The structure of EfpA_BRD-8000.3 complex
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8ynz
Q-score: 0.406
Li D, Zhang X, Yao Y, Sun X, Sun J, Ma X, Yuan K, Bai G, Pang X, Hua R, Guo T, Mi Y, Wu L, Zhang J, Wu Y, Liu Y, Wang P, Wong CCL, Chen XW, Xiao H, Gao GF, Gao F
PNAS (2024) 121 pp. e2412653121-e2412653121 [ DOI: doi:10.1073/pnas.2412653121 Pubmed: 39441632 ]
- Efpa (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- (1s,3s)-n-[6-bromo-5-(pyrimidin-2-yl)pyridin-2-yl]-2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropane-1-carboxamide (401 Da, Ligand)
- Uncharacterized mfs-type transporter efpa (59 kDa, Protein from Mycobacterium tuberculosis H37Rv)
Structure of CRL2APPBP2 bound with RxxGP degron (dimer)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8jal
Q-score: 0.473
Zhao S, Olmayev-Yaakobov D, Ru W, Li S, Chen X, Zhang J, Yao X, Koren I, Zhang K, Xu C
PNAS (2023) 120 pp. e2308870120-e2308870120 [ DOI: doi:10.1073/pnas.2308870120 Pubmed: 37844242 ]
- Crl2appbp2 e3 liganse (400 MDa, Complex from Homo sapiens)
- Leu-thr-arg-asn-lys-gly-pro (1 kDa, Protein from Homo sapiens)
- Elongin-c (12 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Amyloid protein-binding protein 2 (66 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Structure of CRL2APPBP2 bound with RxxGP degron (tetramer)
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 8jaq
Q-score: 0.443
Zhao S, Olmayev-Yaakobov D, Ru W, Li S, Chen X, Zhang J, Yao X, Koren I, Zhang K, Xu C
PNAS (2023) 120 pp. e2308870120-e2308870120 [ DOI: doi:10.1073/pnas.2308870120 Pubmed: 37844242 ]
- Crl2appbp2 e3 liganse (400 MDa, Complex from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1, n-terminally processed (12 kDa, Protein from Homo sapiens)
- Elongin-c (10 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Xp_211896 c-degron (1 kDa, Protein from Homo sapiens)
- Amyloid protein-binding protein 2 (66 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Structure of CRL2APPBP2 bound with RxxGPAA degron (dimer)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8jar
Q-score: 0.468
Zhao S, Olmayev-Yaakobov D, Ru W, Li S, Chen X, Zhang J, Yao X, Koren I, Zhang K, Xu C
PNAS (2023) 120 pp. e2308870120-e2308870120 [ DOI: doi:10.1073/pnas.2308870120 Pubmed: 37844242 ]
- Crl2appbp2 e3 liganse (400 MDa, Complex from Homo sapiens)
- Xp_211896+aa c-degron (1 kDa, Protein from Homo sapiens)
- Elongin-c (10 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Amyloid protein-binding protein 2 (66 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Structure of CRL2APPBP2 bound with RxxGPAA degron (tetramer)
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 8jas
Q-score: 0.366
Zhao S, Olmayev-Yaakobov D, Ru W, Li S, Chen X, Zhang J, Yao X, Koren I, Zhang K, Xu C
PNAS (2023) 120 pp. e2308870120-e2308870120 [ DOI: doi:10.1073/pnas.2308870120 Pubmed: 37844242 ]
- Crl2appbp2 e3 liganse (400 MDa, Complex from Homo sapiens)
- Sumo-xp_211896+aa c-degron (1 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1, n-terminally processed (12 kDa, Protein from Homo sapiens)
- Elongin-c (10 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Amyloid protein-binding protein 2 (66 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (dimer)
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 8jau
Q-score: 0.478
Zhao S, Olmayev-Yaakobov D, Ru W, Li S, Chen X, Zhang J, Yao X, Koren I, Zhang K, Xu C
PNAS (2023) 120 pp. e2308870120-e2308870120 [ DOI: doi:10.1073/pnas.2308870120 Pubmed: 37844242 ]
- Crl2appbp2 e3 liganse (400 MDa, Complex from Homo sapiens)
- Mrpl28 c-degron (1 kDa, Protein from Homo sapiens)
- Elongin-c (10 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Amyloid protein-binding protein 2 (66 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (tetramer)
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8jav
Q-score: 0.421
Zhao S, Olmayev-Yaakobov D, Ru W, Li S, Chen X, Zhang J, Yao X, Koren I, Zhang K, Xu C
PNAS (2023) 120 pp. e2308870120-e2308870120 [ DOI: doi:10.1073/pnas.2308870120 Pubmed: 37844242 ]
- Crl2appbp2 e3 liganse (400 MDa, Complex from Homo sapiens)
- Mrpl28 c-degron (1 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1, n-terminally processed (12 kDa, Protein from Homo sapiens)
- Elongin-c (10 kDa, Protein from Homo sapiens)
- Cullin-2 (87 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Amyloid protein-binding protein 2 (66 kDa, Protein from Homo sapiens)
- Elongin-b (13 kDa, Protein from Homo sapiens)
Structure of the translating Neurospora crassa ribosome arrested by cycloheximide
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7r81
Q-score: 0.539
Shen L, Su Z, Yang K, Wu C, Becker T, Bell-Pedersen D, Zhang J, Sachs MS
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2111862118 Pubmed: 34815343 ]
- 40s ribosomal protein s25 (10 kDa, Protein from Neurospora crassa)
- Cytoplasmic ribosomal protein 10 (28 kDa, Protein from Neurospora crassa)
- Ribosomal protein l19 (22 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l25 (17 kDa, Protein from Neurospora crassa)
- Ubiquitin-40s ribosomal protein s27a (17 kDa, Protein from Neurospora crassa)
- 18s rrna (578 kDa, RNA from Neurospora crassa)
- 40s ribosomal subunit (Complex from Neurospora crassa)
