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 Cortactin-bound to Arp2/3 complex
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8tah
Q-score: 0.514
Fregoso FE, Boczkowska M, Rebowski G, Carman PJ, van Eeuwen T, Dominguez R
Nat Commun (2023) 14 pp. 6894-6894 [ DOI: doi:10.1038/s41467-023-42229-y Pubmed: 37898612 ]
- Cortactin nta bound to arp2/3 complex (223 kDa, Complex from Bos taurus)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Actin-related protein 3 (47 kDa, Protein from Bos taurus)
- 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)
- Src substrate cortactin (8 kDa, Protein from Mus musculus)
- Actin-related protein 2/3 complex subunit 5 (16 kDa, Protein from Bos taurus)
- 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)
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)
Resolution: 3.73 Å
EM Method: Single-particle
Fitted PDBs: 8eax
Q-score: 0.339
Faylo JL, van Eeuwen T, Gupta K, Murakami K, Christianson DW
Biochemistry (2022) 61 pp. 2417-2430 [ Pubmed: 36227241 DOI: doi:10.1021/acs.biochem.2c00509 ]
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)
Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7k01
Q-score: 0.331
van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K
Nat Commun (2021) 12 pp. 3338-3338 [ DOI: doi:10.1038/s41467-021-23684-x Pubmed: 34099686 ]
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ternary complex of tfiih/rad4-rad23-rad33 with aaf damaged dna (420 MDa, Complex)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad3 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad25 (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening
Resolution: 9.25 Å
EM Method: Single-particle
Fitted PDBs: 7k04
Q-score: 0.122
van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K
Nat Commun (2021) 12 pp. 3338-3338 [ DOI: doi:10.1038/s41467-021-23684-x Pubmed: 34099686 ]
- Damaged dna strand (8 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna repair helicase rad3 (89 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Undamaged dna strand (8 kDa, DNA from synthetic construct)
- Dna repair helicase rad25 (95 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna polymerase ii transcription factor b subunit 5 (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Iron/sulfur cluster (351 Da, Ligand)
- Dna repair protein rad33 (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- 10 component complex of rad4-23, rad33 and tfiih on damaged dna (Complex)
- Dna repair protein rad4 (87 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Calcium ion (40 Da, Ligand)
- General transcription and dna repair factor iih subunit tfb1 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex
Resolution: 3.64 Å
EM Method: Single-particle
Fitted PDBs: 6xi8
Q-score: 0.185
van Eeuwen T, Li T, Kim HJ, Gorbea Colon JJ, Parker MI, Dunbrack RL, Garcia BA, Tsai KL, Murakami K
Sci Adv (2021) 7 [ Pubmed: 33827808 DOI: doi:10.1126/sciadv.abd4420 ]
- Rna polymerase ii transcription factor b subunit 3 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Serine/threonine-protein kinase kin28 (34 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ternary complex of kin28-ccl1-tfb3 from saccharomyces cerevisiae. (73 kDa, Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Aluminum fluoride (83 Da, Ligand)
- Cyclin ccl1 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7jth
Q-score: 0.369
Faylo JL, van Eeuwen T, Kim HJ, Gorbea Colon JJ, Garcia BA, Murakami K, Christianson DW
Nat Commun (2021) 12 pp. 3487-3487 [ DOI: doi:10.1038/s41467-021-23589-9 Pubmed: 34108468 ]
- Unliganded phomopsis amygdali fusicoccadiene synthase octamer (392 kDa, Complex from Phomopsis amygdali)
- Fusicoccadiene synthase (83 kDa, Protein from Phomopsis amygdali)