Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 8k18
Q-score: 0.153
To Be Published
- Zcp4c9 light chain (11 kDa, Protein from Homo sapiens)
- Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zcp4c9 heavy chain (13 kDa, Protein from Homo sapiens)
- Neutralization antibody zcp4c9 bound with sars-cov-2 omicron ba.5 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
Liu A, Liu Y, Chen G, Lyu W, Ye F, Wang J, Liao Q, Zhu L, Du Y, Ye RD
PLoS Biol (2024) 22 pp. e3002838-e3002838 [ DOI: doi:10.1371/journal.pbio.3002838 Pubmed: 39466725 ]
- Scfv16 (26 kDa, Protein from Mus musculus)
- Chemerin-like receptor 2 (34 kDa, Protein from Homo sapiens)
- Retinoic acid receptor responder protein 2 (1 kDa, Protein from Homo sapiens)
- Gpr1-c9-gi-scfv16 (Complex from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (6 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
Human spliceosomal PM5 C* complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8c6j
Q-score: 0.353
Dybkov O, Preussner M, El Ayoubi L, Feng VY, Harnisch C, Merz K, Leupold P, Yudichev P, Agafonov DE, Will CL, Girard C, Dienemann C, Urlaub H, Kastner B, Heyd F, Luehrmann R
Sci Adv (2023) 9 pp. eadf1785- [ Pubmed: 36867703 DOI: doi:10.1126/sciadv.adf1785 ]
- Peptidyl-prolyl cis-trans isomerase e (33 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
- Nitric oxide synthase-interacting protein (33 kDa, Protein from Homo sapiens)
- U5 snrna (36 kDa, RNA from Homo sapiens)
- Pre-mrna-splicing factor slu7 (68 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Splicing factor ess-2 homolog (52 kDa, Protein from Homo sapiens)
- Splicing factor c9orf78 (33 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-processing factor 17 (65 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase-like 3 (18 kDa, Protein from Homo sapiens)
- Probable atp-dependent rna helicase ddx41 (69 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
- Atp-dependent rna helicase dhx8 (139 kDa, Protein from Homo sapiens)
- Pre-mrna-processing factor 19 (55 kDa, Protein from Homo sapiens)
- Human spliceosomal c* complex assembled on pm5 pre-mrna (Complex from Homo sapiens)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
- Crooked neck-like protein 1 (83 kDa, Protein from Homo sapiens)
- Intron-binding protein aquarius (171 kDa, Protein from Homo sapiens)
- Pleiotropic regulator 1 (57 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor syf2 (28 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Homo sapiens)
- Serine/arginine repetitive matrix protein 2 (300 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from Homo sapiens)
- U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Splicing regulator sde2 (49 kDa, Protein from Homo sapiens)
- Snw domain-containing protein 1 (61 kDa, Protein from Homo sapiens)
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
- Pm5 5' exon (78 kDa, RNA from Homo sapiens)
- Nf-kappa-b-activating protein (47 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
- U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- U6 snrna (34 kDa, RNA from Homo sapiens)
- Rna-binding protein 8a (19 kDa, Protein from Homo sapiens)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor isy1 homolog (33 kDa, Protein from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- Protein fam50a (40 kDa, Protein from Homo sapiens)
- Sting er exit protein (25 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor spf27 (26 kDa, Protein from Homo sapiens)
- U2 snrna (60 kDa, RNA from Homo sapiens)
- Prkr-interacting protein 1 (21 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Eukaryotic initiation factor 4a-iii (46 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor cwc22 homolog (57 kDa, Protein from Homo sapiens)
- Pm5 intron (74 kDa, RNA from Homo sapiens)
- Splicing factor cactin (88 kDa, Protein from Homo sapiens)
- Protein fam32a (13 kDa, Protein from Homo sapiens)
- Protein mago nashi homolog (17 kDa, Protein from Homo sapiens)
