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 ]
- Dark (Complex)
- Dronc-card (Complex)
- Apaf-1 related killer dark (142 kDa, Protein from Drosophila melanogaster)
- Caspase dronc (12 kDa, Protein from Drosophila melanogaster)
- Structure of the dark/dronc complex (Complex from Drosophila melanogaster)
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 repair factor 1 (prf1) (13 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Uncharacterized protein (9 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)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii protein d1 (39 kDa, Protein from Chlamydomonas reinhardtii)
- Bicarbonate ion (61 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein k (5 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii repair factor 2 (prf2) (12 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chlamydomonas reinhardtii)
- Cryo-em structure of an intermediate-state complex during the process of photosystem ii repair (Complex from Chlamydomonas reinhardtii)
- Thylakoid enriched factor 14 (tef14) (20 kDa, Protein from Chlamydomonas reinhardtii)
- Pheophytin a (871 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Rrr-alpha-tocopherylquinone (446 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chlamydomonas reinhardtii)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- 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 cp43 reaction center protein (50 kDa, Protein from Chlamydomonas reinhardtii)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a (893 Da, Ligand)
- Photosystem ii d2 protein (39 kDa, Protein from Chlamydomonas reinhardtii)
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 ]
- Cytochrome b559 subunit beta (4 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 4.1 kda photosystem ii subunit (9 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)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Chlamydomonas reinhardtii)
- Bicarbonate ion (61 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Photosystem ii reaction center protein k (5 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Cryo-em map of the psii-prf2' complex functioning in the psii-repair cycle (Complex from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chlamydomonas reinhardtii)
- Chains: 1 (10 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii protein d1 (36 kDa, Protein from Chlamydomonas reinhardtii)
- Pheophytin a (871 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii reaction center protein psb30 (3 kDa, Protein from Chlamydomonas reinhardtii)
- Rrr-alpha-tocopherylquinone (446 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chlamydomonas reinhardtii)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- 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 cp43 reaction center protein (50 kDa, Protein from Chlamydomonas reinhardtii)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem ii d2 protein (39 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 [ DOI: doi:10.1073/pnas.2312784121 Pubmed: 38381783 ]
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 ]
- Ced-4 hexamer (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)
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)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Heptameric ced-4/ced-3 catalytic complex (Complex from Caenorhabditis elegans)
- Cell death protein 4 (62 kDa, Protein from Caenorhabditis elegans)
cryo-EM structure of the CED-4/CED-3 holoenzyme
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8jol
Q-score: 0.325
Life Sci Alliance (2023) 6 [ DOI: doi:10.26508/lsa.202302056 Pubmed: 37402593 ]
- Ternary complex of ced-4 with ced-3 card and ced-3 catalytic domain (Complex from Caenorhabditis elegans)
- Cell death protein 3 (56 kDa, Protein from Caenorhabditis elegans)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Cell death protein 4 (62 kDa, Protein from Caenorhabditis elegans)
S protein of SARS-CoV-2 in complex bound with P2B-1A1
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7czp
Q-score: 0.359
Yan R, Wang R, Ju B, Yu J, Zhang Y, Liu N, Wang J, Zhang Q, Chen P, Zhou B, Li Y, Shen Y, Zhang S, Tian L, Guo Y, Xia L, Zhong X, Cheng L, Ge X, Zhao J, Wang HW, Wang X, Zhang Z, Zhang L, Zhou Q
Cell Res (2021) 31 pp. 517-525 [ Pubmed: 33731853 DOI: doi:10.1038/s41422-021-00487-9 ]
- S protein of sars-cov-2 in complex bound with p2b-1a1 (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ig c181_light_iglv2-14_iglj3,igl@ protein (22 kDa, Protein from Homo sapiens)
- Immunoglobulin heavy variable 4-59,chain h of p2b-1a1,anti-rhd monoclonal t125 gamma1 heavy chain (49 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
cryo EM map of the S protein of SARS-CoV-2 in complex bound with P2B-1A10
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7czq
Q-score: 0.385
Yan R, Wang R, Ju B, Yu J, Zhang Y, Liu N, Wang J, Zhang Q, Chen P, Zhou B, Li Y, Shen Y, Zhang S, Tian L, Guo Y, Xia L, Zhong X, Cheng L, Ge X, Zhao J, Wang HW, Wang X, Zhang Z, Zhang L, Zhou Q
Cell Res (2021) 31 pp. 517-525 [ Pubmed: 33731853 DOI: doi:10.1038/s41422-021-00487-9 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- S protein of sars-cov-2 in complex bound with p2b-1a10 (Complex from Homo sapiens)
- Ig c642_heavy_ighv3-53_ighd1-26_ighj6,chain h of p2b-1a10,immunoglobulin gamma-1 heavy chain (49 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Immunoglobulin kappa variable 1-33,uncharacterized protein (23 kDa, Protein from Homo sapiens)