Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 9arv
Q-score: 0.311
Xiang Y, Xu J, McGovern BL, Ranzenigo A, Huang W, Sang Z, Shen J, Diaz-Tapia R, Pham ND, Teunissen AJP, Rodriguez ML, Benjamin J, Taylor DJ, van Leent MMT, White KM, Garcia-Sastre A, Zhang P, Shi Y
Cell (2024) 187 pp. 6966-6980.e23 [ Pubmed: 39447570 DOI: doi:10.1016/j.cell.2024.09.043 ]
- Immunoglobulin j chain (19 kDa, Protein from Homo sapiens)
- Isoform 1 of immunoglobulin heavy constant mu (41 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Adaptive multi-epitope targeting and avidity-enhanced (ameta) nanobody platform (Complex from Homo sapiens)
Cryo-EM structure of BfUbb-ButCD complex
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8ypt
Q-score: 0.577
Tong M, Xu J, Li W, Jiang K, Yang Y, Chen Z, Jiao X, Meng X, Wang M, Hong J, Long H, Liu SJ, Lim B, Gao X
Nat Commun (2024) 15 pp. 8794-8794 [ Pubmed: 39389974 DOI: doi:10.1038/s41467-024-53149-w ]
- Ubiquitin-like protein (8 kDa, Protein from Bacteroides fragilis)
- Tonb-linked outer membrane protein (111 kDa, Protein from Bacteroides fragilis)
- Membrane protein (48 kDa, Protein from Bacteroides fragilis)
- Butcd-bfubb complex (Complex from Bacteroides fragilis)
Cryo-EM structure of ButCD complex
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 8ypu
Q-score: 0.606
Tong M, Xu J, Li W, Jiang K, Yang Y, Chen Z, Jiao X, Meng X, Wang M, Hong J, Long H, Liu SJ, Lim B, Gao X
Nat Commun (2024) 15 pp. 8794-8794 [ DOI: doi:10.1038/s41467-024-53149-w Pubmed: 39389974 ]
- Membrane protein (48 kDa, Protein from Bacteroides fragilis)
- Butcd complex (Complex from Bacteroides fragilis)
- Susc/raga family tonb-linked outer membrane protein (111 kDa, Protein from Bacteroides fragilis)
Cryo-EM structure of ACE2-B0AT1 complex with JX98
Xu J, Hu Z, Dai L, Yadav A, Jiang Y, Broer A, Gardiner MG, McLeod M, Yan R, Broer S
Nat Commun (2024) 15 pp. 7224-7224 [ Pubmed: 39174516 DOI: doi:10.1038/s41467-024-51748-1 ]
- Sodium-dependent neutral amino acid transporter b(0)at1 (72 kDa, Protein from Homo sapiens)
- Angiotensin-converting enzyme 2 (94 kDa, Protein from Homo sapiens)
- Ace2-b0at1 complex with inhibitor jx98 (Complex from Homo sapiens)
- 2-(4-chloranyl-3,5-dimethyl-phenoxy)-~{n}-propan-2-yl-ethanamide (255 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of ACE2-B0AT1 complex with JX225
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8wbz
Q-score: 0.466
Xu J, Hu Z, Dai L, Yadav A, Jiang Y, Broer A, Gardiner MG, McLeod M, Yan R, Broer S
Nat Commun (2024) 15 pp. 7224-7224 [ Pubmed: 39174516 DOI: doi:10.1038/s41467-024-51748-1 ]
- Sodium-dependent neutral amino acid transporter b(0)at1 (72 kDa, Protein from Homo sapiens)
- 2-(4-bromanyl-3-methyl-phenoxy)-~{n}-propyl-ethanamide (286 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Angiotensin-converting enzyme 2 (94 kDa, Protein from Homo sapiens)
- Ace2-b0at1 complex with inhibitor jx225 (Complex from Homo sapiens)
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 8tng
Q-score: 0.402
Xu J, Zhou T, McKee K, Zhang B, Liu C, Nazzari AF, Pegu A, Shen CH, Becker JE, Bender MF, Chan P, Changela A, Chaudhary R, Chen X, Einav T, Kwon YD, Lin BC, Louder MK, Merriam JS, Morano NC, O'Dell S, Olia AS, Rawi R, Roark RS, Stephens T, Teng IT, Tourtellott-Fogt E, Wang S, Yang ES, Shapiro L, Tsybovsky Y, Doria-Rose NA, Casellas R, Kwong PD
Adv Sci (2024) 11 pp. e2309268-e2309268 [ Pubmed: 38704686 DOI: doi:10.1002/advs.202309268 ]
