Human Vault Cage in complex with PARP4
Lodwick JE, Shen R, Erramilli S, Xie Y, Roganowicz K, Kossiakoff AA, Zhao M
bioRxiv (2024) [ DOI: doi:10.1101/2024.06.27.601040 Pubmed: 38979142 ]
- Major vault protein (99 kDa, Protein from Homo sapiens)
- Protein mono-adp-ribosyltransferase parp4 (192 kDa, Protein from Homo sapiens)
- Binary complex of human parp4 bound to oligomerized human mvp (12 MDa, Complex from Homo sapiens)
Human Vault Cage in complex with PARP4 and NAD+
Lodwick JE, Shen R, Erramilli S, Xie Y, Roganowicz K, Kossiakoff AA, Zhao M
bioRxiv (2024) [ DOI: doi:10.1101/2024.06.27.601040 Pubmed: 38979142 ]
- Major vault protein (99 kDa, Protein from Homo sapiens)
- Ternary complex of nad+ and human parp4 bound to oligomerized human mvp (12 MDa, Complex from Homo sapiens)
- Protein mono-adp-ribosyltransferase parp4 (192 kDa, Protein from Homo sapiens)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 9cmi
Q-score: 0.468
Rathnayake SS, Erramilli SK, Kossiakoff AA, Vecchio AJ
Structure (2024) 32 pp. 1936- [ Pubmed: 39383874 DOI: doi:10.1016/j.str.2024.09.015 ]
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Water (18 Da, Ligand)
- Heat-labile enterotoxin b chain (33 kDa, Protein from Clostridium perfringens)
- Cop-1 sfab heavy chain (28 kDa, Protein from Homo sapiens)
- Human claudin-4 complex with clostridium perfringens enterotoxin, sfab cop-1, and nanobody (120 kDa, Complex from synthetic construct)
- Anti-fab nanobody (13 kDa, Protein from Homo sapiens)
- Claudin-4 (22 kDa, Protein from Homo sapiens)
- Cop-1 sfab light chain (25 kDa, Protein from Homo sapiens)
Cryo-EM structure of FLVCR2 in the inward-facing state with choline bound
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 8vzn
Q-score: 0.583
Cater RJ, Mukherjee D, Gil-Iturbe E, Erramilli SK, Chen T, Koo K, Santander N, Reckers A, Kloss B, Gawda T, Choy BC, Zhang Z, Katewa A, Larpthaveesarp A, Huang EJ, Mooney SWJ, Clarke OB, Yee SW, Giacomini KM, Kossiakoff AA, Quick M, Arnold T, Mancia F
Nature (2024) 629 pp. 704-709 [ Pubmed: 38693257 DOI: doi:10.1038/s41586-024-07326-y ]
- Flvcr2 in the inward-facing state complexed with choline and fab flv9 (110 kDa, Complex from Mus musculus)
- Fab flv9 light chain (23 kDa, Protein from synthetic construct)
- Choline ion (104 Da, Ligand)
- Fab flv9 heavy chain (25 kDa, Protein from synthetic construct)
- Feline leukemia virus subgroup c cellular receptor 2 (60 kDa, Protein from Mus musculus)
Cryo-EM structure of FLVCR2 in the outward-facing state with choline bound
Resolution: 2.49 Å
EM Method: Single-particle
Fitted PDBs: 8vzo
Q-score: 0.637
Cater RJ, Mukherjee D, Gil-Iturbe E, Erramilli SK, Chen T, Koo K, Santander N, Reckers A, Kloss B, Gawda T, Choy BC, Zhang Z, Katewa A, Larpthaveesarp A, Huang EJ, Mooney SWJ, Clarke OB, Yee SW, Giacomini KM, Kossiakoff AA, Quick M, Arnold T, Mancia F
Nature (2024) 629 pp. 704-709 [ Pubmed: 38693257 DOI: doi:10.1038/s41586-024-07326-y ]
- Fab flv23 heavy chain (25 kDa, Protein from synthetic construct)
- Flvcr2 in the outward-facing state complexed with choline and fab flv23 (110 kDa, Complex from Mus musculus)
- Fab flv23 light chain (23 kDa, Protein from synthetic construct)
- Choline ion (104 Da, Ligand)
- Feline leukemia virus subgroup c cellular receptor 2 (60 kDa, Protein from Mus musculus)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8the
Q-score: 0.664
Knejski PP, Erramilli SK, Kossiakoff AA
Structure (2024) 32 pp. 411- [ DOI: doi:10.1016/j.str.2024.01.007 Pubmed: 38325368 ]
