CryoEM Structure of Inactive H2R Bound to Famotidine, Nb6M, and NabFab
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7ul3
Q-score: 0.36
Robertson MJ, Papasergi-Scott MM, He F, Seven AB, Meyerowitz JG, Panova O, Peroto MC, Che T, Skiniotis G
Nat Struct Mol Biol (2022) 29 pp. 1188-1195 [ DOI: doi:10.1038/s41594-022-00859-8 Pubmed: 36396979 ]
- Nb6m (Complex from Lama glama)
- Nabfab (Complex from synthetic construct)
- H2r (Complex from Homo sapiens)
- Histamine h2 receptor (44 kDa, Protein from Homo sapiens)
- Nabfab lc (23 kDa, Protein from synthetic construct)
- Nanobody 6m (14 kDa, Protein from synthetic construct)
- Nabfab hc (25 kDa, Protein from synthetic construct)
- Complex of h2r, nb6m, and nabfab (Complex from Homo sapiens)
- Famotidine (339 Da, Ligand)
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 [ Pubmed: 34556869 DOI: doi:10.1038/s41594-021-00656-9 ]
- Dynein light chain lc8_2b (13 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dynein intermediate chain dic2 (77 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain tctex_a (lc2a) (15 kDa, Protein from Tetrahymena thermophila)
- Dynein beta heavy chain (530 kDa, Protein from Tetrahymena thermophila)
- Dynein gamma heavy chain (475 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain 1 (22 kDa, Protein from Tetrahymena thermophila)
- Dynein alpha heavy chain (534 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_1a (lc10) (12 kDa, Protein from Tetrahymena thermophila)
- Magnesium ion (24 Da, Ligand)
- Dynein light chain lc8_2a (lc8e) (10 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_3a (10 kDa, Protein from Tetrahymena thermophila)
- Dynein intermediate chain dic3 (77 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain roadblock lc7b (18 kDa, Protein from Tetrahymena thermophila)
- Free outer-arm dynein (Complex from Tetrahymena thermophila)
- Dynein light chain roadblock lc7a (14 kDa, Protein from Tetrahymena thermophila)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Dynein light chain lc8_3b (12 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain lc8_1b (dlc82) (10 kDa, Protein from Tetrahymena thermophila)
- Dynein light chain tctex_b (13 kDa, Protein from Tetrahymena thermophila)
- Thioredoxin lc3bl (14 kDa, Protein from Tetrahymena thermophila)
ASCT2 in the presence of the inhibitor Lc-BPE in the outward-open conformation.
Resolution: 3.43 Å
EM Method: Single-particle
Fitted PDBs: 7bcq
Q-score: 0.427
Garibsingh RA, Ndaru E, Garaeva AA, Shi Y, Zielewicz L, Zakrepine P, Bonomi M, Slotboom DJ, Paulino C, Grewer C, Schlessinger A
PNAS (2021) 118 [ DOI: doi:10.1073/pnas.2104093118 Pubmed: 34507995 ]
Resolution: 8.45 Å
EM Method: Single-particle
Fitted PDBs: 7phq
Q-score: 0.111
Bloch JS, Mukherjee S, Kowal J, Filippova EV, Niederer M, Pardon E, Steyaert J, Kossiakoff AA, Locher KP
PNAS (2021) 118 [ Pubmed: 34782475 DOI: doi:10.1073/pnas.2115435118 ]
- Water (18 Da, Ligand)
- Complex of staphylococcus capitis divalent metal ion transporter (dmt), chimeric nanobody dmtnb16_4, nabfab, and anti-fab nanobody (Complex from synthetic construct)
- Dmt-nb16_4 (14 kDa, Protein from synthetic construct)
- Nabfab lc (23 kDa, Protein from synthetic construct)
- Divalent metal cation transporter mnth (47 kDa, Protein from Staphylococcus capitis)
- Anti-fab nanobody (13 kDa, Protein from Lama glama)
- Nabfab hc (25 kDa, Protein from synthetic construct)
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 7pij
Q-score: 0.422
Bloch JS, Mukherjee S, Kowal J, Filippova EV, Niederer M, Pardon E, Steyaert J, Kossiakoff AA, Locher KP
PNAS (2021) 118 [ Pubmed: 34782475 DOI: doi:10.1073/pnas.2115435118 ]
- Water (18 Da, Ligand)
- Complex of staphylococcus capitis divalent metal ion transporter (dmt), chimeric nanobody dmtnb16_4, nabfab, and anti-fab nanobody (Complex from synthetic construct)
- Nabfab lc (23 kDa, Protein from synthetic construct)
- Divalent metal cation transporter mnth (47 kDa, Protein from Staphylococcus capitis)
- Anti-fab nanobody (13 kDa, Protein from Lama glama)
- Nabfab hc (25 kDa, Protein from synthetic construct)
- Dmtnb16_4 (14 kDa, Protein from synthetic construct)
VgaA-LC, an antibiotic resistance ABCF, in complex with 70S ribosome from Staphylococcus aureus
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7nhl
Q-score: 0.476
Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O'Neill AJ, Hauryliuk V, Wilson DN
Nat Commun (2021) 12 pp. 3577-3577 [ Pubmed: 34117249 DOI: doi:10.1038/s41467-021-23753-1 ]
- Vgaa-lc in complex with 70s ribosome, mrna, and distorted p-trna from staphylococcus aureus (2 MDa, Complex)
- 50s ribosomal protein l4 (22 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l17 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l31 type b (9 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- Rna (5'-r(p*gp*gp*ap*gp*gp*up*ap*up*g)-3') (4 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s8 (14 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l2 (30 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s2 (29 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l22 (12 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l23 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l27 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- Potassium ion (39 Da, Ligand)
