(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_2 (18 kDa, DNA from Homo sapiens)
- Double stranded dna (Complex from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna_1 (20 kDa, DNA from Homo sapiens)
- Dna mismatch repair protein (Complex from Homo sapiens)
- Mutsbeta-dna-adp complex (Complex)
- Magnesium ion (24 Da, Ligand)
- Dna mismatch repair protein msh2 (104 kDa, Protein from Homo sapiens)
- Dna mismatch repair protein msh3 (127 kDa, Protein 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 ]
- Dimeric complex of v. cholerae ddmd bound with ssdna (Complex from Vibrio cholerae)
- Helicase/uvrb n-terminal domain-containing protein (136 kDa, Protein from Vibrio cholerae)
- Ssdna1 (4 kDa, DNA 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 [ DOI: doi:10.1093/nar/gkae670 Pubmed: 39106165 ]
- Dna2 (DNA from synthetic construct)
- Single-stranded dna-binding protein, mitochondrial (Protein from Homo sapiens)
- Polg, mitochondrial dna polymerase catalytic subunit (Protein from Homo sapiens)
- Dna3 (DNA from synthetic construct)
- Polg2, mitochondrial dna polymerase gamma accessory subunit (Protein from Homo sapiens)
- Dna1 (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)
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 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna polymerase iii subunit tau (41 kDa, Protein from Escherichia coli)
- Dna polymerase iii subunit delta' (37 kDa, Protein from Escherichia coli)
- Dna (27-mer) (9 kDa, DNA from synthetic construct)
- Beta sliding clamp (40 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna polymerase iii subunit delta (38 kDa, Protein from Escherichia coli)
- 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)
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
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna1 (8 kDa, DNA from Homo sapiens)
- Mutsbeta bound to (cag)2 dna (open form) (Complex from Homo sapiens)
- Dna2 (6 kDa, DNA from Homo sapiens)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna mismatch repair protein msh2 (104 kDa, Protein 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
- Mutsbeta bound to 61bp homoduplex dna (Complex from Homo sapiens)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna2 (5 kDa, DNA from Homo sapiens)
- Dna mismatch repair protein msh2 (104 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 ]
- Dna repair protein complementing xp-a cells (Protein from Homo sapiens)
- General transcription factor iih subunit 1 (Protein from Homo sapiens)
- Bulky dna lesion recognition complex 3 (440 kDa, Complex from Homo sapiens)
- Dna2 (DNA from synthetic construct)
- General transcription factor iih subunit 5 (Protein from Homo sapiens)
- General transcription factor iih subunit 2 (Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (Protein from Homo sapiens)
- General transcription factor iih subunit 3 (Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (Protein from Homo sapiens)
- General transcription factor iih subunit 4 (Protein from Homo sapiens)
- Dna1 (DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpb (Protein from Homo sapiens)
Initial DNA-lesion (Cy5) binding by XPC and TFIIH focused
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 factor iih subunit 1 (Protein from Homo sapiens)
- Dna2 (DNA from synthetic construct)
- General transcription factor iih subunit 5 (Protein from Homo sapiens)
- Uv excision repair protein rad23 homolog b (Protein from Homo sapiens)
- General transcription factor iih subunit 2 (Protein from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpd subunit (Protein from Homo sapiens)
- General transcription factor iih subunit 3 (Protein from Homo sapiens)
- Centrin-2 (Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (Protein from Homo sapiens)
- General transcription factor iih subunit 4 (Protein from Homo sapiens)
- Dna1 (DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpb (Protein from Homo sapiens)
- Bulky dna lesion recognition complex 1 (270 kDa, Complex from Homo sapiens)
XPC release from Core7-XPA-DNA (Cy5)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8ebu
Q-score: 0.341
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 factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Bulky dna lesion recognition complex3 (Complex from Homo sapiens)
- Tfiih basal transcription factor complex helicase xpb subunit (89 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-c cells (107 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna repair protein complementing xp-a cells (31 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 2 (46 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (88 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- General transcription factor iih subunit 4, p52 (52 kDa, Protein from Homo sapiens)
- Dna1 (7 kDa, DNA from synthetic construct)
- Dna2 (7 kDa, DNA from synthetic construct)
Type IIS Restriction Endonuclease PaqCI, DNA bound
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8epx
Q-score: 0.545
Kennedy MA, Hosford CJ, Azumaya CM, Luyten YA, Chen M, Morgan RD, Stoddard BL
Nucleic Acids Res (2023) 51 pp. 4467-4487 [ Pubmed: 36987874 DOI: doi:10.1093/nar/gkad228 ]
- Dna 1b (6 kDa, DNA from DNA molecule)
- Dna 2b (5 kDa, DNA from DNA molecule)
- Dna 3a (5 kDa, DNA from DNA molecule)
- Calcium ion (40 Da, Ligand)
- Dna 2a (4 kDa, DNA from DNA molecule)
- Dna 3b (5 kDa, DNA from DNA molecule)
- Type iis restriction endonuclease paqci (56 kDa, Protein from Paucibacter aquatile)
- Dna 4b (4 kDa, DNA from DNA molecule)
- Dna 1a (7 kDa, DNA from DNA molecule)
- Dna 4a (4 kDa, DNA from DNA molecule)
- Homotetramer paqci with associated dna duplexes (Complex from Paucibacter aquatile)