypeptide (26 kDa, Protein from Porphyridium purpureum)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Chlorophyll a-b binding protein of lhcii type iii, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i subunit o (9 kDa, Protein from Porphyridium purpureum)
- Ferredoxin (10 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (39 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein t (3 kDa, Protein from Porphyridium purpureum)
- Psar (8 kDa, Protein from Porphyridium purpureum)
- Lrc5 (30 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit psak (6 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin beta subunit (18 kDa, Protein from Porphyridium purpureum)
- Photosystem ii protein d1 (39 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (29 kDa, Protein from Porphyridium purpureum)
- Carsps1 (31 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Redcap (19 kDa, Protein from Porphyridium purpureum)
- Phycocyanobilin (588 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- 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)
- Phycourobilin (590 Da, Ligand)
- (2s)-2,3-dihydroxypropyl octadecanoate (358 Da, Ligand)
- Photosystem ii cp43 reaction center protein (52 kDa, Protein from Porphyridium purpureum)
- Lpp2 (17 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center x protein (4 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Oxygen-evolving enhancer protein (30 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit xii (3 kDa, Protein from Porphyridium purpureum)
- Phycobiliprotein apce (99 kDa, Protein from Porphyridium purpureum)
- Cytochrome c6 (11 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Porphyridium purpureum)
- Psaa (83 kDa, Protein from Porphyridium purpureum)
- Fucoxanthin-chlorophyll a-c binding protein, chloroplastic (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit xi (14 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta 18 subunit (19 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (36 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit iii (20 kDa, Protein from Porphyridium purpureum)
- Phycoerythrin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- (1r,2s)-4-{(1e,3e,5e,7e,9e,11e,13e,15e,17e)-18-[(4s)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol (568 Da, Ligand)
- Phylloquinone (450 Da, Ligand)
- Psii_pbs31 domain-containing protein (22 kDa, Protein from Porphyridium purpureum)
- Fe (iii) ion (55 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- In situ single-pbs-psii-psi-lhcs megacomplex (Cell from Porphyridium purpureum)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Porphyridium purpureum)
- Lrh (20 kDa, Protein from Porphyridium purpureum)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Porphyridium purpureum)
- Psbm (10 kDa, Protein from Porphyridium purpureum)
- Beta-carotene (536 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Porphyridium purpureum)
- Psb34 (2 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (37 kDa, Protein from Porphyridium purpureum)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- Glycerol (92 Da, Ligand)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Porphyridium purpureum)
- Photosystem ii protein y (3 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein k (5 kDa, Protein from Porphyridium purpureum)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Phycoerythrobilin (588 Da, Ligand)
- Linker4 (14 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (10 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (32 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (31 kDa, Protein from Porphyridium purpureum)
- Chlorophyll a-b binding protein 1b-21, chloroplastic (19 kDa, Protein from Porphyridium purpureum)
- Water (18 Da, Ligand)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod (53 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin gamma subunit (18 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit ii (15 kDa, Protein from Porphyridium purpureum)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Photosystem i reaction center subunit iv (7 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (26 kDa, Protein from Porphyridium purpureum)
- Psbw (3 kDa, Protein from Porphyridium purpureum)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Lpp1 (10 kDa, Protein from Porphyridium purpureum)
- Ps ii complex 12 kda extrinsic protein (16 kDa, Protein from Porphyridium purpureum)
- Cytochrome c550 (17 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein h (7 kDa, Protein from Porphyridium purpureum)
- Carsp2 (36 kDa, Protein from Porphyridium purpureum)
- Lrc4 (16 kDa, Protein from Porphyridium purpureum)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Porphyridium purpureum)
- Lps1 (5 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (34 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (55 kDa, Protein from Porphyridium purpureum)
- Beta-d-glucopyranose (180 Da, Ligand)
- Photosystem ii d2 protein (39 kDa, Protein from Porphyridium purpureum)
- Cnt (10 kDa, Protein from Porphyridium purpureum)
- Photosystem ii reaction center protein j (3 kDa, Protein from Porphyridium purpureum)
- Psbq' (22 kDa, Protein from Porphyridium purpureum)
- Psbl (4 kDa, Protein from Porphyridium purpureum)
- Photosystem i iron-sulfur center (8 kDa, Protein from Porphyridium purpureum)
- Cytochrome b559 subunit beta (5 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta subunit (17 kDa, Protein from Porphyridium purpureum)
PBS of PBS-PSII-PSI-LHCs from Porphyridium purpureum.
