Core particle assembly intermediate 1 purified from Saccharomyces cerevisiae
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 9d0t
Q-score: 0.541
Kaur M, Chen X, Lee SY, Weaver TM, Freudenthal BD, Walters KJ, Roelofs J
bioRxiv (2024) [ DOI: doi:10.1101/2024.11.04.621988 Pubmed: 39574619 ]
- Proteasome subunit alpha type-1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Proteasome subunit alpha type-3 (28 kDa, Protein from Saccharomyces cerevisiae)
- Proteasome subunit alpha type-4 (28 kDa, Protein from Saccharomyces cerevisiae)
- Proteasome subunit alpha type-2 (27 kDa, Protein from Saccharomyces cerevisiae)
- Proteasome subunit alpha type-6 (25 kDa, Protein from Saccharomyces cerevisiae)
- Proteasome maturation factor ump1,myosin light chain kinase 2, skeletal/cardiac muscle (22 kDa, Protein from Saccharomyces cerevisiae)
- Proteasome subunit alpha type-5 (28 kDa, Protein from Saccharomyces cerevisiae)
- Probable proteasome subunit alpha type-7 (31 kDa, Protein from Saccharomyces cerevisiae)
- Proteasome subunit beta type-2 (28 kDa, Protein from Saccharomyces cerevisiae)
- Proteasome subunit beta type-3 (22 kDa, Protein from Saccharomyces cerevisiae)
- Proteasome activator blm10 (246 kDa, Protein from Saccharomyces cerevisiae)
- Proteasome subunit beta type-4 (22 kDa, Protein from Saccharomyces cerevisiae)
- Proteasome assembly intermediate (534 kDa, Complex from Saccharomyces cerevisiae)
Focused map of Cryo-EM structure of Ubiquitin C-degron bound to KLHDC10-EloB/C
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9d8p
Q-score: 0.522
Scott DC, Chittori S, Purser N, King MT, Maiwald SA, Churion K, Nourse A, Lee C, Paulo JA, Miller DJ, Elledge SJ, Harper JW, Kleiger G, Schulman BA
Nat Commun (2024) 15 pp. 9899-9899 [ DOI: doi:10.1038/s41467-024-54126-z Pubmed: 39548056 ]
- Kelch domain-containing protein 10 (45 kDa, Protein from Homo sapiens)
- Ubiquitin-c (8 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
- Trapped arih1-diub-crl2-klhdc10 complex (Complex)
ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9dby
Q-score: 0.39
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9dde
Q-score: 0.456
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Ncprc1rybp bound to h2ak119ub/h1.4 chromatosome (Complex from Homo sapiens)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histones (Complex from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Histone h1.4 (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (Complex from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 9dg3
Q-score: 0.382
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ncprc1rybp delta-linker mutant bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
ncPRC1RYBP bound to unmodified nucleosome
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 9dgg
Q-score: 0.47
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ncprc1rybp bound to unmodified nucleosome (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
(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
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna mismatch repair protein (Complex from Homo sapiens)
- Dna mismatch repair protein msh2 (104 kDa, Protein from Homo sapiens)
- Dna_1 (20 kDa, DNA from Homo sapiens)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
- Mutsbeta-dna-adp complex (Complex)
- Double stranded dna (Complex from Homo sapiens)
- Dna_2 (18 kDa, DNA from Homo sapiens)
MutSbeta-ATPgS with straight MSH2 clamp
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8rz8
Q-score: 0.349
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
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna mismatch repair protein msh2 (104 kDa, Protein from Homo sapiens)
- Mutsbeta-atpgs complex (Complex from Homo sapiens)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
MutSbeta-ATPgS with kinked MSH2 clamp
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 8rz9
Q-score: 0.332
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
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Dna mismatch repair protein msh2 (104 kDa, Protein from Homo sapiens)
- Mutsbeta-atpgs complex (Complex from Homo sapiens)
- Dna mismatch repair protein msh3 (127 kDa, Protein from Homo sapiens)
Resolution: 5.27 Å
EM Method: Single-particle
Fitted PDBs: 9dyg
Q-score: 0.173
Sheng K, Dong X, Aiyer S, Lee J, Djordjevic-Marquardt S, Lyumkis D, Williamson JR
To Be Published
- 23s rrna (565 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- Isat-pna-ra20 50s ribosomal subunit assembly intermediate (Complex from Escherichia coli)
- Large ribosomal subunit protein bl17 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul23 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl19 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul14 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl34 (4 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul3 (21 kDa, Protein from Escherichia coli)