3QHT
 
 | | Crystal Structure of the Monobody ySMB-1 bound to yeast SUMO | | Descriptor: | GLYCEROL, Monobody ySMB-1, Ubiquitin-like protein SMT3 | | Authors: | Koide, S, Gilbreth, R.N. | | Deposit date: | 2011-01-26 | | Release date: | 2011-05-11 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design.
Proc.Natl.Acad.Sci.USA, 108, 2011
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8EZG
 | | Monobody 12D1 bound to KRAS(G12D) | | Descriptor: | GTPase KRas, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Hattori, T, Glasser, E, Akkapeddi, P, Ketavarapu, G, Teng, K.W, Koide, A, Koide, S. | | Deposit date: | 2022-10-31 | | Release date: | 2023-07-19 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.52 Å) | | Cite: | Exploring switch II pocket conformation of KRAS(G12D) with mutant-selective monobody inhibitors.
Proc.Natl.Acad.Sci.USA, 120, 2023
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8F0M
 | | Monobody 12D5 bound to KRAS(G12D) | | Descriptor: | 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE, GUANOSINE-5'-DIPHOSPHATE, Isoform 2B of GTPase KRas, ... | | Authors: | Hattori, T, Glasser, E, Akkapeddi, P, Ketavarapu, G, Teng, K.W, Koide, A, Koide, S. | | Deposit date: | 2022-11-03 | | Release date: | 2023-07-19 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.44 Å) | | Cite: | Exploring switch II pocket conformation of KRAS(G12D) with mutant-selective monobody inhibitors.
Proc.Natl.Acad.Sci.USA, 120, 2023
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5G15
 | | Structure Aurora A (122-403) bound to activating monobody Mb1 and AMPPCP | | Descriptor: | AURORA A KINASE, MAGNESIUM ION, MB1 MONOBODY, ... | | Authors: | Zorba, A, Kutter, S, Kern, D, Koide, S, Koide, A. | | Deposit date: | 2016-03-23 | | Release date: | 2018-03-14 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (2.06 Å) | | Cite: | Allosteric modulation of a human protein kinase with monobodies.
Proc.Natl.Acad.Sci.USA, 116, 2019
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2QBW
 | | The crystal structure of PDZ-Fibronectin fusion protein | | Descriptor: | PDZ-Fibronectin fusion protein, Polypeptide | | Authors: | Huang, J, Makabe, K, Koide, A, Koide, S. | | Deposit date: | 2007-06-18 | | Release date: | 2008-04-22 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Design of protein function leaps by directed domain interface evolution.
Proc.Natl.Acad.Sci.Usa, 105, 2008
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9O55
 | | Structure of a synthetic antibody (RM010) in complex with a class I MHC presenting a hapten-peptide conjugate | | Descriptor: | GTPase KRas, N-terminally processed, MHC class I antigen, ... | | Authors: | Hu, Z, Rajak, E, Maso, L, Koide, S. | | Deposit date: | 2025-04-09 | | Release date: | 2025-07-23 | | Method: | ELECTRON MICROSCOPY (2.88 Å) | | Cite: | Generation of actionable, cancer-specific neoantigens from KRAS(G12C) with adagrasib
To Be Published
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2AF5
 | | 2.5A X-ray Structure of Engineered OspA protein | | Descriptor: | Engineered Outer Surface Protein A (OspA) with the inserted two beta-hairpins | | Authors: | Makabe, K, Mcelheny, D, Tereshko, V, Hilyard, A, Koide, A, Koide, S. | | Deposit date: | 2005-07-25 | | Release date: | 2006-08-01 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Atomic structures of peptide self-assembly mimics.
Proc.Natl.Acad.Sci.Usa, 103, 2006
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7JW7
 | | Structure of monobody 27 human MLKL pseudokinase domain complex | | Descriptor: | Mixed lineage kinase domain-like protein, Monobody 27 | | Authors: | Meng, Y, Garnish, S.E, Koide, A, Koide, S, Czabotar, P.E, Murphy, J.M. | | Deposit date: | 2020-08-25 | | Release date: | 2021-03-10 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.63 Å) | | Cite: | Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis.
Nat Commun, 12, 2021
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7JXU
 | | Structure of monobody 32 human MLKL pseudokinase domain complex | | Descriptor: | 1,2-ETHANEDIOL, Mixed lineage kinase domain-like protein, Monobody 32 | | Authors: | Meng, Y, Garnish, S.E, Koide, A, Koide, S, Czabotar, P.E, Murphy, J.M. | | Deposit date: | 2020-08-28 | | Release date: | 2021-03-10 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.44 Å) | | Cite: | Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis.
