Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8rcu
Q-score: 0.325
Ekundayo B, Arullampalam P, Gerber CE, Hammerli AF, Guichard S, Boukenna M, Ross-Kaschitza D, Lochner M, Rougier JS, Stahlberg H, Abriel H, Ni D
Nat Commun (2025) 16 pp. 833-833 [ DOI: doi:10.1038/s41467-025-56131-2 Pubmed: 39828793 ]
- 4-chloranyl-2-[2-(3-iodanylphenoxy)ethanoylamino]benzoic acid (431 Da, Ligand)
- Homotetramer (500 MDa, Complex from Homo sapiens)
- Transient receptor potential cation channel subfamily m member 4 (83 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
Structure of 5D3-Fab and nanobody(Nb8)-bound ABCG2
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8p7w
Q-score: 0.511
Irobalieva RN, Manolaridis I, Jackson SM, Ni D, Pardon E, Stahlberg H, Steyaert J, Locher KP
J Mol Biol (2023) 435 pp. 168234-168234 [ DOI: doi:10.1016/j.jmb.2023.168234 Pubmed: 37597690 ]
- 5d3(fab) light chain variable domain (23 kDa, Protein from Mus musculus)
- 5d3(fab) heavy chain variable domain (23 kDa, Protein from Mus musculus)
- Nanobody (13 kDa, Protein from Lama glama)
- 5d3(fab) heavy and light chain variable domain (Complex from Mus musculus)
- Structure of nanobody (nb8)-bound abcg2 (Complex)
- Atp-binding cassette sub-family g member 2 (Complex from Homo sapiens)
- Nanobody (Complex from Lama glama)
- Atp-binding cassette sub-family g member 2 (72 kDa, Protein from Homo sapiens)
Structure of 5D3-Fab and nanobody(Nb17)-bound ABCG2
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8p8a
Q-score: 0.52
Irobalieva RN, Manolaridis I, Jackson SM, Ni D, Pardon E, Stahlberg H, Steyaert J, Locher KP
J Mol Biol (2023) 435 pp. 168234-168234 [ DOI: doi:10.1016/j.jmb.2023.168234 Pubmed: 37597690 ]
- 5d3(fab) light chain variable domain (23 kDa, Protein from Mus musculus)
- 5d3(fab) heavy chain variable domain (17 kDa, Protein from Mus musculus)
- Structure of nanobody (nb8)-bound abcg2 (Complex from Homo sapiens)
- Nanobody (13 kDa, Protein from Lama glama)
- Atp-binding cassette sub-family g member 2 (72 kDa, Protein from Homo sapiens)
Structure of 5D3-Fab and nanobody(Nb96)-bound ABCG2
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 8p8j
Q-score: 0.471
Irobalieva RN, Manolaridis I, Jackson SM, Ni D, Pardon E, Stahlberg H, Steyaert J, Locher KP
J Mol Biol (2023) 435 pp. 168234-168234 [ DOI: doi:10.1016/j.jmb.2023.168234 Pubmed: 37597690 ]
- 5d3(fab) light chain variable domain (23 kDa, Protein from Mus musculus)
- 5d3(fab) heavy chain variable domain (23 kDa, Protein from Mus musculus)
- Structure of nanobody (nb96)-bound abcg2 (Complex)
- Nanobody (13 kDa, Protein from Lama glama)
- 5d3(fab) heavy and light chain variable domain (Complex from Mus musculus)
- Atp-binding cassette sub-family g member 2 (Complex from Homo sapiens)
- Nanobody (Complex from Lama glama)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Atp-binding cassette sub-family g member 2 (72 kDa, Protein from Homo sapiens)
elongated Cascade complex from type I-A CRISPR-Cas system
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7r2k
Q-score: 0.324
Ni D, Hu C, Nam KH, Terns M, Stahlberg H, Ke A
To Be Published
- Crispr-associated endonuclease cas3-hd (27 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna (5'-d(p*tp*ap*cp*ap*ap*gp*gp*gp*a)-3') (2 kDa, DNA from Escherichia coli)
- Cas8 (38 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Crispr-associated helicase cas3 (74 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Type i-a crispr-associated protein cas5 (29 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Elongated cascade complex from pyrococcus furiosus type i-a crispr/cas system (550 kDa, Complex)
- Cas11a (12 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Cas7a (36 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Crrna (57-mer) (18 kDa, RNA from Escherichia coli)
- Nickel (ii) ion (58 Da, Ligand)
- Dna (5'-d(p*tp*cp*cp*c)-3') (1 kDa, DNA from Escherichia coli)
cryoEM structure of SPARTA complex ligand-free
