Cryo-EM structure of neutralizing antibody 8G3 in complex with BA.1 RBD
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 9js4
Q-score: 0.434
Liao Y, Ma H, Wang Z, Wang S, He Y, Chang Y, Zong H, Tang H, Wang L, Ke Y, Cai H, Li P, Tang J, Chen H, Drelich A, Peng BH, Hsu J, Tat V, Tseng CK, Song J, Yuan Y, Wu M, Liu J, Yue Y, Zhang X, Wang Z, Yang L, Li J, Ni X, Li H, Xiang Y, Bian Y, Zhang B, Yin H, Dimitrov DS, Gilly J, Han L, Jiang H, Xie Y, Zhu J
PNAS (2025) 122 pp. e2406659122-e2406659122 [ Pubmed: 39908098 DOI: doi:10.1073/pnas.2406659122 ]
- Cryo-em structure of neutralizing antibody 8g3 in complex with ba.1 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Heavy chain of 8g3 (23 kDa, Protein from Homo heidelbergensis)
- Light chain of 8g3 (23 kDa, Protein from Homo sapiens)
structure of C2 projections and MIPs
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7n61
Q-score: 0.405
Han L, Rao Q, Yang R, Wang Y, Chai P, Xiong Y, Zhang K
Nat Struct Mol Biol (2022) 29 pp. 472-482 [ DOI: doi:10.1038/s41594-022-00769-9 Pubmed: 35578022 ]
- Unassigned protein-2 (14 kDa, Protein from Chlamydomonas reinhardtii)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Kinesin-like protein (83 kDa, Protein from Chlamydomonas reinhardtii)
- Fap147 (102 kDa, Protein from Chlamydomonas reinhardtii)
- Tubulin beta (49 kDa, Protein from Chlamydomonas reinhardtii)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Unassigned protein-5 (7 kDa, Protein from Chlamydomonas reinhardtii)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Unassigned protein-4 (3 kDa, Protein from Chlamydomonas reinhardtii)
- Structure of c2 projections and mips (Complex from Chlamydomonas reinhardtii)
- Unassigned protein-1 (14 kDa, Protein from Chlamydomonas reinhardtii)
- Fap65 (233 kDa, Protein from Chlamydomonas reinhardtii)
- Fap70 (111 kDa, Protein from Chlamydomonas reinhardtii)
- Fap239 (57 kDa, Protein from Chlamydomonas reinhardtii)
- Fap213 (22 kDa, Protein from Chlamydomonas reinhardtii)
- Unassigned protein-3 (13 kDa, Protein from Chlamydomonas reinhardtii)
- Fap225 (81 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar wd repeat-containing protein pf20 (65 kDa, Protein from Chlamydomonas reinhardtii)
- Unassigned protein-6 (14 kDa, Protein from Chlamydomonas reinhardtii)
- Fap178 (23 kDa, Protein from Chlamydomonas reinhardtii)
- Fap196 (64 kDa, Protein from Chlamydomonas reinhardtii)
- Tubulin alpha (49 kDa, Protein from Chlamydomonas reinhardtii)
Han L, Rao Q, Yang R, Wang Y, Chai P, Xiong Y, Zhang K
Nat Struct Mol Biol (2022) 29 pp. 472-482 [ DOI: doi:10.1038/s41594-022-00769-9 Pubmed: 35578022 ]
- Fap15 (34 kDa, Protein from Chlamydomonas reinhardtii)
- Fap227 (19 kDa, Protein from Chlamydomonas reinhardtii)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Fap108 (47 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (9 kDa, Protein from Chlamydomonas reinhardtii)
- Fap46 (289 kDa, Protein from Chlamydomonas reinhardtii)
- Fap297 (99 kDa, Protein from Chlamydomonas reinhardtii)
- Fap81 (234 kDa, Protein from Chlamydomonas reinhardtii)
- Fap305 (47 kDa, Protein from Chlamydomonas reinhardtii)
- Fap119 (33 kDa, Protein from Chlamydomonas reinhardtii)
- Heat shock protein 70a (71 kDa, Protein from Chlamydomonas reinhardtii)
- Fap42 (269 kDa, Protein from Chlamydomonas reinhardtii)
- Fap216 (79 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (9 kDa, Protein from Chlamydomonas reinhardtii)
- Tubulin beta (49 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (8 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (7 kDa, Protein from Chlamydomonas reinhardtii)
- Fap279 (43 kDa, Protein from Chlamydomonas reinhardtii)
- Fap360 (80 kDa, Protein from Chlamydomonas reinhardtii)
- Fap74 (204 kDa, Protein from Chlamydomonas reinhardtii)
