Structure of human GlcNAc-1-phosphotransferase complexed with the donor substrate UDP-GlcNAc
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9bgf
Q-score: 0.577
Li H, Doray B, Jennings BC, Lee WS, Liu L, Kornfeld S, Li H
J Biol Chem (2024) 300 pp. 107706-107706 [ Pubmed: 39178950 DOI: doi:10.1016/j.jbc.2024.107706 ]
- Calcium ion (40 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Glcnac-1-phosphotransferase (268 kDa, Complex from Homo sapiens)
- Uridine-diphosphate-n-acetylglucosamine (607 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- N-acetylglucosamine-1-phosphotransferase subunits alpha/beta (134 kDa, Protein from Homo sapiens)
Structure of a hyperactive S1S3 truncation of the human GlcNAc-1-phosphotransferase
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9bgg
Q-score: 0.421
Li H, Doray B, Jennings BC, Lee WS, Liu L, Kornfeld S, Li H
J Biol Chem (2024) 300 pp. 107706-107706 [ Pubmed: 39178950 DOI: doi:10.1016/j.jbc.2024.107706 ]
Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex (pICln PBM local refinement)
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 9e3a
Q-score: 0.48
Jin CY, Hunkeler M, Mulvaney KM, Sellers WR, Fischer ES
J Biol Chem (2025) 301 pp. 108165-108165 [ DOI: doi:10.1016/j.jbc.2025.108165 Pubmed: 39793893 ]
- Methylosome subunit picln (Complex)
- Methylosome protein wdr77 (37 kDa, Protein from Homo sapiens)
- Methylosome subunit picln (26 kDa, Protein from Homo sapiens)
- 6s complex (Complex from Homo sapiens)
- Prmt5/wdr77 in complex with 6s (pbm local refinement) (770 kDa, Complex)
- Small nuclear ribonucleoproteins sm d1, e, f, g (Complex)
- Protein arginine n-methyltransferase 5 (72 kDa, Protein from Homo sapiens)
- Prmt5/wdr77 (Complex from Homo sapiens)
Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 9e3b
Q-score: 0.512
Jin CY, Hunkeler M, Mulvaney KM, Sellers WR, Fischer ES
J Biol Chem (2025) 301 pp. 108165-108165 [ DOI: doi:10.1016/j.jbc.2025.108165 Pubmed: 39793893 ]
- Methylosome subunit picln (Complex)
- Methylosome protein wdr77 (37 kDa, Protein from Homo sapiens)
- Sinefungin (381 Da, Ligand)
- Methylosome subunit picln (26 kDa, Protein from Homo sapiens)
- 6s complex (Complex from Homo sapiens)
- Small nuclear ribonucleoproteins e, f, g (Complex)
- Prmt5/wdr77 in complex with 6s (770 kDa, Complex)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Protein arginine n-methyltransferase 5 (72 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (Complex)
- Prmt5/wdr77 (Complex from Homo sapiens)
Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex (GRG local refine)
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 9e3c
Q-score: 0.508
Jin CY, Hunkeler M, Mulvaney KM, Sellers WR, Fischer ES
J Biol Chem (2025) 301 pp. 108165-108165 [ DOI: doi:10.1016/j.jbc.2025.108165 Pubmed: 39793893 ]
- Methylosome subunit picln (Complex)
- Sinefungin (381 Da, Ligand)
- Prmt5/wdr77 in complex with 6s (grg active site local refine) (770 kDa, Complex)
- 6s complex (Complex from Homo sapiens)
- Small nuclear ribonucleoproteins e, f, g (Complex)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Protein arginine n-methyltransferase 5 (72 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (Complex)
- Prmt5/wdr77 (Complex from Homo sapiens)
Resolution: 1.97 Å
EM Method: Single-particle
Fitted PDBs: 9eh5
Q-score: 0.703
Flesher DA, Shin J, Debus RJ, Brudvig GW
J Biol Chem (2025) pp. 108272-108272 [ DOI: doi:10.1016/j.jbc.2025.108272 Pubmed: 39922494 ]
- Photosystem ii protein d1 2 (38 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii cp43 reaction center protein (50 kDa, Protein from Synechocystis sp. PCC 6803)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem ii manganese-stabilizing polypeptide (29 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii reaction center protein h (7 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii reaction center x protein (4 kDa, Protein from Synechocystis sp. PCC 6803)
- 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)
