6V67
 
 | | Apo Structure of the De Novo PD-1 Binding Miniprotein GR918.2 | | Descriptor: | PD-1 Binding Miniprotein GR918.2 | | Authors: | Bick, M.J, Bryan, C.M, Baker, D, Dimaio, F, Kang, A. | | Deposit date: | 2019-12-04 | | Release date: | 2020-12-09 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.07 Å) | | Cite: | Computational design of a synthetic PD-1 agonist.
Proc.Natl.Acad.Sci.USA, 118, 2021
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6WCW
 | | Structure of human Rubicon RH domain in complex with GTP-bound Rab7 | | Descriptor: | GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, Ras-related protein Rab-7a, ... | | Authors: | Bhargava, H.K, Byck, J.M, Farrell, D.P, Anishchenko, I, DiMaio, F, Im, Y.J, Hurley, J.H. | | Deposit date: | 2020-03-31 | | Release date: | 2020-07-01 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.
Proc.Natl.Acad.Sci.USA, 117, 2020
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5SZS
 | | Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ... | | Authors: | Walls, A.C, Tortorici, M.A, Frenz, B, Snijder, J, Li, W, Rey, F.A, DiMaio, F, Bosch, B.J, Veesler, D. | | Deposit date: | 2016-08-15 | | Release date: | 2016-09-14 | | Last modified: | 2020-07-29 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy.
Nat.Struct.Mol.Biol., 23, 2016
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6W3W
 | | An enumerative algorithm for de novo design of proteins with diverse pocket structures | | Descriptor: | DENOVO NTF2, NITRATE ION | | Authors: | Bera, A.K, Basanta, B, Dimaio, F, Sankaran, B, Baker, D. | | Deposit date: | 2020-03-09 | | Release date: | 2020-04-08 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | An enumerative algorithm for de novo design of proteins with diverse pocket structures.
Proc.Natl.Acad.Sci.USA, 117, 2020
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8UB3
 | | DpHF7 filament | | Descriptor: | DpHF7 filament | | Authors: | Lynch, E.M, Farrell, D, Shen, H, Kollman, J.M, DiMaio, F, Baker, D. | | Deposit date: | 2023-09-22 | | Release date: | 2024-04-10 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | De novo design of pH-responsive self-assembling helical protein filaments.
Nat Nanotechnol, 2024
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8W20
 | | Umb1 umbrella toxin particle | | Descriptor: | Intein C-terminal splicing domain-containing protein, Secreted esterase, Secreted protein | | Authors: | Park, Y.J, Zhao, Q, Seattle Structural Genomics Center for Infectious Disease (SSGCID), DiMaio, F, Mougous, J.D, Veesler, D. | | Deposit date: | 2024-02-19 | | Release date: | 2024-04-17 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (4.3 Å) | | Cite: | Streptomyces umbrella toxin particles block hyphal growth of competing species.
Nature, 629, 2024
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7K3H
 | | Crystal structure of deep network hallucinated protein 0217 | | Descriptor: | Network hallucinated protein 0217 | | Authors: | Pellock, S.J, Anishchenko, I, Chidyausiku, T.M, Bera, A.K, DiMaio, F, Baker, D. | | Deposit date: | 2020-09-11 | | Release date: | 2021-12-22 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | De novo protein design by deep network hallucination.
Nature, 600, 2021
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6Q04
 | | MERS-CoV S structure in complex with 5-N-acetyl neuraminic acid | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, FOLIC ACID, ... | | Authors: | Park, Y.J, Walls, A.C, Wang, Z, Sauer, M, Li, W, Tortorici, M.A, Bosch, B.J, DiMaio, F.D, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID) | | Deposit date: | 2019-08-01 | | Release date: | 2019-12-11 | | Last modified: | 2020-07-29 | | Method: | ELECTRON MICROSCOPY (2.5 Å) | | Cite: | Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors.
Nat.Struct.Mol.Biol., 26, 2019
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6Q06
 | | MERS-CoV S structure in complex with 2,3-sialyl-N-acetyl-lactosamine | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, FOLIC ACID, ... | | Authors: | Park, Y.J, Walls, A.C, Wang, Z, Sauer, M, Li, W, Tortorici, M.A, Bosch, B.J, DiMaio, F.D, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID) | | Deposit date: | 2019-08-01 | | Release date: | 2019-12-11 | | Last modified: | 2020-07-29 | | Method: | ELECTRON MICROSCOPY (2.7 Å) | | Cite: | Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors.