Resolution: 3.97 Å
EM Method: Single-particle
Fitted PDBs: 8oz6
Q-score: 0.222
Ni D, Lu X, Stahlberg H, Ekundayo B
Sci Adv (2023) 9 pp. eadh9002-eadh9002 [ DOI: doi:10.1126/sciadv.adh9002 Pubmed: 37467330 ]
- Rna (5'-r(p*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*u)-3') (5 kDa, RNA from Maribacter polysiphoniae)
- Heter complex of short argonaute-tir antiviral defence system (500 kDa, Complex from Maribacter polysiphoniae)
- Dna (5'-d(*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (4 kDa, DNA from Maribacter polysiphoniae)
- Piwi domain-containing protein (58 kDa, Protein from Maribacter polysiphoniae)
- Tir domain-containing protein (53 kDa, Protein from Maribacter polysiphoniae)
cryoEM structure of SPARTA complex dimer high resolution
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 8oze
Q-score: 0.503
Ni D, Lu X, Stahlberg H, Ekundayo B
Sci Adv (2023) 9 pp. eadh9002-eadh9002 [ DOI: doi:10.1126/sciadv.adh9002 Pubmed: 37467330 ]
- Dna (5'-d(p*ap*tp*ap*cp*ap*ap*cp*cp*tp*ap*cp*tp*ap*cp*cp*tp*c)-3') (5 kDa, DNA from Maribacter polysiphoniae)
- Rna (5'-r(p*up*gp*ap*gp*gp*up*ap*gp*up*ap*gp*gp*up*up*gp*up*ap*up*ap*g)-3') (6 kDa, RNA from Maribacter polysiphoniae)
- Piwi domain-containing protein (58 kDa, Protein from Maribacter polysiphoniae)
- Tir domain-containing protein (53 kDa, Protein from Maribacter polysiphoniae)
- Sparta complex dimer high resolution (300 kDa, Complex from Maribacter polysiphoniae)
cryoEM structure of SPARTA complex Tetramer Post-NAD cleavage-2
Resolution: 3.73 Å
EM Method: Single-particle
Fitted PDBs: 8ozf
Q-score: 0.299
Ni D, Lu X, Stahlberg H, Ekundayo B
Sci Adv (2023) 9 pp. eadh9002-eadh9002 [ DOI: doi:10.1126/sciadv.adh9002 Pubmed: 37467330 ]
- Sparta complex tetramer post-nad cleavage-2 (550 kDa, Complex from Maribacter polysiphoniae)
- Rna (5'-r(p*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*u)-3') (5 kDa, RNA from Maribacter polysiphoniae)
- [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (559 Da, Ligand)
- Dna (5'-d(*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (4 kDa, DNA from Maribacter polysiphoniae)
- Piwi domain-containing protein (58 kDa, Protein from Maribacter polysiphoniae)
- Tir domain-containing protein (53 kDa, Protein from Maribacter polysiphoniae)
cryoEM structure of SPARTA complex Tetramer Post-NAD cleavage-1
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8ozg
Q-score: 0.394
Ni D, Lu X, Stahlberg H, Ekundayo B
Sci Adv (2023) 9 pp. eadh9002-eadh9002 [ DOI: doi:10.1126/sciadv.adh9002 Pubmed: 37467330 ]
- Cryoem structure of sparta complex tetramer post-nad cleavage-1 (500 kDa, Complex from Maribacter polysiphoniae)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(p*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*u)-3') (5 kDa, RNA from Maribacter polysiphoniae)
- [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (559 Da, Ligand)
- Dna (5'-d(*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (4 kDa, DNA from Maribacter polysiphoniae)
- Piwi domain-containing protein (58 kDa, Protein from Maribacter polysiphoniae)
- Tir domain-containing protein (53 kDa, Protein from Maribacter polysiphoniae)
cryoEM structure of SPARTA complex pre-NAD cleavage
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 8ozi
Q-score: 0.439
Ni D, Lu X, Stahlberg H, Ekundayo B
Sci Adv (2023) 9 pp. eadh9002-eadh9002 [ DOI: doi:10.1126/sciadv.adh9002 Pubmed: 37467330 ]
- Sparta complex pre-nad cleavage (560 kDa, Complex from Maribacter polysiphoniae)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Rna (5'-r(p*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*up*u)-3') (5 kDa, RNA from Maribacter polysiphoniae)
- Dna (5'-d(*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (4 kDa, DNA from Maribacter polysiphoniae)
- Piwi domain-containing protein (58 kDa, Protein from Maribacter polysiphoniae)
- Tir domain-containing protein (53 kDa, Protein from Maribacter polysiphoniae)