Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8xk3
Q-score: 0.567
Tao X, Ding H, Wu S, Wang F, Xu H, Li J, Zhai C, Li S, Chen K, Wu S, Liu Y, Ma L
Nucleic Acids Res (2024) 52 pp. 11895-11910 [ DOI: doi:10.1093/nar/gkae820 Pubmed: 39315697 ]
- Kmago (85 kDa, Protein from Kurthia massiliensis)
- Kmago (Complex from Kurthia massiliensis)
- Target dna-1 (2 kDa, DNA from Kurthia massiliensis)
- Water (18 Da, Ligand)
- Guide dna (5 kDa, DNA from Kurthia massiliensis)
- Target dna-2 (2 kDa, DNA from Kurthia massiliensis)
- Manganese (ii) ion (54 Da, Ligand)
(CAG)2 DNA-bound MutSbeta in open form with kinked MSH2 clamp
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8rz7
Q-score: 0.292
Lee J-H, Thomsen M, Daub H, Steinbacher S, Sztyler A, Thieulin-Pardo G, Neudegger T, Plotnikov N, Iyer RR, Wilkinson H, Monteagudo E, Felsenfeld DP, Haque T, Finley M, Dominguez C, Vogt TF, Prasad BC
To Be Published
- Dna mismatch repair protein msh2 (104 kDa, Protein from Homo sapiens)
- Mutsbeta-dna-adp complex (Complex)
- Dna mismatch repair protein (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna_2 (18 kDa, DNA from Homo sapiens)
- Dna_1 (20 kDa, DNA from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
- Double stranded dna (Complex from Homo sapiens)
Structure of V. cholerae DdmD in complex with ssDNA
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 9bf5
Q-score: 0.455
Yang XY, Shen Z, Wang C, Nakanishi K, Fu TM
Cell (2024) 187 pp. 5253-5266.e16 [ DOI: doi:10.1016/j.cell.2024.07.028 Pubmed: 39173632 ]
- Helicase/uvrb n-terminal domain-containing protein (136 kDa, Protein from Vibrio cholerae)
- Ssdna1 (4 kDa, DNA from Vibrio cholerae)
- Dimeric complex of v. cholerae ddmd bound with ssdna (Complex from Vibrio cholerae)
- Ssdna2 (4 kDa, DNA from Vibrio cholerae)
Riccio AA, Bouvette J, Pedersen LC, Somai S, Dutcher RC, Borgnia MJ, Copeland WC
Nucleic Acids Res (2024) 52 pp. 10329-10340 [ Pubmed: 39106165 DOI: doi:10.1093/nar/gkae670 ]
- Polg2, mitochondrial dna polymerase gamma accessory subunit (Protein from Homo sapiens)
- Dna1 (DNA from synthetic construct)
- Single-stranded dna-binding protein, mitochondrial (Protein from Homo sapiens)
- Dna3 (DNA from synthetic construct)
- Dna2 (DNA from synthetic construct)
- The mitchondrial dna polymerase, catalytic (polg) and accessory subunits (polg2), bound to dna in complex with the mitochondrial dna single-stranded binding protein (mtssb) (230 kDa, Complex from Homo sapiens)
- Polg, mitochondrial dna polymerase catalytic subunit (Protein from Homo sapiens)
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
An Q, Wang Y, Tian Z, Han J, Li J, Liao F, Yu F, Zhao H, Wen Y, Zhang H, Deng Z
Cell Res (2024) 34 pp. 545-555 [ Pubmed: 38834762 DOI: doi:10.1038/s41422-024-00981-w ]
- Duf4297-hera-dna-state2 (Complex from Escherichia coli)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Duf4297 (46 kDa, Protein from Escherichia coli)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- S20dna2 (18 kDa, DNA from Escherichia coli)
- Atp-binding protein (64 kDa, Protein from Escherichia coli)
- S20dna1 (18 kDa, DNA 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
An Q, Wang Y, Tian Z, Han J, Li J, Liao F, Yu F, Zhao H, Wen Y, Zhang H, Deng Z
Cell Res (2024) 34 pp. 545-555 [ Pubmed: 38834762 DOI: doi:10.1038/s41422-024-00981-w ]