- Hypothetical protein ncu16635 (el41) (3 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s27 (8 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l16 (26 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l20 (20 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s24 (15 kDa, Protein from Neurospora crassa)
- Ribosomal protein l26 (15 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s17 (16 kDa, Protein from Neurospora crassa)
- Structure of the translating neurospora crassa ribosome arrested by cycloheximide (Complex)
- Mrna (5 kDa, RNA from Neurospora crassa)
- 40s ribosomal protein s26e (13 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l22 (14 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s7 (22 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s30 (6 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l33 (12 kDa, Protein from Neurospora crassa)
- 5s rrna (38 kDa, RNA from Neurospora crassa)
- Trna (Complex from Neurospora crassa)
- 60s ribosomal protein l43 (10 kDa, Protein from Neurospora crassa)
- Guanine nucleotide-binding protein subunit beta-like protein (35 kDa, Protein from Neurospora crassa)
- Nascent peptide (Complex from Neurospora crassa)
- Ribosomal protein l37 (10 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s18 (17 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s1 (29 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l28 (16 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l4-a (38 kDa, Protein from Neurospora crassa)
- Ribosomal_l28e domain-containing protein (16 kDa, Protein from Neurospora crassa)
- Spermidine (145 Da, Ligand)
- 60s ribosomal protein l24 (17 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l36 (11 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l10 (25 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l8 (29 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s19 (16 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l7 (28 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s28 (7 kDa, Protein from Neurospora crassa)
- Ribosomal protein srp1 (18 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l17 (20 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s22 (14 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s5 (23 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s16 (15 kDa, Protein from Neurospora crassa)
- Nascent peptide (358 Da, Protein from Neurospora crassa)
- 60s ribosomal protein l32 (15 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l39 (6 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s8 (23 kDa, Protein from Neurospora crassa)
- Ribosomal protein l14 (15 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s0 (31 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l15 (24 kDa, Protein from Neurospora crassa)
- Ribosomal protein s12 (17 kDa, Protein from Neurospora crassa)
- Trna (24 kDa, RNA from Neurospora crassa)
- 60s ribosomal subunit (Complex from Neurospora crassa)
- 60s ribosomal protein l40 (6 kDa, Protein from Neurospora crassa)
- 4-{(2r)-2-[(1s,3s,5s)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione (281 Da, Ligand)
- Probable 40s ribosomal protein s10-b (18 kDa, Protein from Neurospora crassa)
- 26s rrna (1 MDa, RNA from Neurospora crassa)
- 60s ribosomal protein l27 (el27) (15 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s21 (9 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l2 (27 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l3 (44 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s11 (18 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l23 (14 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s2 (28 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l13 (23 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s13 (16 kDa, Protein from Neurospora crassa)
- Mrna (Complex from Neurospora crassa)
- 40s ribosomal protein s14 (us11) (16 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s9 (21 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l9 (21 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l18 (20 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s29 (6 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l35 (14 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s4 (29 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s12 (16 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l38 (9 kDa, Protein from Neurospora crassa)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l30 (11 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s6 (27 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l5 (34 kDa, Protein from Neurospora crassa)
- 5.8s rrna (50 kDa, RNA from Neurospora crassa)
- 60s ribosomal protein l11 (20 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l34 (13 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l6 (22 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l29 (7 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein l44 (11 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s23 (15 kDa, Protein from Neurospora crassa)
- 40s ribosomal protein s20 (13 kDa, Protein from Neurospora crassa)
- 60s ribosomal protein (14 kDa, Protein from Neurospora crassa)
Cryo-EM structure of amyloid fibril formed by human RIPK3
Resolution: 4.24 Å
EM Method: Helical reconstruction
Fitted PDBs: 7da4
Q-score: 0.353
