III2IV respiratory supercomplex from Saccharomyces cerevisiae
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 9etz
Q-score: 0.639
Lobez AP, Wu F, Di Trani JM, Rubinstein JL, Oliveberg M, Brzezinski P, Moe A
Nat Commun (2024) 15 pp. 8241-8241 [ Pubmed: 39300056 DOI: doi:10.1038/s41467-024-52475-3 ]
- Iii2-iv respiratory supercomplex (Complex from Saccharomyces cerevisiae)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Cytochrome b-c1 complex subunit 1, mitochondrial (47 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b (43 kDa, Protein from Saccharomyces cerevisiae)
- Heme c (618 Da, Ligand)
- Cytochrome c oxidase subunit 12, mitochondrial (8 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- Dinuclear copper ion (127 Da, Ligand)
- Cytochrome c oxidase subunit 26, mitochondrial (5 kDa, Protein from Saccharomyces cerevisiae)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Cytochrome c oxidase subunit 13, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 6, mitochondrial (8 kDa, Protein from Saccharomyces cerevisiae)
- 1,2-diacyl-sn-glycero-3-phoshocholine (734 Da, Ligand)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (20 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 10, mitochondrial (8 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 4, mitochondrial (12 kDa, Protein from Saccharomyces cerevisiae)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase subunit 1 (58 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 5a, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 2, mitochondrial (38 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 8, mitochondrial (5 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c1, heme protein, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 9, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Calcium ion (40 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome b-c1 complex subunit 9, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- 5-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy-6-methyl-benzene-1,4-diol (592 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Cytochrome b-c1 complex subunit 8, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 2 (26 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 3 (30 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 7, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 6, mitochondrial (12 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 7, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
mycobacterial efflux pump, substrate-bound state
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8k1n
Q-score: 0.541
Wang Y, Gao S, Wu F, Gong Y, Mu N, Wei C, Wu C, Wang J, Yan N, Yang H, Zhang Y, Liu J, Wang Z, Yang X, Lam SM, Shui G, Li S, Da L, Guddat LW, Rao Z, Zhang L
PNAS (2024) 121 pp. e2403421121-e2403421121 [ DOI: doi:10.1073/pnas.2403421121 Pubmed: 39226350 ]
- Cardiolipin (1 kDa, Ligand)
- Multidrug efflux system permease protein rv1217c (56 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Ternary complex of an abc transporter rv1217c-1218c (120 kDa, Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Multidrug efflux system atp-binding protein rv1218c (33 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Rifampicin (822 Da, Ligand)
mycobacterial efflux pump, AMPPNP bound state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8k1o
Q-score: 0.597
Wang Y, Gao S, Wu F, Gong Y, Mu N, Wei C, Wu C, Wang J, Yan N, Yang H, Zhang Y, Liu J, Wang Z, Yang X, Lam SM, Shui G, Li S, Da L, Guddat LW, Rao Z, Zhang L
PNAS (2024) 121 pp. e2403421121-e2403421121 [ DOI: doi:10.1073/pnas.2403421121 Pubmed: 39226350 ]
- Multidrug efflux system permease protein rv1217c (56 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Multidrug efflux system atp-binding protein rv1218c (33 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Magnesium ion (24 Da, Ligand)
- Ternary complex of an abc transporter rv1217c-1218c (120 kDa, Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
mycobacterial efflux pump, ADP+vanadate bound state
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8k1p
Q-score: 0.548
To Be Published
- Cardiolipin (1 kDa, Ligand)
- Magnesium ion (24 Da, Ligand)
- Multidrug efflux system permease protein rv1217c (56 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Ternary complex of an abc transporter rv1217c-1218c (120 kDa, Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Multidrug efflux system atp-binding protein rv1218c (33 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Vanadate ion (114 Da, Ligand)
Cryo-EM structure of the Asgard archaeal Argonaute HrAgo1 bound to a guide RNA
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8r3z
Q-score: 0.403
Bastiaanssen C, Bobadilla Ugarte P, Kim K, Finocchio G, Feng Y, Anzelon TA, Kostlbacher S, Tamarit D, Ettema TJG, Jinek M, MacRae IJ, Joo C, Swarts DC, Wu F
Nat Commun (2024) 15 pp. 5499-5499 [ DOI: doi:10.1038/s41467-024-49452-1 Pubmed: 38951509 ]