Nat.Struct.Mol.Biol., 26, 2019
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6Q05
 | | MERS-CoV S structure in complex with sialyl-lewisX | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, FOLIC ACID, ... | | Authors: | Park, Y.J, Walls, A.C, Wang, Z, Sauer, M, Li, W, Tortorici, M.A, Bosch, B.J, DiMaio, F.D, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID) | | Deposit date: | 2019-08-01 | | Release date: | 2019-12-11 | | Last modified: | 2020-07-29 | | Method: | ELECTRON MICROSCOPY (2.8 Å) | | Cite: | Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors.
Nat.Struct.Mol.Biol., 26, 2019
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6Q07
 | | MERS-CoV S structure in complex with 2,6-sialyl-N-acetyl-lactosamine | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, FOLIC ACID, ... | | Authors: | Park, Y.J, Walls, A.C, Wang, Z, Sauer, M, Li, W, Tortorici, M.A, Bosch, B.J, DiMaio, F.D, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID) | | Deposit date: | 2019-08-01 | | Release date: | 2019-12-11 | | Last modified: | 2020-07-29 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors.
Nat.Struct.Mol.Biol., 26, 2019
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5UZB
 | | Cryo-EM structure of the MAL TIR domain filament | | Descriptor: | Toll/interleukin-1 receptor domain-containing adapter protein | | Authors: | Ve, T, Vajjhala, P.R, Hedger, A, Croll, T, DiMaio, F, Horsefield, S, Yu, X, Lavrencic, P, Hassan, Z, Morgan, G.P, Mansell, A, Mobli, M, O'Carrol, A, Chauvin, B, Gambin, Y, Sierecki, E, Landsberg, M.J, Stacey, K.J, Egelman, E.H, Kobe, B. | | Deposit date: | 2017-02-25 | | Release date: | 2017-07-26 | | Last modified: | 2020-01-15 | | Method: | ELECTRON MICROSCOPY (7 Å) | | Cite: | Structural basis of TIR-domain-assembly formation in MAL- and MyD88-dependent TLR4 signaling.
Nat. Struct. Mol. Biol., 24, 2017
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6OG1
 | | Focus classification structure of the hyperactive ClpB mutant K476C, bound to casein, pre-state | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Hyperactive disaggregase ClpB, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER | | Authors: | Rizo, A.R, Lin, J.-B, Gates, S.N, Tse, E, Bart, S.M, Castellano, L.M, Dimaio, F, Shorter, J, Southworth, D.R. | | Deposit date: | 2019-04-01 | | Release date: | 2019-06-12 | | Last modified: | 2024-03-20 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural basis for substrate gripping and translocation by the ClpB AAA+ disaggregase.
Nat Commun, 10, 2019
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7JZV
 | | Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome | | Descriptor: | BRCA1,Ubiquitin-conjugating enzyme E2 D3, BRCA1-associated RING domain protein 1, Histone H2A type 2-A, ... | | Authors: | Witus, S.R, Burrell, A.L, Hansen, J.M, Farrell, D.P, Dimaio, F, Kollman, J.M, Klevit, R.E. | | Deposit date: | 2020-09-02 | | Release date: | 2021-02-17 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1.
Nat.Struct.Mol.Biol., 28, 2021
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5J0L
 | | De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity | | Descriptor: | designed protein 3L6HC2_2 | | Authors: | Sankaran, B, Zwart, P.H, Pereira, J.H, Baker, D, Boyken, S, Chen, Z, Groves, B, Langan, R.A, Oberdorfer, G, Ford, A, Gilmore, J, Xu, C, DiMaio, F, Seelig, G. | | Deposit date: | 2016-03-28 | | Release date: | 2016-07-06 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (2.63 Å) | | Cite: | De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.
Science, 352, 2016
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8W22
 | | Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1) | | Descriptor: | Intein C-terminal splicing domain-containing protein, Secreted esterase, Secreted protein | | Authors: | Park, Y.J, Zhao, Q, Seattle Structural Genomics Center for Infectious Disease (SSGCID), DiMaio, F, Mougous, J.D, Veesler, D. | | Deposit date: | 2024-02-19 | | Release date: | 2024-04-17 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (4 Å) | | Cite: | Streptomyces umbrella toxin particles block hyphal growth of competing species.
