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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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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7TVJ
 | | Crystal Structure of Monobody Mb(SHP2PTP_13)/SHP2 PTP Domain Complex | | Descriptor: | CITRATE ANION, Mb(SHP2PTP_13), Tyrosine-protein phosphatase non-receptor type 11 | | Authors: | Sha, F, Koide, S. | | Deposit date: | 2022-02-05 | | Release date: | 2023-02-15 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.39 Å) | | Cite: | Monobody Inhibitor Selective to the Phosphatase Domain of SHP2 and its Use as a Probe for Quantifying SHP2 Allosteric Regulation.
J.Mol.Biol., 435, 2023
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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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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: | 2020-07-29 | | 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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4M1C
 | | Crystal Structure Analysis of Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Amyloid-Beta (1-40) | | Descriptor: | Amyloid beta A4 protein, Fab-bound IDE, heavy chain, ... | | Authors: | McCord, L.M, Liang, W, Farcasanu, M, Scherpelz, K, Meredith, S.C, Koide, S, Tang, W.J. | | Deposit date: | 2013-08-02 | | Release date: | 2014-08-06 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (3.5007 Å) | | Cite: | Crystal Structure Analysis of Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Amyloid-Beta (1-40)
To be Published
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2IQY
 | | Rat Phosphatidylethanolamine-Binding Protein | | Descriptor: | CALCIUM ION, CHLORIDE ION, Phosphatidylethanolamine-binding protein 1 | | Authors: | Kim, Y, Joachimiak, G, Heil, G.L, Koide, S, Joachimiak, A. | | Deposit date: | 2006-10-14 | | Release date: | 2007-09-25 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Crystal Structure of Rat Phosphatidylethanolamine-Binding Protein
To be Published
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2OCF
 | | Human estrogen receptor alpha ligand-binding domain in complex with estradiol and the E2#23 FN3 monobody | | Descriptor: | ESTRADIOL, Estrogen receptor, Fibronectin | | Authors: | Rajan, S.S, Kuruvilla, S.M, Sharma, S.K, Kim, Y, Huang, J, Koide, A, Koide, S, Joachimiak, A, Greene, G.L. | | Deposit date: | 2006-12-20 | | Release date: | 2007-11-06 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor.
Proc.Natl.Acad.Sci.USA, 99, 2002
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3UYO
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2KIR
 | | Solution structure of a designer toxin, mokatoxin-1 | | Descriptor: | Designer toxin | | Authors: | Biancalana, M, Koide, A, Takacs, Z, Goldstein, S, Koide, S. | | Deposit date: | 2009-05-07 | | Release date: | 2009-12-29 | | Last modified: | 2022-03-16 | | Method: | SOLUTION NMR | | Cite: | A designer ligand specific for Kv1.3 channels from a scorpion neurotoxin-based library.
Proc.Natl.Acad.Sci.USA, 106, 2009
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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: | 2023-10-04 | | 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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3T04
 | | Crystal structure of monobody 7c12/abl1 sh2 domain complex | | Descriptor: | GLYCEROL, MONOBODY 7C12, SULFATE ION, ... | | Authors: | Wojcik, J.B, Wyrzucki, A.M, Koide, S. | | Deposit date: | 2011-07-19 | | Release date: | 2011-11-23 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Targeting the SH2-Kinase Interface in Bcr-Abl Inhibits Leukemogenesis.
Cell(Cambridge,Mass.), 147, 2011
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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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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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7LO8
 | | NorA in complex with Fab36 | | Descriptor: | Fab36 Heavy Chain, Fab36 Light Chain, Quinolone resistance protein NorA | | Authors: | Brawley, D.N, Sauer, D.B, Song, J.M, Koide, A, Koide, S, Traaseth, N.J, Wang, D.N. | | Deposit date: | 2021-02-09 | | Release date: | 2022-04-20 | | Last modified: | 2022-07-13 | | Method: | ELECTRON MICROSCOPY (3.16 Å) | | Cite: | Structural basis for inhibition of the drug efflux pump NorA from Staphylococcus aureus.
Nat.Chem.Biol., 18, 2022
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7LO7
 | | NorA in complex with Fab25 | | Descriptor: | Fab25 Heavy Chain, Fab25 Light Chain, Quinolone resistance protein NorA | | Authors: | Brawley, D.N, Sauer, D.B, Song, J.M, Koide, A, Koide, S, Traaseth, N.J, Wang, D.N. | | Deposit date: | 2021-02-09 | | Release date: | 2022-04-20 | | Last modified: | 2022-07-13 | | Method: | ELECTRON MICROSCOPY (3.74 Å) | | Cite: | Structural basis for inhibition of the drug efflux pump NorA from Staphylococcus aureus.
Nat.Chem.Biol., 18, 2022
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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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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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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: | 2015-09-30 | | Method: | X-RAY DIFFRACTION (2.58 Å) | | Cite: | Crystal Structures of a Double-Barrelled Fluoride Ion Channel.
Nature, 525, 2015
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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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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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7KZX
 | | Cryo-EM structure of YiiP-Fab complex in Apo state | | Descriptor: | Cadmium and zinc efflux pump FieF, Fab2R heavy chain, Fab2R light chain | | Authors: | Lopez-Redondo, M.L, Fan, S, Koide, A, Koide, S, Beckstein, O, Stokes, D.L. | | Deposit date: | 2020-12-10 | | Release date: | 2021-01-06 | | Last modified: | 2021-07-28 | | Method: | ELECTRON MICROSCOPY (4 Å) | | Cite: | Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP.
J.Gen.Physiol., 153, 2021
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7KZZ
 | | Cryo-EM structure of YiiP-Fab complex in Holo state | | Descriptor: | Cadmium and zinc efflux pump FieF, Fab2R heavy chain, Fab2R light chain, ... | | Authors: | Lopez-Redondo, M.L, Fan, S, Koide, A, Koide, S, Beckstein, O, Stokes, D.L. | | Deposit date: | 2020-12-10 | | Release date: | 2021-01-06 | | Last modified: | 2021-07-28 | | Method: | ELECTRON MICROSCOPY (3.42 Å) | | Cite: | Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP.
J.Gen.Physiol., 153, 2021
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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 | | Method: | ELECTRON MICROSCOPY (3.61 Å) | | Cite: | NorA double mutant - E222QD307N at pH 7.5
To Be Published
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