Author results

3J3X
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INDEPENDENT RECONSTRUCTION OF MM-CPN CRYO-EM DENSITY MAP FROM HALF DATASET IN THE CLOSED STATE (TRAINING MAP)
Descriptor:Chaperonin
Authors:DiMaio, F., Zhang, J., Chiu, W., Baker, D.
Deposit date:2013-05-02
Release date:2013-05-29
Modification date:2013-06-12
Method:ELECTRON MICROSCOPY (4.3 Å)
Cite:Cryo-EM model validation using independent map reconstructions.
Protein Sci., 22, 2013
3J9X
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A VIRUS THAT INFECTS A HYPERTHERMOPHILE ENCAPSIDATES A-FORM DNA
Descriptor:coat protein
Authors:DiMaio, F., Yu, X., Rensen, E., Krupovic, M., Prangishvili, D., Egelman, E.
Deposit date:2015-03-21
Release date:2015-06-03
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:A virus that infects a hyperthermophile encapsidates A-form DNA.
Science, 348, 2015
5A2T
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THE MOLECULAR BASIS FOR FLEXIBILITY IN THE FLEXIBLE FILAMENTOUS PLANT VIRUSES
Descriptor:COAT PROTEIN
Authors:DiMaio, F., Chen, C.C., Yu, X., Frenz, B., Hsu, Y.H., Lin, N.S., Egelman, E.H.
Deposit date:2015-05-23
Release date:2015-07-22
Modification date:2015-08-19
Method:ELECTRON MICROSCOPY (5.6 Å)
Cite:The Molecular Basis for Flexibility in the Flexible Filamentous Plant Viruses.
Nat.Struct.Mol.Biol., 22, 2015
5CW9
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CRYSTAL STRUCTURE OF DE NOVO DESIGNED FERREDOXIN-FERREDOXIN DOMAIN INSERTION PROTEIN
Descriptor:De novo designed ferredoxin-ferredoxin domain insertion protein
Authors:DiMaio, F., King, I.C., Gleixner, J., Doyle, L., Stoddard, B., Baker, D.
Deposit date:2015-07-28
Release date:2015-09-23
Modification date:2015-12-23
Method:X-RAY DIFFRACTION (3.108 Å)
Cite:Precise assembly of complex beta sheet topologies from de novo designed building blocks.
Elife, 4, 2015
3SQF
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CRYSTAL STRUCTURE OF MONOMERIC M-PMV RETROVIRAL PROTEASE
Descriptor:Protease (E.C.3.4.23.-)
Authors:Jaskolski, M., Kazmierczyk, M., Gilski, M., Krzywda, S., Pichova, I., Zabranska, H., Khatib, F., DiMaio, F., Cooper, S., Thompson, J., Popovic, Z., Baker, D., Group, Foldit Contenders
Deposit date:2011-07-05
Release date:2011-09-21
Modification date:2012-03-21
Method:X-RAY DIFFRACTION (1.6324 Å)
Cite:Crystal structure of a monomeric retroviral protease solved by protein folding game players.
Nat.Struct.Mol.Biol., 18, 2011
4RZP
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CRYSTAL STRUCTURE OF ENGINEERED PROTEIN. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET OR366.
Descriptor:Engineered Protein OR366
Authors:Vorobiev, S., Parmeggiani, F., Dimaio, F., Seetharaman, J., Sahdev, S., Xiao, R., Kogan, S., Everett, J.K., Acton, T.B., Baker, D., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)
Deposit date:2014-12-23
Release date:2015-01-07
Modification date:2015-03-04
Method:X-RAY DIFFRACTION (2.804 Å)
Cite:Crystal Structure of Engineered Protein OR366
To be Published
2XYY
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DE NOVO MODEL OF BACTERIOPHAGE P22 PROCAPSID COAT PROTEIN
Descriptor:COAT PROTEIN
Authors:Chen, D.-H., Baker, M.L., Hryc, C.F., DiMaio, F., Jakana, J., Wu, W., Dougherty, M., Haase-Pettingell, C., Schmid, M.F., Jiang, W., Baker, D., King, J.A., Chiu, W.