- Asgard archaeal argonaute hrago1 in complex with the 5'-end of a guide rna (Complex from Candidatus Harpocratesius repetitus)
- Magnesium ion (24 Da, Ligand)
- Hrago1 (95 kDa, Protein from Candidatus Harpocratesius repetitus)
- Rna (5'-r(p*up*gp*ap*gp*gp*u*(mg))-3') (6 kDa, RNA from Candidatus Harpocratesius repetitus)
Membrane bound PRTase, C3 symmetry, donor bound
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8j8j
Q-score: 0.601
Gao S, Wu F, Gurcha SS, Batt SM, Besra GS, Rao Z, Zhang L
Nat Microbiol (2024) 9 pp. 976-987 [ DOI: doi:10.1038/s41564-024-01643-8 Pubmed: 38491273 ]
- Magnesium ion (24 Da, Ligand)
- 1-o-pyrophosphono-5-o-phosphono-alpha-d-ribofuranose (390 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- Decaprenyl-phosphate phosphoribosyltransferase (32 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Trimeric phosphoribosyltransferase (97 kDa, Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 7dty
Q-score: 0.436
Zhao F, Zhang C, Zhou Q, Hang K, Zou X, Chen Y, Wu F, Rao Q, Dai A, Yin W, Shen DD, Zhang Y, Xia T, Stevens RC, Xu HE, Yang D, Zhao L, Wang MW
eLife (2021) 10 [ DOI: doi:10.7554/eLife.68719 Pubmed: 34254582 ]
- Guanine nucleotide-binding protein g(s) subunit alpha isoforms short (45 kDa, Protein from Bos taurus)
- Gastric inhibitory polypeptide (4 kDa, Protein from Homo sapiens)
- Nanobody-35 (15 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (40 kDa, Protein from Rattus norvegicus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Human glucose-dependent insulinotropic polypeptide receptor (64 kDa, Protein from Homo sapiens)
- Cryo-em structure of the human glucose-dependent insulinotropic polypeptide receptor in complex with gip and g protein (Complex from Homo sapiens)
- Cholesterol (386 Da, Ligand)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7bvc
Q-score: 0.564
Zhang L, Zhao Y, Gao Y, Wu L, Gao R, Zhang Q, Wang Y, Wu C, Wu F, Gurcha SS, Veerapen N, Batt SM, Zhao W, Qin L, Yang X, Wang M, Zhu Y, Zhang B, Bi L, Zhang X, Yang H, Guddat LW, Xu W, Wang Q, Li J, Besra GS, Rao Z
Science (2020) 368 pp. 1211-1219 [ Pubmed: 32327601 DOI: doi:10.1126/science.aba9102 ]
- [(2z,6e,10e,14z,18e,22z,26z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2s,3s,4s,5r)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate (911 Da, Ligand)
- Meromycolate extension acyl carrier protein (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Acpm (Complex from Mycolicibacterium smegmatis MC2 155)
- 4'-phosphopantetheine (358 Da, Ligand)
- Ethambutol (204 Da, Ligand)
- Mycobacterium smegmatis arabinosyltransferase emba-embb-acpm2 in complex with ethambutol (Complex)
- Integral membrane indolylacetylinositol arabinosyltransferase embb (119 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Emba-embb (Complex from Mycolicibacterium smegmatis MC2 155)
- Calcium ion (40 Da, Ligand)
- Integral membrane indolylacetylinositol arabinosyltransferase emba (116 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Phosphate ion (94 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 7bve
Q-score: 0.552
Zhang L, Zhao Y, Gao Y, Wu L, Gao R, Zhang Q, Wang Y, Wu C, Wu F, Gurcha SS, Veerapen N, Batt SM, Zhao W, Qin L, Yang X, Wang M, Zhu Y, Zhang B, Bi L, Zhang X, Yang H, Guddat LW, Xu W, Wang Q, Li J, Besra GS, Rao Z
Science (2020) 368 pp. 1211-1219 [ Pubmed: 32327601 DOI: doi:10.1126/science.aba9102 ]
- N~3~-[(2s)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-n-(2-sulfanylethyl)-beta-alaninamide (358 Da, Ligand)
- Integral membrane indolylacetylinositol arabinosyltransferase embc (116 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Mycobacterium smegmatis arabinosyltransferase embc2-acpm2 in complex with ethambutol (Complex)
- Meromycolate extension acyl carrier protein (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Acpm (Complex from Mycolicibacterium smegmatis MC2 155)
- Ethambutol (204 Da, Ligand)
- Embc (Complex from Mycolicibacterium smegmatis MC2 155)
- Calcium ion (40 Da, Ligand)
- Phosphate ion (94 Da, Ligand)
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 7bvf
Q-score: 0.58
Zhang L, Zhao Y, Gao Y, Wu L, Gao R, Zhang Q, Wang Y, Wu C, Wu F, Gurcha SS, Veerapen N, Batt SM, Zhao W, Qin L, Yang X, Wang M, Zhu Y, Zhang B, Bi L, Zhang X, Yang H, Guddat LW, Xu W, Wang Q, Li J, Besra GS, Rao Z
Science (2020) 368 pp. 1211-1219 [ Pubmed: 32327601 DOI: doi:10.1126/science.aba9102 ]
- Cardiolipin (1 kDa, Ligand)
- Mono-trans, octa-cis decaprenyl-phosphate (779 Da, Ligand)
- Mycobacterium tuberculosis arabinosyltransferase emba-embb-acpm2 in complex with ethambutol (Complex)
- Meromycolate extension acyl carrier protein (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Probable arabinosyltransferase a (116 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Acpm (Complex from Mycolicibacterium smegmatis MC2 155)
- Probable arabinosyltransferase b (120 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Ethambutol (204 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Emba and embb (Complex from Mycobacterium tuberculosis H37Rv)