Structure of a class A GPCR/Fab complex
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8tlm
Q-score: 0.527
Sun D, Sun Y, Janezic E, Zhou T, Johnson M, Azumaya C, Noreng S, Chiu C, Seki A, Arenzana TL, Nicoludis JM, Shi Y, Wang B, Ho H, Joshi P, Tam C, Payandeh J, Comps-Agrar L, Wang J, Rutz S, Koerber JT, Masureel M
Nat Commun (2023) 14 pp. 7940-7940 [ DOI: doi:10.1038/s41467-023-43601-8 Pubmed: 38040762 ]
- Fab heavy chain (23 kDa, Protein from Oryctolagus cuniculus)
- C-c chemokine receptor type 8, green fluorescent protein fusion (76 kDa, Protein from Aequorea victoria)
- Ccr8_fab complex (Complex from Homo sapiens)
- Fab light chain (23 kDa, Protein from Oryctolagus cuniculus)
Structure of a class A GPCR/agonist complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8u1u
Q-score: 0.515
Sun D, Sun Y, Janezic E, Zhou T, Johnson M, Azumaya C, Noreng S, Chiu C, Seki A, Arenzana TL, Nicoludis JM, Shi Y, Wang B, Ho H, Joshi P, Tam C, Payandeh J, Comps-Agrar L, Wang J, Rutz S, Koerber JT, Masureel M
Nat Commun (2023) 14 pp. 7940-7940 [ DOI: doi:10.1038/s41467-023-43601-8 Pubmed: 38040762 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (43 kDa, Protein from Homo sapiens)
- Ccr8 in complex with ccl1 and gi (Complex from Homo sapiens)
- C-c motif chemokine 1,c-c chemokine receptor type 8,egfp fusion protein (83 kDa, Protein from Human adenovirus C serotype 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Scfv fragment (28 kDa, Protein from Mus musculus)
Local refined cryo-EM reconstruction of Omicron BA.5 RBD in complex with 8-9D Fab
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8j1t
Q-score: 0.455
Tai W, Yang K, Liu Y, Li R, Feng S, Chai B, Zhuang X, Qi S, Shi H, Liu Z, Lei J, Ma E, Wang W, Tian C, Le T, Wang J, Chen Y, Tian M, Xiang Y, Yu G, Cheng G
Nat Commun (2023) 14 pp. 8042-8042 [ DOI: doi:10.1038/s41467-023-43798-8 Pubmed: 38052844 ]
- Severe acute respiratory syndrome coronavirus 2 omicron ba.5 rbd bound 8-9d fab (22 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov2 omicron ba.5 rbd (Complex)
- 8-9d heavy chain (12 kDa, Protein from Homo sapiens)
- 8-9d light chain (11 kDa, Protein from Homo sapiens)
- 8-9d fab (Complex from Homo sapiens)
- Spike protein (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM reconstruction of SARS-CoV2 Omicron BA.5 spike in complex with 8-9D Fabs
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8j1v
Q-score: 0.374
Tai W, Yang K, Liu Y, Li R, Feng S, Chai B, Zhuang X, Qi S, Shi H, Liu Z, Lei J, Ma E, Wang W, Tian C, Le T, Wang J, Chen Y, Tian M, Xiang Y, Yu G, Cheng G
Nat Commun (2023) 14 pp. 8042-8042 [ DOI: doi:10.1038/s41467-023-43798-8 Pubmed: 38052844 ]
- Sars-cov2 omicron ba.5 spike ectodomain (Complex)
- 8-9d heavy chain (12 kDa, Protein from Homo sapiens)
- Severe acute respiratory syndrome coronavirus 2 omicron ba.5 spike bound 8-9d fab (369 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 8-9d light chain (11 kDa, Protein from Homo sapiens)
- Spike protein s2' (123 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 8-9d fab variable region (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of EDS1 and SAG101 with ATP-APDR
Resolution: 2.71 Å
EM Method: Single-particle
Fitted PDBs: 7xjp
Q-score: 0.488
Jia A, Huang S, Song W, Wang J, Meng Y, Sun Y, Xu L, Laessle H, Jirschitzka J, Hou J, Zhang T, Yu W, Hessler G, Li E, Ma S, Yu D, Gebauer J, Baumann U, Liu X, Han Z, Chang J, Parker JE, Chai J
Science (2022) 377 pp. eabq8180-eabq8180 [ DOI: doi:10.1126/science.abq8180 Pubmed: 35857644 ]
- Protein eds1 (71 kDa, Protein from Arabidopsis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Isopropyl alcohol (60 Da, Ligand)
- Adenosine-5-diphosphoribose (559 Da, Ligand)
- Binary complex of eds1 and sag101 with molecule atp-adpr (Complex from Arabidopsis)
- Senescence-associated carboxylesterase 101 (62 kDa, Protein from Arabidopsis)
PlmCasX-sgRNAv1-dsDNA ternary complex at nts loading state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7way