Nat Commun, 12, 2021
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6D0N
 | | Crystal structure of a CLC-type fluoride/proton antiporter, V319G mutant | | Descriptor: | (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID, CLC-type fluoride/proton antiporter, DECYL-BETA-D-MALTOPYRANOSIDE, ... | | Authors: | Last, N.B, Stockbridge, R.B, Wilson, A.E, Shane, T, Kolmakova-Partensky, L, Koide, A, Koide, S, Miller, C. | | Deposit date: | 2018-04-10 | | Release date: | 2018-07-04 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (3.12 Å) | | Cite: | A CLC-type F-/H+antiporter in ion-swapped conformations.
Nat. Struct. Mol. Biol., 25, 2018
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6D0K
 | | Crystal structure of a CLC-type fluoride/proton antiporter, E118Q mutant | | Descriptor: | (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID, CLC-type fluoride/proton antiporter, DECYL-BETA-D-MALTOPYRANOSIDE, ... | | Authors: | Last, N.B, Stockbridge, R.B, Wilson, A.E, Shane, T, Kolmakova-Partensky, L, Koide, A, Koide, S, Miller, C. | | Deposit date: | 2018-04-10 | | Release date: | 2018-07-04 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (3.35 Å) | | Cite: | A CLC-type F-/H+antiporter in ion-swapped conformations.
Nat. Struct. Mol. Biol., 25, 2018
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6D0J
 | | Crystal structure of a CLC-type fluoride/proton antiporter | | Descriptor: | (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID, CLC-type fluoride/proton antiporter, DECYL-BETA-D-MALTOPYRANOSIDE, ... | | Authors: | Last, N.B, Stockbridge, R.B, Wilson, A.E, Shane, T, Kolmakova-Partensky, L, Koide, A, Koide, S, Miller, C. | | Deposit date: | 2018-04-10 | | Release date: | 2018-07-04 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | A CLC-type F-/H+antiporter in ion-swapped conformations.
Nat. Struct. Mol. Biol., 25, 2018
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3UYO
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5WOB
 | | Crystal Structure Analysis of Fab1-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Insulin | | Descriptor: | IDE-bound Fab heavy chain, IDE-bound Fab light chain, Insulin, ... | | Authors: | McCord, L.A, Liang, W.G, Farcasanu, M, Wang, A.G, Koide, S, Tang, W.J. | | Deposit date: | 2017-08-01 | | Release date: | 2018-04-18 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (3.95 Å) | | Cite: | Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme.
Elife, 7, 2018
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5KVM
 | | Extracellular region of mouse GPR56/ADGRG1 in complex with FN3 monobody | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Adhesion G-protein coupled receptor G1, ... | | Authors: | Salzman, G.S, Ding, C, Koide, S, Arac, D. | | Deposit date: | 2016-07-14 | | Release date: | 2016-09-28 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (2.449 Å) | | Cite: | Structural Basis for Regulation of GPR56/ADGRG1 by Its Alternatively Spliced Extracellular Domains.
Neuron, 91, 2016
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5V7P
 | | Atomic structure of the eukaryotic intramembrane Ras methyltransferase ICMT (isoprenylcysteine carboxyl methyltransferase), in complex with a monobody | | Descriptor: | DECANE, Protein-S-isoprenylcysteine O-methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, ... | | Authors: | Long, S.B, Diver, M.M, Pedi, L, Koide, A, Koide, S. | | Deposit date: | 2017-03-20 | | Release date: | 2018-01-17 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT.
Nature, 553, 2018
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5VG9
 | | Structure of the eukaryotic intramembrane Ras methyltransferase ICMT (isoprenylcysteine carboxyl methyltransferase) without a monobody | | Descriptor: | Protein-S-isoprenylcysteine O-methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE | | Authors: | Long, S.B, Diver, M.M, Pedi, L, Koide, A, Koide, S. | | Deposit date: | 2017-04-10 | | Release date: | 2018-01-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (4 Å) | | Cite: | Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT.