cryo-EM structure of sea urchin sperm doublet microtubule (48-nm periodicity)
Leung MR, Zeng J, Wang X, Roelofs MC, Huang W, Zenezini Chiozzi R, Hevler JF, Heck AJR, Dutcher SK, Brown A, Zhang R, Zeev-Ben-Mordehai T
Cell (2023) 186 pp. 2880- [ Pubmed: 37327785 DOI: doi:10.1016/j.cell.2023.05.026 ]
- Tex33 (40 kDa, Protein from Strongylocentrotus purpuratus)
- Tex43 (14 kDa, Protein from Strongylocentrotus purpuratus)
- Coiled-coil domain-containing protein 105 (49 kDa, Protein from Strongylocentrotus purpuratus)
- Cfap90(c5orf49) (19 kDa, Protein from Strongylocentrotus purpuratus)
- Rib35 (34 kDa, Protein from Strongylocentrotus purpuratus)
- Spata45 (9 kDa, Protein from Strongylocentrotus purpuratus)
- Cilia- and flagella-associated protein 97 (27 kDa, Protein from Strongylocentrotus purpuratus)
- Protein phosphatase 1 regulatory subunit 32 (52 kDa, Protein from Strongylocentrotus purpuratus)
- Flagellar protofilament ribbon protein rib74 (74 kDa, Protein from Strongylocentrotus purpuratus)
- C4orf45 (32 kDa, Protein from Strongylocentrotus purpuratus)
- Tex49 (17 kDa, Protein from Strongylocentrotus purpuratus)
- Cilia- and flagella-associated protein 45 (64 kDa, Protein from Strongylocentrotus purpuratus)
- Nucleoside diphosphate kinase (42 kDa, Protein from Strongylocentrotus purpuratus)
- Spata48 (23 kDa, Protein from Strongylocentrotus purpuratus)
- Outer dense fiber protein 3 (27 kDa, Protein from Strongylocentrotus purpuratus)
- Helo_like_n(loc577943) (34 kDa, Protein from Strongylocentrotus purpuratus)
- Magnesium ion (24 Da, Ligand)
- Cilia- and flagella-associated protein 77 (27 kDa, Protein from Strongylocentrotus purpuratus)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Cfap276 (19 kDa, Protein from Strongylocentrotus purpuratus)
- Tubulin alpha chain (50 kDa, Protein from Strongylocentrotus purpuratus)
- Flagellar flij protein (14 kDa, Protein from Strongylocentrotus purpuratus)
- Cfap144(fam183a) (16 kDa, Protein from Strongylocentrotus purpuratus)
- Meiosis-specific nuclear structural protein 1 (61 kDa, Protein from Strongylocentrotus purpuratus)
- Meiosis-specific nuclear structural protein 1 (17 kDa, Protein from Strongylocentrotus purpuratus)
- Cilia- and flagella-associated protein 52 (70 kDa, Protein from Strongylocentrotus purpuratus)
- Cilia- and flagella-associated protein 126 (15 kDa, Protein from Strongylocentrotus purpuratus)
- Cfap68(upf0686, c11orf1) (17 kDa, Protein from Strongylocentrotus purpuratus)
- Rib43a-like with coiled-coils protein 2 (45 kDa, Protein from Strongylocentrotus purpuratus)
- Cfa20 domain-containing protein (22 kDa, Protein from Strongylocentrotus purpuratus)
- Outer dense fiber protein 3 (30 kDa, Protein from Strongylocentrotus purpuratus)
- Fam166c (23 kDa, Protein from Strongylocentrotus purpuratus)
- Tektin (49 kDa, Protein from Strongylocentrotus purpuratus)
- C20orf85 (23 kDa, Protein from Strongylocentrotus purpuratus)
- Tex36(cfap95, c9orf135) (25 kDa, Protein from Strongylocentrotus purpuratus)
- Tex26(loc100888047) (19 kDa, Protein from Strongylocentrotus purpuratus)
- Cfap96(c4orf47) (33 kDa, Protein from Strongylocentrotus purpuratus)
- Pacrg (26 kDa, Protein from Strongylocentrotus purpuratus)
- Tektin (46 kDa, Protein from Strongylocentrotus purpuratus)
- Cilia- and flagella-associated protein 161 (32 kDa, Protein from Strongylocentrotus purpuratus)
- Testicular haploid expressed gene protein-like (30 kDa, Protein from Strongylocentrotus purpuratus)
- Coiled-coil domain-containing protein 81 (79 kDa, Protein from Strongylocentrotus purpuratus)
- Atp6v1fnb (21 kDa, Protein from Strongylocentrotus purpuratus)
- Sea urchin sperm doublet microtubule (Cellular component from Strongylocentrotus purpuratus)
- Ef-hand domain-containing family member c2 (85 kDa, Protein from Strongylocentrotus purpuratus)
- Tex49_homologue(loc580808) (20 kDa, Protein from Strongylocentrotus purpuratus)
- Protein fam166b (48 kDa, Protein from Strongylocentrotus purpuratus)
- Pierce1 (13 kDa, Protein from Strongylocentrotus purpuratus)
