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Structure of human mitochondrial RNase P in complex with mitochondrial pre-tRNA-His(5,Ser)
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8cbk
Q-score: 0.452
Meynier V, Hardwick SW, Catala M, Roske JJ, Oerum S, Chirgadze DY, Barraud P, Yue WW, Luisi BF, Tisne C
Nat Commun (2024) 15 pp. 4683-4683 [ Pubmed: 38824131 DOI: doi:10.1038/s41467-024-49132-0 ]
- 3-hydroxyacyl-coa dehydrogenase type-2 (26 kDa, Protein from Homo sapiens)
- Human mitochondrial rnase p in complex with mitochondrial pre-trnahis-ser (269 kDa, Complex from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Mitochondrial ribonuclease p catalytic subunit (61 kDa, Protein from Homo sapiens)
- Trna methyltransferase 10 homolog c (48 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Mitochondrial precursor trna-his(5,ser) (29 kDa, RNA from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Holvec S, Barchet C, Lechner A, Frechin L, Hazemann I, Wolff P, von Loeffelholz O, De Silva N, Klaholz BP
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01274-x ]
- 60s ribosomal protein l28 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l26 (17 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 28s rrna (3773-mer) (1 MDa, RNA from Homo sapiens)
- 60s ribosomal protein l30 (12 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- Ubiquitin-like fubi-ribosomal protein es30 fusion protein (14 kDa, Protein from Homo sapiens)
- 5s rrna (120-mer) (38 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l19 (23 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l24 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l8 (28 kDa, Protein from Homo sapiens)
- Human 80s ribosome (4 MDa, Complex from Homo sapiens)
- 60s ribosomal protein l13a (23 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul18 (34 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l15 (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l32 (15 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l14 (23 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul4 (41 kDa, Protein from Homo sapiens)
- 18s rrna (1740-mer) (603 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l10-like (24 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l27 (15 kDa, Protein from Homo sapiens)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l18 (21 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37a (10 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l23a (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35a (12 kDa, Protein from Homo sapiens)
- Ubiquitin-60s ribosomal protein l40 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l31 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l29 (17 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l17 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l37 (11 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul3 (46 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l22 (14 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul30 (29 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein es19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36a (12 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l38 (8 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l36 (12 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul15 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l7a (30 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l35 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l9 (21 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 60s ribosomal protein l13 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l39 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l34 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l18a (20 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l21 (18 kDa, Protein from Homo sapiens)
- 5.8s rrna (156-mer) (50 kDa, RNA from Homo sapiens)
Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8u5h
Q-score: 0.443
To Be Published
- Nucleosome dna (55 kDa, DNA from Homo sapiens)
- Histone h3.3c (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dnmt3a n-terminal domain and h2ak119ub nucleosome complex (Complex from Homo sapiens)
- Nucleosome dna (55 kDa, DNA from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3a (11 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
Cryo-EM structure of the SPARTA oligomer with guide RNA and target DNA
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8u72
Q-score: 0.533
Kottur J, Malik R, Aggarwal AK
Nat Commun (2024) [ ]
- Dna (5'-d(p*tp*ap*tp*ap*cp*ap*ap*cp*cp*tp*ap*cp*tp*ap*cp*cp*tp*c)-3') (13 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Piwi domain-containing protein (58 kDa, Protein from Thermoflavifilum thermophilum)
- Sparta complex with grna/tdna (Complex from Thermoflavifilum thermophilum)
- Tir domain-containing protein (53 kDa, Protein from Thermoflavifilum thermophilum)
- Rna (5'-r(p*up*gp*ap*gp*gp*up*ap*gp*up*ap*gp*gp*up*up*gp*up*ap*up*a)-3') (6 kDa, RNA from synthetic construct)
SpCas9-MMLV RT-pegRNA-target DNA complex (termination)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8wus
Q-score: 0.454
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Rna (115-mer) (37 kDa, RNA from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Dna (40-mer) (12 kDa, DNA from Streptococcus pyogenes)
SpCas9-MMLV RT-pegRNA-target DNA complex (initiation)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8wut
Q-score: 0.364
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Rna (115-mer) (37 kDa, RNA from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Dna/rna (35-mer) (10 kDa, Macromolecule from Streptococcus pyogenes)
SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 16-nt)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8wuv
Q-score: 0.354
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Rna (137-mer) (44 kDa, RNA from Streptococcus pyogenes)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Dna (50-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
Structure of the Mumps Virus L Protein (state2) Bound by Phosphoprotein Tetramer (composite map)
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8x01
Q-score: 0.495
Li T, Liu M, Gu Z, Su X, Liu Y, Lin J, Zhang Y, Shen QT
Nat Commun (2024) 15 pp. 4189-4189 [ Pubmed: 38760379 DOI: doi:10.1038/s41467-024-48389-9 ]
- Zinc ion (65 Da, Ligand)
- Phosphoprotein (41 kDa, Protein from Mumps orthorubulavirus)
- The muv polymerase complex of rna-directed rna polymerase l with tetrameric phosphoproteins (Complex from Mumps orthorubulavirus)
- Rna-directed rna polymerase l (256 kDa, Protein from Mumps orthorubulavirus)
SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 28-nt)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8ygj
Q-score: 0.354
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Rna (137-mer) (44 kDa, RNA from Streptococcus pyogenes)
- Dna (62-mer) (19 kDa, DNA from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Dna (5'-d(p*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
HSV-1 DNA polymerase-processivity factor complex in exonuclease state with 1-bp DNA mismatch
Resolution: 2.12 Å
EM Method: Single-particle
Fitted PDBs: 9enp
Q-score: 0.588
Gustavsson E, Grunewald K, Elias P, Hallberg BM
Nucleic Acids Res (2024) [ Pubmed: 38806233 DOI: doi:10.1093/nar/gkae374 ]
- Dna (46-mer) (13 kDa, DNA from synthetic construct)
- Dna (67-mer) (20 kDa, DNA from synthetic construct)
- Calcium ion (40 Da, Ligand)
- Dna polymerase processivity factor (51 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Dna (Complex from synthetic construct)
- Hsv-1 dna polymerase-processivity factor complex in exonuclease state with 1-bp dna mismatch (Complex)
- Dna polymerase-processivity factor (Complex from Human alphaherpesvirus 1 strain KOS)
- Dna polymerase catalytic subunit (136 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Water (18 Da, Ligand)