- 50s ribosomal protein l34 (5 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l29 (8 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s3 (24 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 16s rrna (501 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
- 5s rrna (36 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
- 23s rrna (946 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l21 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l13 (16 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l33 2 (5 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l25 (23 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- Vgaa-lc (Complex from Staphylococcus haemolyticus)
- 30s ribosomal protein s10 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s18 (9 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s12 (15 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s9 (14 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s20 (9 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- Lincosamide-streptogramin a resistance protein (63 kDa, Protein from Staphylococcus haemolyticus)
- 50s ribosomal protein l15 (15 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s5 (17 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s13 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s15 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l6 (19 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s7 (17 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l32 (6 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l19 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l28 (6 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s11 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l20 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l36 (4 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- P-trna fmet (24 kDa, RNA from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s14 type z (7 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l16 (16 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l35 (7 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l14 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 30s ribosomal protein s4 (23 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s19 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 70s ribosome (Complex from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s17 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l3 (23 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l18 (13 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l30 (6 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s16 (10 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l5 (20 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 30s ribosomal protein s6 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
- 50s ribosomal protein l24 (11 kDa, Protein from Staphylococcus aureus subsp. aureus NCTC 8325)
Outer Dynein Arm-Shulin complex - Shulin region from Tetrahymena thermophila
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6zyx
Q-score: 0.398
Mali GR, Ali FA, Lau CK, Begum F, Boulanger J, Howe JD, Chen ZA, Rappsilber J, Skehel M, Carter AP
Science (2021) 371 pp. 910-916 [ DOI: doi:10.1126/science.abe0526 Pubmed: 33632841 ]
- Dynein (Complex from Tetrahymena thermophila CU428)
- Shulin (Complex from Tetrahymena thermophila CU428)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain (12 kDa, Protein from Tetrahymena thermophila CU428)
- Flagellar outer dynein arm intermediate protein, putative (77 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein heavy chain, outer arm protein (534 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain (10 kDa, Protein from Tetrahymena thermophila CU428)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Shulin region from outer dynein arm-shulin complex (tetrahymena thermophila). contains shulin (excluding c3 finger), lc8e, lc8f, lc8d, lc8, lc2a, lc9, dic n-termini and portion of dyh3 tail. (Complex)
- Dynein light chain (13 kDa, Protein from Tetrahymena thermophila CU428)
- Shulin (139 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain tctex-type 1 protein (13 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein light chain 2a (15 kDa, Protein from Tetrahymena thermophila CU428)
- Dynein intermediate chain 2 (77 kDa, Protein from Tetrahymena thermophila CU428)
Outer dynein arm bound to doublet microtubules from C. reinhardtii
Resolution: 7.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 7kzm
Q-score: 0.315
Nat Commun (2021) 12 pp. 477-477 [ DOI: doi:10.1038/s41467-020-20735-7 Pubmed: 33473120 ]