Nature, 553, 2018
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2R8S
 | | High resolution structure of a specific synthetic FAB bound to P4-P6 RNA ribozyme domain | | Descriptor: | Fab heavy chain, Fab light chain, MAGNESIUM ION, ... | | Authors: | Ye, J.D, Tereshko, V, Sidhu, S.S, Koide, S, Kossiakoff, A.A, Piccirilli, J.A. | | Deposit date: | 2007-09-11 | | Release date: | 2007-12-04 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Synthetic antibodies for specific recognition and crystallization of structured RNA
Proc.Natl.Acad.Sci.Usa, 105, 2008
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8VQD
 | | HER2 S310F in complex with TL1 Fab | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Receptor tyrosine-protein kinase erbB-2/hIgG1 Fc domain fusion, Variable Heavy chain of TL1 Fab, ... | | Authors: | Bang, I, Koide, S. | | Deposit date: | 2024-01-18 | | Release date: | 2024-10-09 | | Last modified: | 2025-05-14 | | Method: | ELECTRON MICROSCOPY (2.61 Å) | | Cite: | Selective targeting of oncogenic hotspot mutations of the HER2 extracellular domain.
Nat.Chem.Biol., 21, 2025
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8VQE
 | | Homodimeric structure of HER2 S310F extracellular region | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Receptor tyrosine-protein kinase erbB-2/hIgG1 Fc domain fusion | | Authors: | Bang, I, Koide, S. | | Deposit date: | 2024-01-18 | | Release date: | 2024-11-06 | | Last modified: | 2025-05-14 | | Method: | ELECTRON MICROSCOPY (2.67 Å) | | Cite: | Selective targeting of oncogenic hotspot mutations of the HER2 extracellular domain.
Nat.Chem.Biol., 21, 2025
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5A43
 | | Crystal structure of a dual topology fluoride ion channel. | | Descriptor: | DECYL-BETA-D-MALTOPYRANOSIDE, FLUORIDE ION, MONOBODIES, ... | | Authors: | Stockbridge, R.B, Kolmakova-Partensky, L, Shane, T, Koide, A, Koide, S, Miller, C, Newstead, S. | | Deposit date: | 2015-06-04 | | Release date: | 2015-09-02 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (2.58 Å) | | Cite: | Crystal Structures of a Double-Barrelled Fluoride Ion Channel.
Nature, 525, 2015
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5A40
 | | Crystal structure of a dual topology fluoride ion channel. | | Descriptor: | MERCURY (II) ION, MONOBODIES, PUTATIVE FLUORIDE ION TRANSPORTER CRCB | | Authors: | Stockbridge, R.B, Kolmakova-Partensky, L, Shane, T, Koide, A, Koide, S, Miller, C, Newstead, S. | | Deposit date: | 2015-06-04 | | Release date: | 2015-09-02 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (3.6 Å) | | Cite: | Crystal Structures of a Double-Barrelled Fluoride Ion Channel.
Nature, 525, 2015
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6CPG
 | | Structure of dephosphorylated Aurora A (122-403) in complex with inhibiting monobody and AT9283 in an inactive conformation | | Descriptor: | 1-cyclopropyl-3-{3-[5-(morpholin-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl}urea, Aurora kinase A, Monobody | | Authors: | Otten, R, Kutter, S, Zorba, A, Padua, R.A.P, Koide, A, Koide, S, Kern, D. | | Deposit date: | 2018-03-13 | | Release date: | 2018-06-27 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Dynamics of human protein kinase Aurora A linked to drug selectivity.
Elife, 7, 2018
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8TTF
 | | NorA double mutant - E222QD307N at pH 7.5 | | Descriptor: | Heavy Chain of FabDA1 Variable Domain, Light Chain of FabDA1 Variable Domain, Quinolone resistance protein NorA | | Authors: | Li, J.P, Li, Y, Koide, A, Kuang, H.H, Torres, V.J, Koide, S, Wang, D.N, Traaseth, N.J. | | Deposit date: | 2023-08-13 | | Release date: | 2024-05-29 | | Last modified: | 2025-05-21 | | Method: | ELECTRON MICROSCOPY (3.61 Å) | | Cite: | Proton-coupled transport mechanism of the efflux pump NorA.
Nat Commun, 15, 2024
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8TTH
 | | NorA single mutant - D307N at pH 7.5 | | Descriptor: | Heavy Chain of FabDA1 Variable Domain, Light Chain of FabDA1 Variable Domain, Quinolone resistance protein NorA | | Authors: | Li, J.P, Li, Y, Koide, A, Kuang, H.H, Torres, V.J, Koide, S, Wang, D.N, Traaseth, N.J. | | Deposit date: | 2023-08-13 | | Release date: | 2024-05-29 | | Last modified: | 2025-06-04 | | Method: | ELECTRON MICROSCOPY (3.54 Å) | | Cite: | Proton-coupled transport mechanism of the efflux pump NorA.
Nat Commun, 15, 2024
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