- Water (18 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (2~{r},4~{r},5~{s},6~{s})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-2-[[(2~{r},3~{s},4~{s},5~{r},6~{s})-5-[[(3~{r})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{r},3~{r},4~{r},5~{s},6~{s})-3-oxidanyl-5-[[(3~{r})-3-oxidanyltetradecanoyl]amino]-4-[(3~{r})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{s})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-4,5-bis(oxidanyl)oxane-2-carboxylic acid (2 kDa, Ligand)
- Synthetic antibody heavy chain (25 kDa, Protein from Homo sapiens)
- Heme bound p. aeruginosa phur with bound synthetic antibody (Complex from Pseudomonas aeruginosa)
- Heme/hemoglobin uptake outer membrane receptor phur (86 kDa, Protein from Pseudomonas aeruginosa)
- Synthetic antibody light chain (23 kDa, Protein from Homo sapiens)
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8u4v
Q-score: 0.572
Erramilli SK, Dominik PK, Ogbu CP, Kossiakoff AA, Vecchio AJ
Commun Biol (2024) 7 pp. 733-733 [ DOI: doi:10.1038/s42003-024-06437-6 Pubmed: 38886509 ]
- Lauryl maltose neopentyl glycol (1 kDa, Ligand)
- Claudin-4 (22 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Heat-labile enterotoxin b chain (14 kDa, Protein from Clostridium perfringens)
- Cop-1 sfab heavy chain (28 kDa, Protein from Homo sapiens)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- Cop-1 sfab light chain (23 kDa, Protein from Homo sapiens)
- Human claudin-4 complex with clostridium perfringens enterotoxin c-terminal domain, sfab cop-1, and nanobody (100 kDa, Complex from Homo sapiens)
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 8pg0
Q-score: 0.528
Ciuta AD, Nosol K, Kowal J, Mukherjee S, Ramirez AS, Stieger B, Kossiakoff AA, Locher KP
Nat Commun (2023) 14 pp. 5774-5774 [ DOI: doi:10.1038/s41467-023-41552-8 Pubmed: 37723174 ]
- Bicarbonate ion (61 Da, Ligand)
- Solute carrier organic anion transporter family member 1b3 (77 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Fab19 (light chain, variable region) (23 kDa, Protein from Homo sapiens)
- Human oatp1b3 (180 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fab19 (heavy chain, variable region) (25 kDa, Protein from Homo sapiens)
LRRC8A:C conformation 1 (round) top focus
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 8drk
Q-score: 0.47
Kern DM, Bleier J, Mukherjee S, Hill JM, Kossiakoff AA, Isacoff EY, Brohawn SG
Nat Struct Mol Biol (2023) 30 pp. 841-852 [ Pubmed: 36928458 DOI: doi:10.1038/s41594-023-00944-6 ]
- Water (18 Da, Ligand)
- Volume-regulated anion channel subunit lrrc8c (93 kDa, Protein from Mus musculus)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Volume-regulated anion channel subunit lrrc8a,soluble cytochrome b562 (105 kDa, Protein from Mus musculus)
- Lrrc8a:c (620 kDa, Complex from Mus musculus)
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 7zlg
Q-score: 0.454
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP
Nat Chem Biol (2023) 19 pp. 575-584 [ Pubmed: 36604564 DOI: doi:10.1038/s41589-022-01219-9 ]
- Synthetic octapeptide wehi 1886493 (821 Da, Protein from synthetic construct)
- Cmt2-fab heavy chain (25 kDa, Protein from synthetic construct)
- Water (18 Da, Ligand)
- C-mannosyltransferase cedpy19, in complex with acceptor peptide and bound to cmt2-fab and anti-fab nanobody (Complex from Caenorhabditis elegans)
- C-mannosyltransferase dpy-19 (80 kDa, Protein from Caenorhabditis elegans)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- Cmt2-fab light chain (23 kDa, Protein from synthetic construct)