Nature, 629, 2024
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6OR5
 | | Full-length S. pombe Mdn1 in the presence of AMPPNP (ring region) | | Descriptor: | Midasin, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER | | Authors: | Chen, Z, Suzuki, H, Wang, A.C, DiMaio, F, Walz, T, Kapoor, T.M. | | Deposit date: | 2019-04-29 | | Release date: | 2019-05-29 | | Last modified: | 2024-03-13 | | Method: | ELECTRON MICROSCOPY (4 Å) | | Cite: | Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis.
Cell, 175, 2018
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5J73
 | | De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity | | Descriptor: | protein design 2L4HC2_9 | | Authors: | Sankaran, B, Zwart, P.H, Pereira, J.H, Baker, D, Boyken, S, Chen, Z, Groves, B, Langan, R.A, Oberdorfer, G, Ford, A, Gilmore, J, Xu, C, DiMaio, F, Seelig, G. | | Deposit date: | 2016-04-05 | | Release date: | 2016-05-25 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (2.56 Å) | | Cite: | De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.
Science, 352, 2016
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6VPT
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7RNR
 | | Yeast CTP Synthase (Ura8) Bundle Bound to Substrates at Low pH | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, CTP synthase, MAGNESIUM ION, ... | | Authors: | Hansen, J.M, Lynch, E.M, Farrell, D.P, DiMaio, F, Quispe, J, Kollman, J.M. | | Deposit date: | 2021-07-29 | | Release date: | 2021-11-24 | | Last modified: | 2024-06-05 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation.
Elife, 10, 2021
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7RMC
 | | Yeast CTP Synthase (Ura7) filament bound to CTP at low pH | | Descriptor: | CTP synthase 1, CYTIDINE-5'-TRIPHOSPHATE | | Authors: | Hansen, J.M, Lynch, E.M, Farrell, D.P, DiMaio, F, Quispe, J, Kollman, J.M. | | Deposit date: | 2021-07-27 | | Release date: | 2021-11-24 | | Last modified: | 2024-06-05 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation.
Elife, 10, 2021
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7RMO
 | | Yeast CTP Synthase (Ura7) Bundle bound to Products at low pH | | Descriptor: | CTP synthase, CYTIDINE-5'-TRIPHOSPHATE | | Authors: | Hansen, J.M, Lynch, E.M, Farrell, D.P, DiMaio, F, Quispe, J, Kollman, J.M. | | Deposit date: | 2021-07-27 | | Release date: | 2021-11-24 | | Last modified: | 2024-06-05 | | Method: | ELECTRON MICROSCOPY (7 Å) | | Cite: | Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation.
Elife, 10, 2021
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5J0J
 | | De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity | | Descriptor: | designed protein 2L6HC3_6 | | Authors: | Sankaran, B, Zwart, P.H, Pereira, J.H, Baker, D, Boyken, S, Chen, Z, Groves, B, Langan, R.A, Oberdorfer, G, Ford, A, Gilmore, J, Xu, C, DiMaio, F, Seelig, G. | | Deposit date: | 2016-03-28 | | Release date: | 2016-05-25 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (2.256 Å) | | Cite: | De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.
Science, 352, 2016
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5V4S
 | | CryoEM Structure of a Prokaryotic Cyclic Nucleotide-Gated Ion Channel | | Descriptor: | Transporter, cation channel family / cyclic nucleotide-binding domain multi-domain protein | | Authors: | James, Z.M, Borst, A.J, Haitin, Y, Frenz, B, DiMaio, F, Zagotta, W.N, Veesler, D. | | Deposit date: | 2017-03-10 | | Release date: | 2017-04-12 | | Last modified: | 2024-03-13 | | Method: | ELECTRON MICROSCOPY (4.2 Å) | | Cite: | CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel.
Proc. Natl. Acad. Sci. U.S.A., 114, 2017
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5J0I
 | | De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity | | Descriptor: | Designed protein 2L6HC3_12 | | Authors: | Sankaran, B, Zwart, P.H, Pereira, J.H, Baker, D, Boyken, S, Chen, Z, Groves, B, Langan, R.A, Oberdorfer, G, Ford, A, Gilmore, J, Xu, C, DiMaio, F, Seelig, G. | | Deposit date: | 2016-03-28 | | Release date: | 2016-05-25 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (2.202 Å) | | Cite: | De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.
Science, 352, 2016
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