- Fap92 (153 kDa, Protein from Chlamydomonas reinhardtii)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Fap54 (332 kDa, Protein from Chlamydomonas reinhardtii)
- Fap275 (18 kDa, Protein from Chlamydomonas reinhardtii)
- Fap7 (54 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (4 kDa, Protein from Chlamydomonas reinhardtii)
- Fap69 (114 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (14 kDa, Protein from Chlamydomonas reinhardtii)
- Cpc1 (205 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (9 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (3 kDa, Protein from Chlamydomonas reinhardtii)
- Hydin (425 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (11 kDa, Protein from Chlamydomonas reinhardtii)
- Fap289 (46 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (1 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (4 kDa, Protein from Chlamydomonas reinhardtii)
- C1 microtubule and its associated projection of central pair (Complex from Chlamydomonas reinhardtii)
- Fap101 (85 kDa, Protein from Chlamydomonas reinhardtii)
- Pf16 (54 kDa, Protein from Chlamydomonas reinhardtii)
- Fap114 (31 kDa, Protein from Chlamydomonas reinhardtii)
- Phosphopyruvate hydratase (51 kDa, Protein from Chlamydomonas reinhardtii)
- Calmodulin (18 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (5 kDa, Protein from Chlamydomonas reinhardtii)
- Fap47 (319 kDa, Protein from Chlamydomonas reinhardtii)
- Tubulin alpha (49 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (16 kDa, Protein from Chlamydomonas reinhardtii)
- Pf6 (237 kDa, Protein from Chlamydomonas reinhardtii)
- Fap76 (172 kDa, Protein from Chlamydomonas reinhardtii)
- Dpy30 (11 kDa, Protein from Chlamydomonas reinhardtii)
- Fap246 (120 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (15 kDa, Protein from Chlamydomonas reinhardtii)
- Hth_9 domain-containing protein (109 kDa, Protein from Chlamydomonas reinhardtii)
- Unknown protein (4 kDa, Protein from Chlamydomonas reinhardtii)
- Fap194 (57 kDa, Protein from Chlamydomonas reinhardtii)
- Fap99 (90 kDa, Protein from Chlamydomonas reinhardtii)
Structure of outer-arm dyneins bound to microtubule with microtubule binding state 1(MTBS-1)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7k58
Q-score: 0.357
Rao Q, Han L, Wang Y, Chai P, Kuo YW, Yang R, Hu F, Yang Y, Howard J, Zhang K
Nat Struct Mol Biol (2021) 28 pp. 799-810 [ DOI: doi:10.1038/s41594-021-00656-9 Pubmed: 34556869 ]
- Outer-arm dynein (2 MDa, Complex from Tetrahymena thermophila)
- Dynein light chain roadblock-type 2 protein (12 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain 2a (14 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (11 kDa, Protein from Tetrahymena thermophila)
- Thioredoxin (12 kDa, Protein from Tetrahymena thermophila)
- Dynein intermediate chain 2 (69 kDa, Protein from Tetrahymena thermophila)
- Gamma heavy chain (450 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dynein light chain (11 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain 1 (21 kDa, Protein from Tetrahymena thermophila)
- Dynein heavy chain, outer arm protein (533 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (11 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Flagellar outer dynein arm intermediate protein, putative (63 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain roadblock (10 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)
- Outer arm dynein beta heavy chain (529 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain tctex-type 1 protein (12 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
Structure of outer-arm dynein bound to microtubule doublet in microtubule binding state 2 (MTBS-2)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7k5b
Q-score: 0.264
