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Cryo-EM structure of an anti-phage defense complex bound to AMPPNP and DNA at state 1
Resolution: 2.73 Å
EM Method: Single-particle
Fitted PDBs: 8xaw
Q-score: 0.553
To Be Published
- Magnesium ion (24 Da, Ligand)
- S20dna2 (18 kDa, DNA from Escherichia coli)
- Duf4297-hera-dna-state2 (Complex from Escherichia coli)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp-binding protein (64 kDa, Protein from Escherichia coli)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- S20dna1 (18 kDa, DNA from Escherichia coli)
- Duf4297 (46 kDa, Protein from Escherichia coli)
Cryo-EM structure of an anti-phage defense complex bound to AMPPNP and DNA at state 2
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 8xax
Q-score: 0.516
To Be Published
- Magnesium ion (24 Da, Ligand)
- S20dna2 (18 kDa, DNA from Escherichia coli)
- Duf4297-hera-dna state1 (Complex from Escherichia coli)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Atp-binding protein (64 kDa, Protein from Escherichia coli)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- S20dna1 (18 kDa, DNA from Escherichia coli)
- Duf4297 (46 kDa, Protein from Escherichia coli)
The Cryo-EM structure of MPXV E5 apo conformation
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 8xj6
Q-score: 0.362
Cell Discov (2024) [ ]
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Monkeypox virus (Virus from Monkeypox virus)
- Amp phosphoramidate (426 Da, Ligand)
- Monkeypox virus e5 (90 kDa, Protein from Monkeypox virus)
- Zinc ion (65 Da, Ligand)
The Cryo-EM structure of MPXV E5 in complex with DNA
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 8xj7
Q-score: 0.541
Cell Discov (2024) [ ]
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Monkeypox virus (Virus from Monkeypox virus)
- Dna (70-mer) (21 kDa, DNA from Monkeypox virus)
- Magnesium ion (24 Da, Ligand)
- Monkeypox virus e5 (90 kDa, Protein from Monkeypox virus)
The Cryo-EM structure of MPXV E5 C-terminal in complex with DNA
Resolution: 2.67 Å
EM Method: Single-particle
Fitted PDBs: 8xj8
Q-score: 0.189
Cell Discov (2024) [ ]
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Monkeypox virus (Virus from Monkeypox virus)
- Dna (70-mer) (21 kDa, DNA from Monkeypox virus)
- Magnesium ion (24 Da, Ligand)
- Monkeypox virus e5 (53 kDa, Protein from Monkeypox virus)
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 8gk7
Q-score: 0.364
Wang H, Ishchenko A, Skudlarek J, Shen P, Dzhekieva L, Painter RE, Chen YT, Bukhtiyarova M, Leithead A, Tracy R, Babaoglu K, Bahnck-Teets C, Buevich A, Cabalu TD, Labroli M, Lange H, Lei Y, Li W, Liu J, Mann PA, Meng T, Mitchell HJ, Mulhearn J, Scapin G, Sha D, Shaw AW, Si Q, Tong L, Wu C, Wu Z, Xiao JC, Xu M, Zhang LK, McKenney D, Miller RR, Black TA, Cooke A, Balibar CJ, Klein DJ, Raheem I, Walker SS
Nat Microbiol (2024) 9 pp. 1244-1255 [ DOI: doi:10.1038/s41564-024-01667-0 Pubmed: 38649414 ]
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Lipid a export atp-binding/permease protein msba (66 kDa, Protein from Acinetobacter baumannii)
- Msba complexed with cerastecin c (450 kDa, Complex from Acinetobacter baumannii)
- 2-[(4-butylbenzene-1-sulfonyl)amino]-5-[(3-{4-[(4-butylbenzene-1-sulfonyl)amino]-3-carboxyanilino}-3-oxopropyl)carbamoyl]benzoic acid (778 Da, Ligand)
Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-catalytic intermediate state
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8j5s
Q-score: 0.566
Yang X, Hu T, Liang J, Xiong Z, Lin Z, Zhao Y, Zhou X, Gao Y, Sun S, Yang X, Guddat LW, Yang H, Rao Z, Zhang B
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01256-z Pubmed: 38548954 ]
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Uncharacterized abc transporter atp-binding protein rv1281c (65 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1282c (31 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Iron/sulfur cluster (351 Da, Ligand)