- Flagellar outer dynein arm light chain 2 (15 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar outer dynein arm heavy chain beta (520 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein 11 kda light chain, flagellar outer arm (13 kDa, Protein from Chlamydomonas reinhardtii)
- Oda complex (Complex from Chlamydomonas reinhardtii)
- Dynein, 70 kda intermediate chain, flagellar outer arm (63 kDa, Protein from Chlamydomonas reinhardtii)
- Outer dynein arm-docking complex subunit 1 (83 kDa, Protein from Chlamydomonas reinhardtii)
- Magnesium ion (24 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Dynein light chain roadblock lc7b (11 kDa, Protein from Chlamydomonas reinhardtii)
- Outer dynein arm-docking complex protein dc3 (21 kDa, Protein from Chlamydomonas reinhardtii)
- Dc2 (14 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein 8 kda light chain, flagellar outer arm (10 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein light chain 10 (12 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein light chain roadblock lc7a (11 kDa, Protein from Chlamydomonas reinhardtii)
- Dc1 (13 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein gamma chain, flagellar outer arm (513 kDa, Protein from Chlamydomonas reinhardtii)
- Tubulin beta (49 kDa, Protein from Chlamydomonas reinhardtii)
- Outer dynein arm protein 1 (62 kDa, Protein from Chlamydomonas reinhardtii)
- Heavy chain alpha (504 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein, 78 kda intermediate chain, flagellar outer arm (76 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein light chain 9 (12 kDa, Protein from Chlamydomonas reinhardtii)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dynein 18 kda light chain, flagellar outer arm (17 kDa, Protein from Chlamydomonas reinhardtii)
- Tubulin alpha (49 kDa, Protein from Chlamydomonas reinhardtii)
Outer dynein arm core subcomplex from C. reinhardtii
Resolution: 4.0 Å
EM Method: Helical reconstruction
Fitted PDBs: 7kzn
Q-score: 0.376
Nat Commun (2021) 12 pp. 477-477 [ DOI: doi:10.1038/s41467-020-20735-7 Pubmed: 33473120 ]
- Dynein light chain roadblock lc7a (11 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein gamma chain, flagellar outer arm (513 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar outer dynein arm light chain 2 (15 kDa, Protein from Chlamydomonas reinhardtii)
- Dc1 (10 kDa, Protein from Chlamydomonas reinhardtii)
- Flagellar outer dynein arm heavy chain beta (520 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein light chain roadblock lc7b (11 kDa, Protein from Chlamydomonas reinhardtii)
- Outer dynein arm-docking complex protein dc3 (21 kDa, Protein from Chlamydomonas reinhardtii)
- Oda core subcomplex (Complex from Chlamydomonas reinhardtii)
- Dynein 18 kda light chain, flagellar outer arm (17 kDa, Protein from Chlamydomonas reinhardtii)
- Dc2 (14 kDa, Protein from Chlamydomonas reinhardtii)
- Heavy chain alpha (504 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein, 78 kda intermediate chain, flagellar outer arm (76 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein 8 kda light chain, flagellar outer arm (10 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein 11 kda light chain, flagellar outer arm (13 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein light chain 9 (12 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein, 70 kda intermediate chain, flagellar outer arm (63 kDa, Protein from Chlamydomonas reinhardtii)
- Dynein light chain 10 (12 kDa, Protein from Chlamydomonas reinhardtii)
Structure of the phycobilisome from the red alga Porphyridium purpureum
Ma JF, You X, Sun S, Wang XX, Qin S, Sui SF
Nature (2020) 579 pp. 146-151 [ DOI: doi:10.1038/s41586-020-2020-7 Pubmed: 32076272 ]
- Lrc4 (16 kDa, Protein from Red alga)
- Lr9 (31 kDa, Protein from Red alga)
- Lr4 (31 kDa, Protein from Red alga)
- Lr3 (37 kDa, Protein from Red alga)
- Lr1 (39 kDa, Protein from Red alga)
- Allophycocyanin beta subunit (17 kDa, Protein from Red alga)
- Lr5 (29 kDa, Protein from Red alga)
- Lr2_hb (43 kDa, Protein from Red alga)
- Lrc6 (26 kDa, Protein from Red alga)
- Allophycocyanin beta 18 subunit (19 kDa, Protein from Red alga)
- Lrc3 (55 kDa, Protein from Red alga)
- Phycoerythrin alpha subunit (17 kDa, Protein from Red alga)
- C-phycocyanin alpha subunit (17 kDa, Protein from Red alga)
- B-phycoerythrin beta chain (18 kDa, Protein from Red alga)
- Lr8 (31 kDa, Protein from Red alga)
- C-phycocyanin beta subunit (18 kDa, Protein from Red alga)
- Lrc2 (53 kDa, Protein from Red alga)
- Allophycocyanin alpha subunit (17 kDa, Protein from Red alga)
- Phycoerythrobilin (588 Da, Ligand)
- Lr2 (32 kDa, Protein from Red alga)
- Lr7 (36 kDa, Protein from Red alga)
- Phycobilisome rod-core linker polypeptide (26 kDa, Protein from Red alga)
- Complex of phycobilisome from red alga p.purpureum. (Complex from Porphyridium purpureum)
- Phycocyanobilin (588 Da, Ligand)
- Allophycocyanin gamma subunit (18 kDa, Protein from Red alga)
- Lc (10 kDa, Protein from Red alga)
- Lrc5 (30 kDa, Protein from Red alga)
- Phycourobilin (590 Da, Ligand)
- Phycobilisome linker polypeptide (99 kDa, Protein from Red alga)