V-K CAST Transpososome from Scytonema hofmanni, major configuration
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8ea3
Q-score: 0.356
Park JU, Tsai AW, Rizo AN, Truong VH, Wellner TX, Schargel RD, Kellogg EH
Nature (2023) 613 pp. 775-782 [ Pubmed: 36442503 DOI: doi:10.1038/s41586-022-05573-5 ]
- Non-target_r (21 kDa, DNA from synthetic construct)
- Sg_rna (85 kDa, RNA from synthetic construct)
- Cas12k (73 kDa, Protein from Scytonema hofmannii)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- Tniq (19 kDa, Protein from Scytonema hofmannii)
- Re_r1 (15 kDa, DNA from synthetic construct)
- Re_f (23 kDa, DNA from synthetic construct)
- 12_tnsc shcast transpososome (Complex from Scytonema hofmannii)
- Target_le (43 kDa, DNA from synthetic construct)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Le_r (15 kDa, DNA from synthetic construct)
- Tnsb (66 kDa, Protein from Scytonema hofmannii)
- Tnsc (31 kDa, Protein from Scytonema hofmannii)
- Magnesium ion (24 Da, Ligand)
- Re_r2 (6 kDa, DNA from synthetic construct)
V-K CAST Transpososome from Scytonema hofmanni, minor configuration
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8ea4
Q-score: 0.302
Park JU, Tsai AW, Rizo AN, Truong VH, Wellner TX, Schargel RD, Kellogg EH
Nature (2023) 613 pp. 775-782 [ Pubmed: 36442503 DOI: doi:10.1038/s41586-022-05573-5 ]
- Non-target_r (21 kDa, DNA from synthetic construct)
- Cas12k (73 kDa, Protein from Scytonema hofmannii)
- Sg_rna (85 kDa, RNA from synthetic construct)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- Tniq (19 kDa, Protein from Scytonema hofmannii)
- Re_r1 (15 kDa, DNA from synthetic construct)
- Re_f (23 kDa, DNA from synthetic construct)
- Sh_cast transpososome (Complex from [Scytonema hofmanni] UTEX 2349)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Le_r (15 kDa, DNA from synthetic construct)
- Target-le (43 kDa, DNA from synthetic construct)
- Tnsb (66 kDa, Protein from Scytonema hofmannii)
- Tnsc (31 kDa, Protein from Scytonema hofmannii)
- Magnesium ion (24 Da, Ligand)
- Re_r2 (6 kDa, DNA from synthetic construct)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7svu
Q-score: 0.379
Park J, Tsai AWT, Rizo AN, Truong VH, Wellner TX, Schargel RD, Kellogg EH
Nature (2023) 613 pp. 775-782 [ Pubmed: 36442503 DOI: doi:10.1038/s41586-022-05573-5 ]
- Tnsb-ctd (1 kDa, Protein from [Scytonema hofmanni] UTEX 2349)
- Atp-bound tnsbctd-tnsc-tniq complex from shcast element (400 kDa, Complex from [Scytonema hofmanni] UTEX 2349)
- Dna (29-mer) (9 kDa, DNA from synthetic construct)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dna (28-mer) (8 kDa, DNA from synthetic construct)
- Tnsc (31 kDa, Protein from [Scytonema hofmanni] UTEX 2349)
- Tniq (19 kDa, Protein from [Scytonema hofmanni] UTEX 2349)
- Magnesium ion (24 Da, Ligand)
Skd3_ATPyS_FITC-casein Hexamer, AAA+ only
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 7ttr
Q-score: 0.451
Cupo RR, Rizo AN, Braun GA, Tse E, Chuang E, Gupta K, Southworth DR, Shorter J
Cell Rep (2022) 40 pp. 111408-111408 [ DOI: doi:10.1016/j.celrep.2022.111408 Pubmed: 36170828 ]
- Skd3 complex bound to fitc-casein (Complex)
- Beta-casein (24 kDa, Protein from Bos taurus)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Caseinolytic peptidase b protein homolog (66 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7tts
Q-score: 0.165
Cupo RR, Rizo AN, Braun GA, Tse E, Chuang E, Gupta K, Southworth DR, Shorter J