- Endogenous oligopeptide (698 Da, Protein from Mycolicibacterium smegmatis MC2 155)
- Uncharacterized protein rv1280c (64 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Magnesium ion (24 Da, Ligand)
- Cryo-em structure of mycobacterium tuberculosis oppabcd in the pre-catalytic intermediate state (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1283c (35 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Composite structure of Dynein-Dynactin-JIP3-LIS1
Resolution: 10.0 Å
EM Method: Single-particle
Fitted PDBs: 8ptk
Q-score: 0.202
Singh K, Lau CK, Manigrasso G, Gama JB, Gassmann R, Carter AP
Science (2024) 383 pp. eadk8544-eadk8544 [ DOI: doi:10.1126/science.adk8544 Pubmed: 38547289 ]
- Dynactin 6 (20 kDa, Protein from Sus scrofa)
- Actin, cytoplasmic 1 (41 kDa, Protein from Sus scrofa)
- C-jun-amino-terminal kinase-interacting protein 3 (65 kDa, Protein from Homo sapiens)
- Arp11 (46 kDa, Protein from Sus scrofa)
- Dynactin subunits (Complex from Sus scrofa)
- Dynein light chain tctex-type 1 (12 kDa, Protein from Homo sapiens)
- F-actin-capping protein subunit beta (30 kDa, Protein from Sus scrofa)
- Cytoplasmic dynein 1 intermediate chain 2 (68 kDa, Protein from Homo sapiens)
- Composite structure of dynein-dynactin-jip3-lis1 (Complex)
- Dynein light chain 1, cytoplasmic (10 kDa, Protein from Homo sapiens)
- Dynactin subunit 2 (44 kDa, Protein from Sus scrofa)
- Platelet-activating factor acetylhydrolase ib subunit beta (46 kDa, Protein from Homo sapiens)
- Cytoplasmic dynein 1 light intermediate chain 2 (54 kDa, Protein from Homo sapiens)
- Dynactin subunit 5 (20 kDa, Protein from Sus scrofa)
- Cytoplasmic dynein 1 heavy chain 1 (533 kDa, Protein from Homo sapiens)
- Dynein and jip3 (Complex from Homo sapiens)
- Dynactin subunit 3 (21 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Arp1 actin related protein 1 homolog a (42 kDa, Protein from Sus scrofa)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dynactin subunit 1 (142 kDa, Protein from Sus scrofa)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dynein light chain roadblock-type 1 (10 kDa, Protein from Homo sapiens)
- Dynactin subunit 4 (52 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Capping protein (actin filament) muscle z-line, alpha 1 (33 kDa, Protein from Sus scrofa)
Cryo-EM structure of H. thermophilus GroEL-GroES2 asymmetric football complex
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8wuw
Q-score: 0.444
Liao Z, Gopalasingam CC, Kameya M, Gerle C, Shigematsu H, Ishii M, Arakawa T, Fushinobu S
Structure (2024) [ Pubmed: 38492570 DOI: doi:10.1016/j.str.2024.02.012 ]
- Co-chaperonin groes (Complex)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Chaperonin groel (56 kDa, Protein from Hydrogenobacter thermophilus TK-6)
- Potassium ion (39 Da, Ligand)
- Co-chaperonin groes (10 kDa, Protein from Hydrogenobacter thermophilus TK-6)
- Magnesium ion (24 Da, Ligand)
- H. thermophilus groel-groes2 asymmetric football complex (Complex from Hydrogenobacter thermophilus TK-6)
- Chaperonin groel (Complex)
Cryo-EM structure of H. thermophilus GroEL-GroES bullet complex
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8wux
Q-score: 0.453
Liao Z, Gopalasingam CC, Kameya M, Gerle C, Shigematsu H, Ishii M, Arakawa T, Fushinobu S
Structure (2024) [ Pubmed: 38492570 DOI: doi:10.1016/j.str.2024.02.012 ]
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- H. thermophilus groel-groes bullet complex (Complex from Hydrogenobacter thermophilus TK-6)
- Chaperonin groel (56 kDa, Protein from Hydrogenobacter thermophilus TK-6)
- Co-chaperonin groes (10 kDa, Protein from Hydrogenobacter thermophilus TK-6)
- Potassium ion (39 Da, Ligand)
- Chaperonin groel (Complex)
- Co-chaperonin groes (Complex)
- Magnesium ion (24 Da, Ligand)