- Duf4297-hera-dna state1 (Complex from Escherichia coli)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Duf4297 (46 kDa, Protein from Escherichia coli)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- S20dna2 (18 kDa, DNA from Escherichia coli)
- Atp-binding protein (64 kDa, Protein from Escherichia coli)
- S20dna1 (18 kDa, DNA from Escherichia coli)
Structure of the E. coli clamp loader bound to the beta clamp in a Closed-DNA2 conformation
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8var
Q-score: 0.422
Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA
J Biol Chem (2024) 300 pp. 107166-107166 [ DOI: doi:10.1016/j.jbc.2024.107166 Pubmed: 38490435 ]
- Structure of the e. coli clamp loader bound to the beta clamp in an closed-dna2 conformation (Complex from Escherichia coli)
- Dna (5'-d(p*gp*cp*ap*gp*ap*cp*ap*cp*tp*ap*cp*gp*ap*gp*tp*ap*cp*ap*tp*a)-3') (6 kDa, DNA from synthetic construct)
- Beta sliding clamp (40 kDa, Protein from Escherichia coli)
- Dna polymerase iii subunit delta (38 kDa, Protein from Escherichia coli)
- Beryllium trifluoride ion (66 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna polymerase iii subunit delta' (37 kDa, Protein from Escherichia coli)
- Dna (27-mer) (9 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna polymerase iii subunit tau (41 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
MutSbeta bound to (CAG)2 DNA (open form)
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 8om9
Q-score: 0.249
Lee J-H, Thomsen M, Daub H, Steinbacher S, Sztyler A, Thieulin-Pardo G, Neudegger T, Plotnikov N, Iyer RR, Wilkinson H, Monteagudo E, Felsenfeld DP, Haque T, Finley M, Dominguez C, Vogt TF, Prasad BC
To Be Published
- Dna mismatch repair protein msh2 (104 kDa, Protein from Homo sapiens)
- Mutsbeta bound to (cag)2 dna (open form) (Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna1 (8 kDa, DNA from Homo sapiens)
- Dna2 (6 kDa, DNA from Homo sapiens)
MutSbeta bound to 61bp homoduplex DNA
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8oma
Q-score: 0.177
Lee J-H, Thomsen M, Daub H, Steinbacher S, Sztyler A, Thieulin-Pardo G, Neudegger T, Plotnikov N, Iyer RR, Wilkinson H, Monteagudo E, Felsenfeld DP, Haque T, Finley M, Dominguez C, Vogt TF, Prasad BC
To Be Published
- Dna mismatch repair protein msh2 (104 kDa, Protein from Homo sapiens)
- Dna2 (5 kDa, DNA from Homo sapiens)
- Mutsbeta bound to 61bp homoduplex dna (Complex from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
- Dna1 (5 kDa, DNA from Homo sapiens)
Bulky DNA lesion recognition complex 3
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023) 617 pp. 170-175 [ Pubmed: 37076618 DOI: doi:10.1038/s41586-023-05959-z ]
- General transcription and dna repair factor iih helicase subunit xpb (Protein from Homo sapiens)
- Dna1 (DNA from synthetic construct)
- General transcription factor iih subunit 3 (Protein from Homo sapiens)
- General transcription factor iih subunit 4 (Protein from Homo sapiens)
- General transcription factor iih subunit 5 (Protein from Homo sapiens)
- Dna2 (DNA from synthetic construct)
- Tfiih basal transcription factor complex helicase xpd subunit (Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (Protein from Homo sapiens)
- Bulky dna lesion recognition complex 3 (440 kDa, Complex from Homo sapiens)
- General transcription factor iih subunit 2 (Protein from Homo sapiens)
- General transcription factor iih subunit 1 (Protein from Homo sapiens)