Structure of the Dark/Dronc complex
Resolution: 7.0 Å
EM Method: Single-particle
Fitted PDBs: 8y6q
Q-score: 0.154
PNAS (2024) 121 pp. e2312784121-e2312784121 [ DOI: doi:10.1073/pnas.2312784121 Pubmed: 38381783 ]
- Structure of the dark/dronc complex (Complex from Drosophila melanogaster)
- Dark (Complex)
- Apaf-1 related killer dark (142 kDa, Protein from Drosophila melanogaster)
- Caspase dronc (12 kDa, Protein from Drosophila melanogaster)
- Dronc-card (Complex)
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 ]
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Bicarbonate ion (61 Da, Ligand)
- Photosystem ii cp43 reaction center protein (50 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein h (9 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chlamydomonas reinhardtii)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein k (5 kDa, Protein from Chlamydomonas reinhardtii)
- Cryo-em structure of an intermediate-state complex during the process of photosystem ii repair (Complex from Chlamydomonas reinhardtii)
- Uncharacterized protein (9 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii repair factor 1 (prf1) (13 kDa, Protein from Chlamydomonas reinhardtii)
- Thylakoid enriched factor 14 (tef14) (20 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)
- Pheophytin a (871 Da, Ligand)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii d2 protein (39 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a (893 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chlamydomonas reinhardtii)
- Rrr-alpha-tocopherylquinone (446 Da, Ligand)
- Photosystem ii reaction center protein z (6 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)
- Photosystem ii protein d1 (39 kDa, Protein from Chlamydomonas reinhardtii)
- Protoporphyrin ix containing fe (616 Da, Ligand)
Overall cryo-EM map of an intermediate-state complex during the process of photosystem II repair
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8zee
Q-score: 0.518
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 z (6 kDa, Protein from Chlamydomonas reinhardtii)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein psb30 (3 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Cryo-em map of the psii-prf2' complex functioning in the psii-repair cycle (Complex from Chlamydomonas reinhardtii)
- 4.1 kda photosystem ii subunit (9 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein k (5 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein m (3 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii d2 protein (39 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein h (9 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii cp43 reaction center protein (50 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii protein d1 (36 kDa, Protein from Chlamydomonas reinhardtii)
- Bicarbonate ion (61 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a (893 Da, Ligand)
- Protoporphyrin ix containing fe (616 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)
- Rrr-alpha-tocopherylquinone (446 Da, Ligand)
- Chains: 1 (10 kDa, Protein from Chlamydomonas reinhardtii)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chlamydomonas reinhardtii)
Structure of the auto-inhibited Dark monomer
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8y6p
Q-score: 0.376
PNAS (2024) 121 pp. e2312784121-e2312784121 [ Pubmed: 38381783 DOI: doi:10.1073/pnas.2312784121 ]
cryo-EM structure of a CED-4 hexamer
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 8jns
Q-score: 0.263
Life Sci Alliance (2023) 6 [ DOI: doi:10.26508/lsa.202302056 Pubmed: 37402593 ]
- Cell death protein 4 (62 kDa, Protein from Caenorhabditis elegans)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Ced-4 hexamer (Complex from Caenorhabditis elegans)
- Magnesium ion (24 Da, Ligand)
The Cryo-EM structure of a heptameric CED-4/CED-3 catalytic complex
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8jo0
Q-score: 0.303
Life Sci Alliance (2023) 6 [ DOI: doi:10.26508/lsa.202302056 Pubmed: 37402593 ]
- Cell death protein 4 (12 kDa, Protein from Caenorhabditis elegans)
- Heptameric ced-4/ced-3 catalytic complex (Complex from Caenorhabditis elegans)
- Cell death protein 4 (62 kDa, Protein from Caenorhabditis elegans)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)