- Complex between hiv-1 env bg505 ds-sosip and llama nanobody r27 (252 kDa, Complex from Lama glama)
- Hiv-1 bg505 ds-sosip gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- Cd4-binding site targeting nanobody r27 (12 kDa, Protein from Lama glama)
- Envelope glycoproteihiv-1 bg505 ds-sosip gp41n gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 8tnh
Q-score: 0.43
Xu J, Zhou T, McKee K, Zhang B, Liu C, Nazzari AF, Pegu A, Shen CH, Becker JE, Bender MF, Chan P, Changela A, Chaudhary R, Chen X, Einav T, Kwon YD, Lin BC, Louder MK, Merriam JS, Morano NC, O'Dell S, Olia AS, Rawi R, Roark RS, Stephens T, Teng IT, Tourtellott-Fogt E, Wang S, Yang ES, Shapiro L, Tsybovsky Y, Doria-Rose NA, Casellas R, Kwong PD
Adv Sci (2024) 11 pp. e2309268-e2309268 [ Pubmed: 38704686 DOI: doi:10.1002/advs.202309268 ]
- Cd4-binding site nanobody g36 (13 kDa, Protein from Lama glama)
- Hiv-1 bg505 ds-sosip gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Hiv-1 bg505 ds-sosip gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Complex between hiv-1 env bg505 ds-sosip and llama nanobody g36 (252 kDa, Complex from Lama glama)
Resolution: 3.61 Å
EM Method: Single-particle
Fitted PDBs: 8tni
Q-score: 0.391
Xu J, Zhou T, McKee K, Zhang B, Liu C, Nazzari AF, Pegu A, Shen CH, Becker JE, Bender MF, Chan P, Changela A, Chaudhary R, Chen X, Einav T, Kwon YD, Lin BC, Louder MK, Merriam JS, Morano NC, O'Dell S, Olia AS, Rawi R, Roark RS, Stephens T, Teng IT, Tourtellott-Fogt E, Wang S, Yang ES, Shapiro L, Tsybovsky Y, Doria-Rose NA, Casellas R, Kwong PD
Adv Sci (2024) 11 pp. e2309268-e2309268 [ Pubmed: 38704686 DOI: doi:10.1002/advs.202309268 ]
- Hiv-1 bg505 ds-sosip gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- Light chain of bi-specific antibody cap256l-r27 (36 kDa, Protein from Homo sapiens)
- Complex between hiv-1 env bg505 ds-sosip and bi-specific antibody cap256l-r27 (405 kDa, Complex from Homo sapiens)
- Heavy chain of bi-specific antibody cap256l-r27 (26 kDa, Protein from Homo sapiens)
- Hiv-1 bg505 ds-sosip gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8sy5
Q-score: 0.552
Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D
Nat Commun (2023) 14 pp. 8219-8219 [ Pubmed: 38086811 DOI: doi:10.1038/s41467-023-43735-9 ]
- Non-template single stranded dna (5 kDa, DNA from synthetic construct)
- Template single stranded dna (8 kDa, DNA from synthetic construct)
- E. coli rnap transcription elongation complex bound the unnatural ds-btp base pair in the active site (500 kDa, Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Rna oligomer (2 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 2-oxo-2-hydroadenosine 5'-(tetrahydrogen triphosphate) (523 Da, Ligand)
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 8sy6
Q-score: 0.449
Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D
Nat Commun (2023) 14 pp. 8219-8219 [ Pubmed: 38086811 DOI: doi:10.1038/s41467-023-43735-9 ]
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Uridine 5'-triphosphate (484 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- 2'-deoxyguanosine-5'-monophosphate (347 Da, Ligand)
- Template single stranded dna (8 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta' (158 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Non-template single stranded dna (5 kDa, DNA from synthetic construct)
- E. coli rnap transcription elongation complex bound the unnatural db-utp base pair in the active site (500 kDa, Complex from Escherichia coli)
- Rna oligomer (2 kDa, RNA from synthetic construct)