- Cfap107 (27 kDa, Protein from Strongylocentrotus purpuratus)
- Trichohyalin-plectin-homology domain-containing protein (62 kDa, Protein from Strongylocentrotus purpuratus)
- Saxo3(loc115918676) (37 kDa, Protein from Strongylocentrotus purpuratus)
- Tepp protein (21 kDa, Protein from Strongylocentrotus purpuratus)
- Ef-hand domain-containing protein (66 kDa, Protein from Strongylocentrotus purpuratus)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Enkurin domain-containing protein (30 kDa, Protein from Strongylocentrotus purpuratus)
- Sperm-associated antigen 8 (23 kDa, Protein from Strongylocentrotus purpuratus)
- Tektin (53 kDa, Protein from Strongylocentrotus purpuratus)
- Trichohyalin-plectin-homology domain-containing protein (65 kDa, Protein from Strongylocentrotus purpuratus)
- Tubulin beta chain (50 kDa, Protein from Strongylocentrotus purpuratus)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8b0g
Q-score: 0.399
Couves EC, Gardner S, Voisin TB, Bickel JK, Stansfeld PJ, Tate EW, Bubeck D
Nat Commun (2023) 14 pp. 890-890 [ DOI: doi:10.1038/s41467-023-36441-z Pubmed: 36797260 ]
- Complement component c8 beta chain (67 kDa, Protein from Homo sapiens)
- Cd59 glycoprotein (9 kDa, Protein from Homo sapiens)
- Complement component c8 gamma chain (22 kDa, Protein from Homo sapiens)
- Complement component c6 (104 kDa, Protein from Homo sapiens)
- 2c9, cd59 inhibited mac complex (Complex from Homo sapiens)
- Complement component c7 (93 kDa, Protein from Homo sapiens)
- Complement c5 (188 kDa, Protein from Homo sapiens)
- Complement component c8 alpha chain (65 kDa, Protein from Homo sapiens)
- Complement component c9 (63 kDa, Protein from Homo sapiens)
2C9, C5b9-CD59 cryoEM structure
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8b0h
Q-score: 0.405
Couves EC, Gardner S, Voisin TB, Bickel JK, Stansfeld PJ, Tate EW, Bubeck D
Nat Commun (2023) 14 pp. 890-890 [ DOI: doi:10.1038/s41467-023-36441-z Pubmed: 36797260 ]
- Complement component c8 beta chain (67 kDa, Protein from Homo sapiens)
- Complement component c8 gamma chain (22 kDa, Protein from Homo sapiens)
- Complement component c6 (104 kDa, Protein from Homo sapiens)
- 2c9, cd59 inhibited mac complex (Complex)
- Complement component c7 (93 kDa, Protein from Homo sapiens)
- Cd59 glycoprotein (14 kDa, Protein from Homo sapiens)
- Complement component c8 alpha chain (65 kDa, Protein from Homo sapiens)
- Complement c5 (188 kDa, Protein from Homo sapiens)
- Cd59 glycoprotein (Complex from Homo sapiens)
- Complement component c9 (63 kDa, Protein from Homo sapiens)
- Complement components c5, c6, c7, c8 and c9 (Complex from Homo sapiens)
2C9, C5b9-CD59 cryoEM structure; focus refinement map
Couves EC, Gardner S, Voisin TB, Bickel JK, Stansfeld PJ, Tate EW, Bubeck D
Nat Commun (2023) 14 pp. 890-890 [ DOI: doi:10.1038/s41467-023-36441-z Pubmed: 36797260 ]
3C9, C5b9-CD59 cryoEM structure; focus refinement map
Couves EC, Gardner S, Voisin TB, Bickel JK, Stansfeld PJ, Tate EW, Bubeck D
Nat Commun (2023) 14 pp. 890-890 [ DOI: doi:10.1038/s41467-023-36441-z Pubmed: 36797260 ]
Oligomeric C9 in complex with aE11 Fab
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8de6
Q-score: 0.519
Bayly-Jones C, Ho BHT, Lau C, Leung EWW, D'Andrea L, Lupton CJ, Ekkel SM, Venugopal H, Whisstock JC, Mollnes TE, Spicer BA, Dunstone MA
Commun Biol (2023) 6 pp. 42-42 [ Pubmed: 36639734 DOI: doi:10.1038/s42003-023-04431-y ]
- Ae11 fab vh (15 kDa, Protein from Mus musculus)
- Ae11 fab vl (13 kDa, Protein from Mus musculus)
- Complement component c9 (63 kDa, Protein from Homo sapiens)
- Beta-d-mannopyranose (180 Da, Ligand)
- Quaternary complex of ae11 fab and polyc9 (2 MDa, Complex from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
PolyC9 in complex with aE11 Fab
Bayly-Jones C, Ho BHT, Lau C, Leung EWW, D'Andrea L, Lupton CJ, Ekkel SM, Venugopal H, Whisstock JC, Mollnes TE, Spicer BA, Dunstone MA
Commun Biol (2023) 6 pp. 42-42 [ Pubmed: 36639734 DOI: doi:10.1038/s42003-023-04431-y ]