Cell Rep (2022) 40 pp. 111408-111408 [ DOI: doi:10.1016/j.celrep.2022.111408 Pubmed: 36170828 ]
- Skd3 bound to fitc-casein (Complex)
- Beta-casein (24 kDa, Protein from Bos taurus)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Caseinolytic peptidase b protein homolog (66 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8dv1
Q-score: 0.415
Remesh SG, Merz GE, Brilot AF, Chio US, Rizo AN, Pospiech Jr TH, Lui I, Laurie MT, Glasgow J, Le CQ, Zhang Y, Diwanji D, Hernandez E, Lopez J, Mehmood H, Pawar KI, Pourmal S, Smith AM, Zhou F, DeRisi J, Kortemme T, Rosenberg OS, Glasgow A, Leung KK, Wells JA, Verba KA
Structure (2023) 31 pp. 253- [ Pubmed: 36805129 DOI: doi:10.1016/j.str.2023.01.009 ]
- Angiotensin-converting enzyme 2,immunoglobulin gamma-1 heavy chain fusion,immunoglobulin gamma-1 heavy chain (110 kDa, Protein from Homo sapiens)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 wuhan-hu-1-spike bound to linker variant of affinity matured ace2 mimetic cvd432 (Complex)
- Angiotensin-converting enzyme 2,immunoglobulin gamma-1 heavy chain fusion (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to computationally engineered ACE2 mimetic CVD293
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8dv2
Q-score: 0.394
Remesh SG, Merz GE, Brilot AF, Chio US, Rizo AN, Pospiech Jr TH, Lui I, Laurie MT, Glasgow J, Le CQ, Zhang Y, Diwanji D, Hernandez E, Lopez J, Mehmood H, Pawar KI, Pourmal S, Smith AM, Zhou F, DeRisi J, Kortemme T, Rosenberg OS, Glasgow A, Leung KK, Wells JA, Verba KA
Structure (2023) 31 pp. 253- [ Pubmed: 36805129 DOI: doi:10.1016/j.str.2023.01.009 ]
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2,immunoglobulin gamma-1 heavy chain fusion (113 kDa, Protein from Homo sapiens)
- Angiotensin-converting enzyme 2,immunoglobulin gamma-1 heavy chain fusion (Complex)
- Sars-cov-2 wuhan-hu-1-spike bound to linker variant of affinity matured ace2 mimetic cvd293 (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (Complex from Homo sapiens)
SARS-CoV-2 Spike bound to Nb6 in closed conformation
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 7kkk
Q-score: 0.463
Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbolle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, Garcia-Sastre A, Ott M, Vignuzzi M, QCRG Structural Biology Consortium, Walter P, Manglik A
Science (2020) 370 pp. 1473-1479 [ Pubmed: 33154106 DOI: doi:10.1126/science.abe3255 ]
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Synthetic nanobody nb6 (Complex from synthetic construct)
- Spike s2p glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Complex of spike s2p glycoprotein with synthetic nanobody nb6 (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Synthetic nanobody nb6 (12 kDa, Protein from synthetic construct)
SARS-CoV-2 Spike bound to Nb6 in open conformation
Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbolle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, Garcia-Sastre A, Ott M, Vignuzzi M, QCRG Structural Biology Consortium, Walter P, Manglik A
Science (2020) 370 pp. 1473-1479 [ Pubmed: 33154106 DOI: doi:10.1126/science.abe3255 ]
SARS-CoV-2 Spike bound to Nb11 in closed conformation
Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbolle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, Garcia-Sastre A, Ott M, Vignuzzi M, QCRG Structural Biology Consortium, Walter P, Manglik A
Science (2020) 370 pp. 1473-1479 [ Pubmed: 33154106 DOI: doi:10.1126/science.abe3255 ]