Gag CA-SP1 immature lattice from intact enveloped virus-like particles
Resolution: 2.42 Å
EM Method: Single-particle
Fitted PDBs: 9cwv
Q-score: 0.581
Wu C, Meuser ME, Rey JS, Meshkin H, Yang R, Devarkar SC, Freniere C, Shi J, Aiken C, Perilla JR, Xiong Y
bioRxiv (2024) [ Pubmed: 39416065 DOI: doi:10.1101/2024.10.09.617473 ]
- Water (18 Da, Ligand)
- Inositol hexakisphosphate (660 Da, Ligand)
- Human immunodeficiency virus type 1 group m subtype b (isolate ny5) (hiv-1) (Virus from Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (HIV-1))
- Gag (25 kDa, Protein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Gag CA-SP1 immature lattice bound with Lenacapavir and Bevirimat from enveloped virus like particles
Resolution: 2.1 Å
EM Method: Single-particle
Fitted PDBs: 9d6c
Q-score: 0.612
Wu C, Meuser ME, Rey JS, Meshkin H, Yang R, Devarkar SC, Freniere C, Shi J, Aiken C, Perilla JR, Xiong Y
bioRxiv (2024) [ Pubmed: 39416065 DOI: doi:10.1101/2024.10.09.617473 ]
- Gag (25 kDa, Protein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
- Inositol hexakisphosphate (660 Da, Ligand)
- 3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid (584 Da, Ligand)
- Human immunodeficiency virus type 1 (new york-5 isolate) (Virus from Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE))
- Water (18 Da, Ligand)
- Lenacapavir (968 Da, Ligand)
Gag CA-SP1 immature lattice bound with Lenacapavir from enveloped virus like particles
Resolution: 2.18 Å
EM Method: Single-particle
Fitted PDBs: 9d6d
Q-score: 0.587
Wu C, Meuser ME, Rey JS, Meshkin H, Yang R, Devarkar SC, Freniere C, Shi J, Aiken C, Perilla JR, Xiong Y
bioRxiv (2024) [ Pubmed: 39416065 DOI: doi:10.1101/2024.10.09.617473 ]
- Inositol hexakisphosphate (660 Da, Ligand)
- Human immunodeficiency virus type 1 (new york-5 isolate) (Virus from Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE))
- Water (18 Da, Ligand)
- Gag polyprotein (25 kDa, Protein from Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE))
- Lenacapavir (968 Da, Ligand)
Gag CA-SP1 immature lattice bound with Bevirimat from enveloped virus like particles
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 9d6e
Q-score: 0.467
Wu C, Meuser ME, Rey JS, Meshkin H, Yang R, Devarkar SC, Freniere C, Shi J, Aiken C, Perilla JR, Xiong Y
bioRxiv (2024) [ Pubmed: 39416065 DOI: doi:10.1101/2024.10.09.617473 ]
- Human immunodeficiency virus type 1 (new york-5 isolate) (Virus from Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE))
- Inositol hexakisphosphate (660 Da, Ligand)
- Gag polyprotein (25 kDa, Protein from Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE))
- 3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid (584 Da, Ligand)
Gag CA-SP1 immature lattice from enveloped and perforated virus like particles
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 9d88
Q-score: 0.474
Wu C, Meuser ME, Rey JS, Meshkin H, Yang R, Devarkar SC, Freniere C, Shi J, Aiken C, Perilla JR, Xiong Y
bioRxiv (2024) [ Pubmed: 39416065 DOI: doi:10.1101/2024.10.09.617473 ]
Gag CA-SP1 immature lattice bound with Lenacapavir from enveloped virus like particles (T8I)
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 9dwd
Q-score: 0.501
Wu C, Meuser ME, Rey JS, Meshkin H, Yang R, Devarkar SC, Freniere C, Shi J, Aiken C, Perilla JR, Xiong Y
bioRxiv (2024) [ Pubmed: 39416065 DOI: doi:10.1101/2024.10.09.617473 ]
- Human immunodeficiency virus type 1 (new york-5 isolate) (Virus from Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE))
- Inositol hexakisphosphate (660 Da, Ligand)
- Lenacapavir (968 Da, Ligand)
- Gag (25 kDa, Protein from Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE))
Cutibacterium acnes 50S ribosomal subunit with Clindamycin bound
Lomakin IB, Devarkar SC, Grada A, Bunick CG
J Invest Dermatol. (2024) 144 pp. 2553-2561.e3 [ DOI: doi:10.1016/j.jid.2024.07.013 Pubmed: 39122144 ]
- 50s ribosomal protein l28 (6 kDa, Protein from Cutibacterium acnes)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Cutibacterium acnes)
- 23s rrna (1 MDa, RNA from Cutibacterium acnes)
- 50s ribosomal protein l2 (30 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l18 (13 kDa, Protein from Cutibacterium acnes)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l27 (9 kDa, Protein from Cutibacterium acnes)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l19 (13 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l3 (23 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l32 (6 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l25 (22 kDa, Protein from Cutibacterium acnes)
- Clindamycin (424 Da, Ligand)
- 50s ribosomal protein l31 (7 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l36 (4 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l29 (8 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l16 (15 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l20 (13 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l13 (16 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l34 (5 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l4 (32 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l14 (13 kDa, Protein from Cutibacterium acnes)
- 50s subunit with clindamycin bound (Complex from Cutibacterium acnes)
- 50s ribosomal protein l15 (15 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein bl37 (2 kDa, Protein from Cutibacterium acnes)
- Large ribosomal subunit protein ul24 (13 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l6 (19 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l22 (16 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l23 (11 kDa, Protein from Cutibacterium acnes)
- Large ribosomal subunit protein bl17 (20 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l30 (6 kDa, Protein from Cutibacterium acnes)
- 5s rrna (38 kDa, RNA from Cutibacterium acnes)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l33 (6 kDa, Protein from Cutibacterium acnes)
- 50s ribosomal protein l5 (23 kDa, Protein from Cutibacterium acnes)
MERS-CoV Nsp1 protein bound to the Human 40S Ribosomal subunit
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8t4s
Q-score: 0.59
Devarkar SC, Vetick M, Balaji S, Lomakin IB, Yang L, Jin D, Gilbert WV, Chen S, Xiong Y
Cell Rep (2023) 42 pp. 113156-113156 [ DOI: doi:10.1016/j.celrep.2023.113156 Pubmed: 37733586 ]
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- Mers-cov nsp1 bound to human 40s ribosomal subunit (Complex from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 18s rrna (602 kDa, RNA from Homo sapiens)
- Fau ubiquitin-like and ribosomal protein s30 (14 kDa, Protein from Homo sapiens)
- Replicase polyprotein 1ab (21 kDa, Protein from Middle East respiratory syndrome-related coronavirus)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
MERS-CoV Nsp1 protein binds the human 40S ribosome - Consensus Reconstruction
Devarkar SC, Vetick M, Balaji S, Lomakin IB, Yang L, Jin D, Gilbert WV, Chen S, Xiong Y
Cell Rep (2023) 42 pp. 113156-113156 [ Pubmed: 37733586 DOI: doi:10.1016/j.celrep.2023.113156 ]
MERS-CoV Nsp1 protein bound to the human 40S ribosome: Focus Refined 40S Head Map
Devarkar SC, Vetick M, Balaji S, Lomakin IB, Yang L, Jin D, Gilbert WV, Chen S, Xiong Y
Cell Rep (2023) 42 pp. 113156-113156 [ Pubmed: 37733586 DOI: doi:10.1016/j.celrep.2023.113156 ]