DNA-bound Type IV-A3 CRISPR effector in complex with DinG helicase from K. pneumoniae (state I)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8s35
Q-score: 0.381
Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P
Nat Commun (2024) 15 pp. 9306-9306 [ Pubmed: 39468082 DOI: doi:10.1038/s41467-024-53778-1 ]
- Zinc ion (65 Da, Ligand)
- Crispr type aferr-associated protein csf2 (38 kDa, Protein from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf3 (25 kDa, Protein from Klebsiella pneumoniae)
- Crrna (19 kDa, RNA from Klebsiella pneumoniae)
- Type iv-a3 crispr-cas effector complex with ding from klebsiella pneumoniae bound to crrna and target dna (428 kDa, Complex)
- Ts-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Dead/deah box helicase (70 kDa, Protein from Klebsiella pneumoniae)
- Crispr effector in complex with a ding helicase and crrna (Complex from Klebsiella pneumoniae)
- Nts-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf1 (29 kDa, Protein from Klebsiella pneumoniae)
- Double-stranded dna (Complex from Klebsiella pneumoniae)
DNA-bound Type IV-A3 CRISPR effector in complex with DinG helicase from K. pneumoniae (state II)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8s36
Q-score: 0.388
Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P
Nat Commun (2024) 15 pp. 9306-9306 [ Pubmed: 39468082 DOI: doi:10.1038/s41467-024-53778-1 ]
- Zinc ion (65 Da, Ligand)
- Crispr type aferr-associated protein csf2 (38 kDa, Protein from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf3 (25 kDa, Protein from Klebsiella pneumoniae)
- Crrna (19 kDa, RNA from Klebsiella pneumoniae)
- Type iv-a3 crispr-cas effector complex with ding from klebsiella pneumoniae bound to crrna and target dna (Complex)
- Ts-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Nts-nda (18 kDa, DNA from Klebsiella pneumoniae)
- Dead/deah box helicase (70 kDa, Protein from Klebsiella pneumoniae)
- Crispr effector in complex with a ding helicase and crrna (Complex from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf1 (29 kDa, Protein from Klebsiella pneumoniae)
- Double-stranded dna (Complex from Klebsiella pneumoniae)
DNA-bound Type IV-A3 CRISPR effector in complex with DinG helicase from K. pneumoniae (state III)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8s37
Q-score: 0.371
Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P
Nat Commun (2024) 15 pp. 9306-9306 [ Pubmed: 39468082 DOI: doi:10.1038/s41467-024-53778-1 ]
- Zinc ion (65 Da, Ligand)
- Crispr type aferr-associated protein csf2 (38 kDa, Protein from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf3 (25 kDa, Protein from Klebsiella pneumoniae)
- Crrna (19 kDa, RNA from Klebsiella pneumoniae)
- Type iv-a3 crispr-cas effector complex with ding from klebsiella pneumoniae bound to crrna and target dna (Complex)
- Ts-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Dead/deah box helicase (70 kDa, Protein from Klebsiella pneumoniae)
- Crispr effector in complex with a ding helicase and crrna (Complex from Klebsiella pneumoniae)
- Nts-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf1 (29 kDa, Protein from Klebsiella pneumoniae)
- Double-stranded dna (Complex from Klebsiella pneumoniae)
Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Diphosphomethylphosphonic acid adenosyl ester (505 Da, Ligand)
- Cognate substrate bound in the entry site (es) of human mitochondrial transcription elongation complex (227 kDa, Complex from Homo sapiens)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Template strand dna (ts31mt) (10 kDa, DNA from synthetic construct)
- Non-template strand dna (nt27mt) (10 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 8u8v
Q-score: 0.405
Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Substrate atp bound to insertion site (is) of human mitochondrial transcription elongation complex (227 kDa, Complex from Homo sapiens)
- Diphosphomethylphosphonic acid adenosyl ester (505 Da, Ligand)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Template strand dna (ts31mt) (10 kDa, DNA from synthetic construct)
- Non-template strand dna (nt27mt) (10 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
Cryo-EM Structure of the TEFM-bound Human Mitochondrial Transcription Substrate Rejection Complex
Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Non-template strand dna (nt27mt_+1t) (10 kDa, DNA from synthetic construct)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Structure of the transcription elongation complex of human mitochondrial polymerase with the closed conformation of the fingers domain (227 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
- Template strand dna (ts31mt_+1a) (10 kDa, DNA from synthetic construct)
Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Non-cognate substrate bound in the entry site (es) of human mitochondrial transcription elongation complex (227 kDa, Complex from Homo sapiens)
- Non-template strand dna (nt27mt_+1t) (10 kDa, DNA from synthetic construct)
- Diphosphomethylphosphonic acid adenosyl ester (505 Da, Ligand)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
- Template strand dna (ts31mt_+1a) (10 kDa, DNA from synthetic construct)
Structure of CbCas9 bound to 20-nucleotide complementary DNA substrate
Resolution: 2.46 Å
EM Method: Single-particle
Fitted PDBs: 8iyq
Q-score: 0.513
Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JG
Nature (2024) 630 pp. 484-492 [ DOI: doi:10.1038/s41586-024-07486-x Pubmed: 38811729 ]
- Sgrna (40 kDa, RNA from Chryseobacterium)
- Structure of cbcas9 bound to 20-nucleotide complementary dna substrate (228 kDa, Complex from Chryseobacterium)
- Ts (8 kDa, DNA from Chryseobacterium)
- Deadcbcas9 (170 kDa, Protein from Chryseobacterium)
- Nts (8 kDa, DNA from Chryseobacterium)
Structure of CbCas9 bound to 6-nucleotide complementary DNA substrate
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8wmh
Q-score: 0.279
Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JG
Nature (2024) 630 pp. 484-492 [ DOI: doi:10.1038/s41586-024-07486-x Pubmed: 38811729 ]
- Ts (8 kDa, DNA from Chryseobacterium)
- Sgrna (40 kDa, RNA from Chryseobacterium)
- Deadcbcas9 (170 kDa, Protein from Chryseobacterium)
- Structure of cbcas9 bound to 6-nucleotide complementary dna substrate (228 kDa, Complex from Chryseobacterium)
- Nts (8 kDa, DNA from Chryseobacterium)
Structure of CbCas9-PcrIIC1 complex bound to 28-bp DNA substrate (20-nt complementary)
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8wmm
Q-score: 0.342
Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JG
Nature (2024) 630 pp. 484-492 [ DOI: doi:10.1038/s41586-024-07486-x Pubmed: 38811729 ]
- Pcriic1 (15 kDa, Protein from Chryseobacterium)
- Sgrna (40 kDa, RNA from Chryseobacterium)
- Ts (8 kDa, DNA from Chryseobacterium)
- Structure of cbcas9-pcriic1 complex bound to 28-bp dna substrate (20-nt complementary) (469 kDa, Complex from Chryseobacterium)
- Deadcbcas9 (170 kDa, Protein from Chryseobacterium)
- Nts (8 kDa, DNA from Chryseobacterium)
- Magnesium ion (24 Da, Ligand)