You X, Zhang X, Cheng J, Xiao Y, Ma J, Sun S, Zhang X, Wang HW, Sui SF
Nature (2023) 616 pp. 199-206 [ Pubmed: 36922595 DOI: doi:10.1038/s41586-023-05831-0 ]
- B-phycoerythrin beta chain (18 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (36 kDa, Protein from Porphyridium purpureum)
- Lpp2 (17 kDa, Protein from Porphyridium purpureum)
- Phycobilisome rod-core linker polypeptide (26 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (26 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (45 kDa, Protein from Porphyridium purpureum)
- Phycobiliprotein apce (99 kDa, Protein from Porphyridium purpureum)
- Carsps2 (35 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (39 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin beta 18 subunit (19 kDa, Protein from Porphyridium purpureum)
- Lrc4 (16 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (36 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 27.9 kda linker polypeptide, phycoerythrin-associated, rod (34 kDa, Protein from Porphyridium purpureum)
- Phycoerythrin alpha subunit (17 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (55 kDa, Protein from Porphyridium purpureum)
- Lrc5 (30 kDa, Protein from Porphyridium purpureum)
- Phycoerythrobilin (588 Da, Ligand)
- Linker4 (14 kDa, Protein from Porphyridium purpureum)
- C-phycocyanin beta subunit (18 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 31.8 kda linker polypeptide, phycoerythrin-associated, rod (32 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 7.8 kda linker polypeptide, allophycocyanin-associated, core (10 kDa, Protein from Porphyridium purpureum)
- Fas1 domain-containing protein (31 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (31 kDa, Protein from Porphyridium purpureum)
- R-phycoerythrin gamma chain, chloroplastic (29 kDa, Protein from Porphyridium purpureum)
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod (53 kDa, Protein from Porphyridium purpureum)
- In situ pbs from porphyridium purpureum (Cell from Porphyridium purpureum)
- Phycocyanobilin (588 Da, Ligand)
- Carsps1 (28 kDa, Protein from Porphyridium purpureum)
- Phycourobilin (590 Da, Ligand)
- Allophycocyanin beta subunit (17 kDa, Protein from Porphyridium purpureum)
- Allophycocyanin gamma subunit (18 kDa, Protein from Porphyridium purpureum)
Human 20S proteasome core particle
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7nan
Q-score: 0.531
Zhao J, Makhija S, Zhou C, Zhang H, Wang Y, Muralidharan M, Huang B, Cheng Y
PNAS (2022) 119 pp. e2207200119-e2207200119 [ DOI: doi:10.1073/pnas.2207200119 Pubmed: 35858375 ]
- Proteasome subunit beta type-3 (22 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-1 (26 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-3 (28 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-5 (26 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-7 (27 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-4 (29 kDa, Protein from Homo sapiens)
- 20s proteasome core particle (Complex from Homo sapiens)
- Proteasome subunit alpha type-1 (29 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-2 (22 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-6 (25 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-7 (30 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-5 (28 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-2 (25 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-4 (29 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-6 (27 kDa, Protein from Homo sapiens)
Cryo-EM structure of the supercoiled EPEC H6 flagellar filament core Curly I waveform
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8cvi
Q-score: 0.486
Kreutzberger MAB, Sonani RR, Liu J, Chatterjee S, Wang F, Sebastian AL, Biswas P, Ewing C, Zheng W, Poly F, Frankel G, Luisi BF, Calladine CR, Krupovic M, Scharf BE, Egelman EH
Cell (2022) 185 pp. 3487-3500.e14 [ DOI: doi:10.1016/j.cell.2022.08.009 Pubmed: 36057255 ]
- Flagellin (56 kDa, Protein from Escherichia coli)
- Bacterial flagellar filament core (Complex from Escherichia coli)
Cryo-EM structure of the supercoiled E. coli K12 flagellar filament core, Normal waveform
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 8cxm
Q-score: 0.494
Kreutzberger MAB, Sonani RR, Liu J, Chatterjee S, Wang F, Sebastian AL, Biswas P, Ewing C, Zheng W, Poly F, Frankel G, Luisi BF, Calladine CR, Krupovic M, Scharf BE, Egelman EH
Cell (2022) 185 pp. 3487-3500.e14 [ DOI: doi:10.1016/j.cell.2022.08.009 Pubmed: 36057255 ]
- E. coli k12 flagellar filament core (Complex from Escherichia coli K-12)
- Flagellin (51 kDa, Protein from Escherichia coli K-12)
Human telomerase catalytic core structure at 3.3 Angstrom
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7trd
Q-score: 0.447
Liu B, He Y, Wang Y, Song H, Zhou ZH, Feigon J
Nature (2022) 604 pp. 578-583 [ Pubmed: 35418675 DOI: doi:10.1038/s41586-022-04582-8 ]
- Telomerase rna, partial sequence (145 kDa, RNA from Homo sapiens)
- Human telomerase catalytic core with dna-substrate (Complex from Homo sapiens)
- Telomerase reverse transcriptase (130 kDa, Protein from Homo sapiens)
- Telomeric repeat substrate (5 kDa, DNA from Homo sapiens)
Human telomerase catalytic core RNP with H2A/H2B
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7trf
Q-score: 0.369
Liu B, He Y, Wang Y, Song H, Zhou ZH, Feigon J
Nature (2022) 604 pp. 578-583 [ Pubmed: 35418675 DOI: doi:10.1038/s41586-022-04582-8 ]
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Telomerase rna, partial sequence (145 kDa, RNA from Homo sapiens)
- Telomerase reverse transcriptase (130 kDa, Protein from Homo sapiens)
- Telomeric repeat substrate (5 kDa, DNA from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Active human telomerase catalytic core with shelterin protein tpp1 (Complex from Homo sapiens)