Rao Q, Han L, Wang Y, Chai P, Kuo YW, Yang R, Hu F, Yang Y, Howard J, Zhang K
Nat Struct Mol Biol (2021) 28 pp. 799-810 [ DOI: doi:10.1038/s41594-021-00656-9 Pubmed: 34556869 ]
- Dynein light chain 2a (14 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (11 kDa, Protein from Tetrahymena thermophila)
- Thioredoxin (12 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain roadblock-type 2 protein (14 kDa, Protein from Tetrahymena thermophila)
- Dynein intermediate chain 2 (69 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dynein light chain (12 kDa, Protein from Tetrahymena thermophila)
- Gamma heavy chain (450 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain roadblock-type 2 protein (17 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dynein light chain 1 (21 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (11 kDa, Protein from Tetrahymena thermophila)
- Dynein heavy chain, outer arm protein (533 kDa, Protein from Tetrahymena thermophila)
- Flagellar outer dynein arm intermediate protein, putative (63 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)
- Dynein light chain tctex-type 1 protein (12 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain 4a (16 kDa, Protein from Tetrahymena thermophila)
- Outer-arm dynein bound to microtubule doublet in microtubule binding state 2 (mtbs-2) (Complex from Tetrahymena thermophila)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila)
- Outer arm dynein beta heavy chain (529 kDa, Protein from Tetrahymena thermophila)
Structure of the free outer-arm dynein in pre-parallel state
Resolution: 8.0 Å
EM Method: Single-particle
Fitted PDBs: 7kek
Q-score: 0.082
Rao Q, Han L, Wang Y, Chai P, Kuo YW, Yang R, Hu F, Yang Y, Howard J, Zhang K
Nat Struct Mol Biol (2021) 28 pp. 799-810 [ DOI: doi:10.1038/s41594-021-00656-9 Pubmed: 34556869 ]
- Dynein light chain tctex_b (13 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_3a (10 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Free outer-arm dynein (Complex from Tetrahymena thermophila)
- Thioredoxin lc3bl (14 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain 1 (22 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dynein light chain lc8_1a (lc10) (12 kDa, Protein from Tetrahymena thermophila)
- Dynein gamma heavy chain (475 kDa, Protein from Tetrahymena thermophila)
- Dynein intermediate chain dic3 (77 kDa, Protein from Tetrahymena thermophila)
- Dynein beta heavy chain (530 kDa, Protein from Tetrahymena thermophila)
- Dynein alpha heavy chain (534 kDa, Protein from Tetrahymena thermophila)
- Dynein intermediate chain dic2 (77 kDa, Protein from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)
- Dynein light chain roadblock lc7a (14 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_1b (dlc82) (10 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain roadblock lc7b (18 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_2a (lc8e) (10 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain tctex_a (lc2a) (15 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_3b (12 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_2b (13 kDa, Protein from Tetrahymena thermophila)
16-nm repeat microtubule doublet
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7mwg
Q-score: 0.438
Rao Q, Han L, Wang Y, Chai P, Kuo YW, Yang R, Hu F, Yang Y, Howard J, Zhang K
Nat Struct Mol Biol (2021) 28 pp. 799-810 [ DOI: doi:10.1038/s41594-021-00656-9 Pubmed: 34556869 ]
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Tubulin beta chain (49 kDa, Protein from Tetrahymena thermophila)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Tubulin alpha chain (49 kDa, Protein from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)
- 16-nm repeat microtubule doublet (Complex from Tetrahymena thermophila)
- Water (18 Da, Ligand)