- (3r)-beta,beta-caroten-3-ol (552 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Bicarbonate ion (61 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii reaction center protein ycf12 (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii protein y (4 kDa, Protein from Synechocystis sp. PCC 6803)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii reaction center protein j (3 kDa, Protein from Synechocystis sp. PCC 6803)
- Water (18 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Photosystem ii reaction center protein t (3 kDa, Protein from Synechocystis sp. PCC 6803)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Photosystem ii cp47 reaction center protein (55 kDa, Protein from Synechocystis sp. PCC 6803)
- Cytochrome b559 subunit beta (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii d2 protein (39 kDa, Protein from Synechocystis sp. PCC 6803)
- Cytochrome c-550 (17 kDa, Protein from Synechocystis sp. PCC 6803)
- Calcium ion (40 Da, Ligand)
- Photosystem ii reaction center protein k (5 kDa, Protein from Synechocystis sp. PCC 6803)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem ii reaction center protein z (6 kDa, Protein from Synechocystis sp. PCC 6803)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Synechocystis sp. PCC 6803)
- Sll1638 protein (16 kDa, Protein from Synechocystis sp. PCC 6803)
- Photosystem ii (Complex from Synechocystis sp. PCC 6803)
- Photosystem ii 12 kda extrinsic protein (14 kDa, Protein from Synechocystis sp. PCC 6803)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosystem ii reaction center protein i (4 kDa, Protein from Synechocystis sp. PCC 6803)
- Ca-mn4-o5 cluster (339 Da, Ligand)
Cryo-EM structure of the reduced cytochrome bd oxidase from M. tuberculosis
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 9fka
Q-score: 0.526
van der Velden TT, Kayastha K, Waterham CYJ, Brunle S, Jeuken LJC
J Biol Chem (2024) 301 pp. 108094-108094 [ DOI: doi:10.1016/j.jbc.2024.108094 Pubmed: 39706268 ]
- Menaquinone-9 (785 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Cis-heme d hydroxychlorin gamma-spirolactone (632 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Probable integral membrane cytochrome d ubiquinol oxidase (subunit i) cyda (cytochrome bd-i oxidase subunit i) (53 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Probable integral membrane cytochrome d ubiquinol oxidase (subunit ii) cydb (cytochrome bd-i oxidase subunit ii) (37 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome bd-i oxidase (942 kDa, Complex from Mycobacterium tuberculosis)
- Cardiolipin (1 kDa, Ligand)
Human calpain-3 forms a homohexamer
Ye Q, Henrickson A, Demeler B, Balasco Serrao VH, Davies PL
J Biol Chem (2024) 301 pp. 108133-108133 [ Pubmed: 39725035 DOI: doi:10.1016/j.jbc.2024.108133 ]
- Human calpain-3 (Protein from Homo sapiens)
- Calpain-3 hexamer particle (514 kDa, Complex from Homo sapiens)
Blood cell-specific tubulin in complex with Cryptophycin-52
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9c6r
Q-score: 0.488
Montecinos F, Eren E, Watts NR, Sackett DL, Wingfield PT
J Biol Chem (2024) 301 pp. 108132-108132 [ Pubmed: 39725029 DOI: doi:10.1016/j.jbc.2024.108132 ]
- Chicken erythrocytes tubulin in complex with cryptophycin-52 (734 kDa, Complex from Gallus gallus)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Cryptophycin 52 (669 Da, Ligand)
- Detyrosinated tubulin alpha-1a chain (50 kDa, Protein from Gallus gallus)
- Tubulin beta-6 chain (50 kDa, Protein from Gallus gallus)
18-mer blood cell-specific tubulin in complex with Cryptophycin-52
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 9c6s
Q-score: 0.381
Montecinos F, Eren E, Watts NR, Sackett DL, Wingfield PT
J Biol Chem (2024) 301 pp. 108132-108132 [ Pubmed: 39725029 DOI: doi:10.1016/j.jbc.2024.108132 ]
- 18-mer hematopoietic tubulin in complex with cryptophycin-52 (840 kDa, Complex from Gallus gallus)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Cryptophycin 52 (669 Da, Ligand)
- Detyrosinated tubulin alpha-1a chain (50 kDa, Protein from Gallus gallus)
- Tubulin beta-6 chain (50 kDa, Protein from Gallus gallus)