Q-score: 0.522
Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brotzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG
Mol Cell (2022) 82 pp. 1199-1209.e6 [ Pubmed: 35219382 DOI: doi:10.1016/j.molcel.2022.02.002 ]
- Dna (33-mer) (12 kDa, DNA from Planctomycetes bacterium)
- Dplmcasx (112 kDa, Protein from Planctomycetes bacterium)
- Rna (39 kDa, RNA from Planctomycetes bacterium)
- Sgrnav1 (Complex from Planctomycetes)
- Dna (27-mer) (12 kDa, DNA from Planctomycetes bacterium)
- Plmcasx (Complex)
- Dsdna (Complex from Planctomycetes)
- Plmcasx-sgrnav1-dsdna ternary complex at nts loading state (Complex from Planctomycetes)
PlmCasX-sgRNAv1-dsDNA ternary complex at ts loading state
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7waz
Q-score: 0.246
Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brotzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG
Mol Cell (2022) 82 pp. 1199-1209.e6 [ Pubmed: 35219382 DOI: doi:10.1016/j.molcel.2022.02.002 ]
- Dplmcasx (112 kDa, Protein from Planctomycetes bacterium)
- Rna (115-mer) (39 kDa, RNA from Planctomycetes bacterium)
- Dna (Complex from Planctomycetes bacterium)
- Nts-dna (12 kDa, DNA from Planctomycetes bacterium)
- Plmcasx (Complex from Planctomycetes bacterium)
- Ts-dna (12 kDa, DNA from Planctomycetes bacterium)
- Plmcasx-sgrnav1-dsdna ternary complex at nts loading state (Complex from Planctomycetes bacterium)
- Rna (Complex)
PlmCasX-sgRNAv1-dsDNA ternary complex at nts loading state with flexible H2 domain
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7wb0
Q-score: 0.374
Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brotzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG
Mol Cell (2022) 82 pp. 1199-1209.e6 [ Pubmed: 35219382 DOI: doi:10.1016/j.molcel.2022.02.002 ]
- Dplmcasx (112 kDa, Protein from Planctomycetes bacterium)
- Rna (115-mer) (39 kDa, RNA from Planctomycetes bacterium)
- Rna (Complex from Planctomycetes bacterium)
- Plmcasx (Complex)
- Dna (Complex from Planctomycetes bacterium)
- Nts-dna (12 kDa, DNA from Planctomycetes bacterium)
- Ts-dna (12 kDa, DNA from Planctomycetes bacterium)
- Plmcasx-sgrnav1-dsdna ternary complex at nts loading state (Complex from Planctomycetes bacterium)
PlmCasX-sgRNAv2-dsDNA ternary complex at nts loading state
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7wb1
Q-score: 0.369
Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brotzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG
Mol Cell (2022) 82 pp. 1199-1209.e6 [ Pubmed: 35219382 DOI: doi:10.1016/j.molcel.2022.02.002 ]
- Dplmcasx (112 kDa, Protein from Planctomycetes bacterium)
- Plmcasx-sgrnav2-dsdna ternary complex at nts loading state (Complex from Planctomycetes)
- Sgrnav2 (Complex from Planctomycetes)
- Rna (121-mer) (38 kDa, RNA from Planctomycetes bacterium)
- Plmcasx (Complex)
- Dsdna (Complex from Planctomycetes)
- Nts-dna (12 kDa, DNA from Planctomycetes bacterium)
- Ts-dna (12 kDa, DNA from Planctomycetes bacterium)
Double nuclear outer ring from the isolated yeast NPC
Resolution: 11.6 Å
EM Method: Single-particle
Fitted PDBs: 7n84
Q-score: 0.063
Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP
Cell (2022) 185 pp. 361-378.e25 [ Pubmed: 34982960 DOI: doi:10.1016/j.cell.2021.12.015 ]
- Unknown (5 kDa, Protein from Saccharomyces cerevisiae)
- Yeast double outer ring (10 MDa, Complex from Saccharomyces cerevisiae)
- Nucleoporin nup133 (133 kDa, Protein from Saccharomyces cerevisiae)
- Protein transport protein sec13 (33 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin 145c (81 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin seh1 (39 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nup84 (83 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nup188 (188 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nup120 (120 kDa, Protein from Saccharomyces cerevisiae)
- Nucleoporin nup85 (84 kDa, Protein from Saccharomyces cerevisiae)