Single particle reconstruction of the human LINE-1 ORF2p without substrate (apo)
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS
Nature (2024) 626 pp. 194-206 [ DOI: doi:10.1038/s41586-023-06947-z Pubmed: 38096902 ]
Structure of LINE-1 ORF2p with template:primer hybrid
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8sxt
Q-score: 0.339
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS
Nature (2024) 626 pp. 194-206 [ DOI: doi:10.1038/s41586-023-06947-z Pubmed: 38096902 ]
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Long interspersed nuclear element (line)-1 orf2 protein (Complex from Homo sapiens)
- Dna primer (3 kDa, DNA from synthetic construct)
- Rna template (5 kDa, RNA from synthetic construct)
- Line-1 retrotransposable element orf2 protein (149 kDa, Protein from Homo sapiens)
Structure of LINE-1 ORF2p with an oligo(A) template
Resolution: 3.66 Å
EM Method: Single-particle
Fitted PDBs: 8sxu
Q-score: 0.185
Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS
Nature (2024) 626 pp. 194-206 [ DOI: doi:10.1038/s41586-023-06947-z Pubmed: 38096902 ]
- Long interspersed nuclear element (line)-1 orf2 protein (Complex from Homo sapiens)
- Rna (25-mer) (8 kDa, RNA from synthetic construct)
- Line-1 retrotransposable element orf2 protein (149 kDa, Protein from Homo sapiens)
Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7t5q
Q-score: 0.385
van Eeuwen T, Boczkowska M, Rebowski G, Carman PJ, Fregoso FE, Dominguez R
PNAS (2023) 120 pp. e2306165120-e2306165120 [ DOI: doi:10.1073/pnas.2306165120 Pubmed: 37549294 ]
- Magnesium ion (24 Da, Ligand)
- Actin skeletal muscle (Complex from Oryctolagus cuniculus)
- F-actin-capping protein subunit beta/actin nucleation-promoting factor wasl chimera (37 kDa, Protein from Mus musculus)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- F-actin-capping protein subunit alpha-1/actin nucleation-promoting factor wasl chimera (39 kDa, Protein from Mus musculus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Actin-related protein 3 (47 kDa, Protein from Bos taurus)
- Bovine arp2/3 complex and actin, capz (248 kDa, Complex)
- Actin-related protein 2/3 complex subunit 3 (20 kDa, Protein from Bos taurus)
- Actin-related protein 2/3 complex subunit 4 (19 kDa, Protein from Bos taurus)
- Bovine arp2/3 (Complex from Bos taurus)
- Actin-related protein 2/3 complex subunit 5 (16 kDa, Protein from Bos taurus)
- Actin, alpha skeletal muscle (41 kDa, Protein from Oryctolagus cuniculus)
- Actin-related protein 2/3 complex subunit 2 (34 kDa, Protein from Bos taurus)
- Actin-related protein 2 (44 kDa, Protein from Bos taurus)
- Actin-related protein 2/3 complex subunit 1a (41 kDa, Protein from Bos taurus)
- F-actin-capping protein (Complex from Homo sapiens)
Cryo-EM structure of Arpin-bound Arp2/3 complex
Resolution: 3.24 Å
EM Method: Single-particle
Fitted PDBs: 7jpn
Q-score: 0.433
Fregoso FE, van Eeuwen T, Simanov G, Rebowski G, Boczkowska M, Zimmet A, Gautreau AM, Dominguez R
Nat Commun (2022) 13 pp. 628-628 [ Pubmed: 35110533 DOI: doi:10.1038/s41467-022-28112-2 ]
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Arpin (Complex from Homo sapiens)
- Arpin (3 kDa, Protein from Homo sapiens)
- Actin-related protein 3 (46 kDa, Protein from Bos taurus)
- Bovine arp2/3 complex with arpin (248 kDa, Complex)
- Actin-related protein 2/3 complex subunit 3 (20 kDa, Protein from Bos taurus)
- Actin-related protein 2/3 complex subunit 4 (19 kDa, Protein from Bos taurus)
- Actin-related protein 2/3 complex subunit 5 (15 kDa, Protein from Bos taurus)
- Bovine arp2/3 (Complex from Bos taurus)
- Actin-related protein 2/3 complex subunit 1b (41 kDa, Protein from Bos taurus)
- Actin-related protein 2/3 complex subunit 2 (34 kDa, Protein from Bos taurus)
- Actin-related protein 2 (42 kDa, Protein from Bos taurus)
CryoEM structure of human Arp2/3 complex with bound NPFs
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6uhc
Q-score: 0.353
Zimmet A, Van Eeuwen T, Boczkowska M, Rebowski G, Murakami K, Dominguez R
Sci Adv (2020) 6 pp. eaaz7651-eaaz7651 [ DOI: doi:10.1126/sciadv.aaz7651 Pubmed: 32548263 ]
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Actin-related protein 2/3 complex subunit 2 (34 kDa, Protein from Homo sapiens)
- Actin-related protein 2/3 complex subunit 1b (41 kDa, Protein from Homo sapiens)
- Neural wiskott-aldrich syndrome protein (54 kDa, Protein from Mus musculus)
- Actin-related protein 2/3 complex subunit 5 (16 kDa, Protein from Homo sapiens)
- Actin-related protein 2/3 complex subunit 3 (23 kDa, Protein from Homo sapiens)
- Actin-related protein 3 (47 kDa, Protein from Homo sapiens)
- Cryo-em structure of human arp2/3 complex with bound npfs (243 MDa, Complex from Spodoptera aff. frugiperda 1 BOLD-2017)
- Actin-related protein 2/3 complex subunit 4 (19 kDa, Protein from Homo sapiens)
- Actin-related protein 2 (44 kDa, Protein from Homo sapiens)
CENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6muo
Q-score: 0.369
Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M, Braitbard M, Xu C, Kalisman N, Murakami K, Black BE
Curr Biol (2019) 29 pp. 2625-2639.e5 [ Pubmed: 31353180 DOI: doi:10.1016/j.cub.2019.06.062 ]
- Cenp-a chromatin complex bound with cenp-c and cenp-n of ccan kinetochore components (276 kDa, Cellular component from Homo sapiens)
- Histone h2b type 2-f (10 kDa, Protein from Homo sapiens)
- Histone h4 (10 kDa, Protein from Homo sapiens)
- Dna/rna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3-like centromeric protein a (11 kDa, Protein from Homo sapiens)
- Centromere protein c (2 kDa, Protein from Homo sapiens)
- Centromere protein n (25 kDa, Protein from Homo sapiens)
- Dna/rna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2a type 1-c (11 kDa, Protein from Homo sapiens)
CENP-A nucleosome bound by two copies of CENP-C(CD) and two copies CENP-N(NT)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6mup
Q-score: 0.401
Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M, Braitbard M, Xu C, Kalisman N, Murakami K, Black BE
Curr Biol (2019) 29 pp. 2625-2639.e5 [ Pubmed: 31353180 DOI: doi:10.1016/j.cub.2019.06.062 ]
- Cenp-a chromatin complex bound with cenp-c and cenp-n of ccan kinetochore components (276 kDa, Cellular component from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2b type 2-f (10 kDa, Protein from Homo sapiens)
- Histone h4 (10 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3-like centromeric protein a (11 kDa, Protein from Homo sapiens)
- Centromere protein c (2 kDa, Protein from Homo sapiens)
- Centromere protein n (25 kDa, Protein from Homo sapiens)
- Histone h2a type 1-c (11 kDa, Protein from Homo sapiens)
CENP-A nucleosome bound by two copies of CENP-C(CD) and two copies CENP-N(NT) with local refinement
Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M, Braitbard M, Xu C, Kalisman N, Murakami K, Black BE
Curr Biol (2019) 29 pp. 2625-2639.e5 [ Pubmed: 31353180 DOI: doi:10.1016/j.cub.2019.06.062 ]
- Chromatin complex (276 kDa, Cellular component from Homo sapiens)