Deposit date:2010-11-19
Release date:2011-02-02
Modification date:2011-02-09
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:Structural Basis for Scaffolding-Mediated Assembly and Maturation of a DsDNA Virus.
Proc.Natl.Acad.Sci.USA, 108, 2011
2XYZ
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DE NOVO MODEL OF BACTERIOPHAGE P22 VIRION COAT PROTEIN
Descriptor:COAT PROTEIN
Authors:Chen, D.-H., Baker, M.L., Hryc, C.F., DiMaio, F., Jakana, J., Wu, W., Dougherty, M., Haase-Pettingell, C., Schmid, M.F., Jiang, W., Baker, D., King, J.A., Chiu, W.
Deposit date:2010-11-19
Release date:2011-02-02
Modification date:2011-02-09
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Structural Basis for Scaffolding-Mediated Assembly and Maturation of a DsDNA Virus.
Proc.Natl.Acad.Sci.USA, 108, 2011
3J02
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LIDLESS D386A MM-CPN IN THE PRE-HYDROLYSIS ATP-BOUND STATE
Descriptor:Lidless D386A Mm-cpn variant
Authors:Zhang, J., Ma, B., DiMaio, F., Douglas, N.R., Joachimiak, L., Baker, D., Frydman, J., Levitt, M., Chiu, W.
Deposit date:2011-02-10
Release date:2011-05-18
Modification date:2012-03-21
Method:ELECTRON MICROSCOPY (8 Å)
Cite:Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.
Structure, 19, 2011
3J03
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LIDLESS MM-CPN IN THE CLOSED STATE WITH ATP/ALFX
Descriptor:Lidless Mm-cpn
Authors:Zhang, J., Ma, B., DiMaio, F., Douglas, N.R., Joachimiak, L., Baker, D., Frydman, J., Levitt, M., Chiu, W.
Deposit date:2011-02-10
Release date:2011-05-18
Modification date:2012-03-21
Method:ELECTRON MICROSCOPY (4.8 Å)
Cite:Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.
Structure, 19, 2011
3J83
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HEPTAMERIC ESPB ROSETTA MODEL GUIDED BY EM DENSITY
Descriptor:ESX-1 secretion-associated protein EspB
Authors:Solomonson, M., DiMaio, F., Strynadka, N.C.J.
Deposit date:2014-09-30
Release date:2015-03-11
Modification date:2015-03-18
Method:ELECTRON MICROSCOPY (30 Å)
Cite:Structure of EspB from the ESX-1 Type VII Secretion System and Insights into its Export Mechanism.
Structure, 23, 2015
3J89
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STRUCTURAL PLASTICITY OF HELICAL NANOTUBES BASED ON COILED-COIL ASSEMBLIES
Descriptor:synthetic peptide
Authors:Egelman, E.H., Xu, C., DiMaio, F., Magnotti, E., Modlin, C., Yu, X., Wright, E., Baker, D., Conticello, V.P.
Deposit date:2014-10-07
Release date:2015-02-11
Modification date:2015-02-18
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Structural plasticity of helical nanotubes based on coiled-coil assemblies.
Structure, 23, 2015
3J9G
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ATOMIC MODEL OF THE VIPA/VIPB, THE TYPE SIX SECRETION SYSTEM CONTRACTILE SHEATH OF VIBRIO CHOLERAE FROM CRYO-EM
Descriptor:VipA, VipB
Authors:Kudryashev, M., Wang, R.Y.-R., Brackmann, M., Scherer, S., Maier, T., Baker, D., DiMaio, F., Stahlberg, H., Egelman, E.H., Basler, M.
Deposit date:2015-01-16
Release date:2015-03-11
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Structure of the Type VI Secretion System Contractile Sheath.
Cell(Cambridge,Mass.), 160, 2015
3J9J
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STRUCTURE OF THE CAPSAICIN RECEPTOR, TRPV1, DETERMINED BY SINGLE PARTICLE ELECTRON CRYO-MICROSCOPY
Descriptor:Transient receptor potential cation channel subfamily V member 1
Authors:Wang, R.Y.-R., Barad, B.A., Fraser, J.S., DiMaio, F.
Deposit date:2015-02-02
Release date:2015-09-02
Modification date:2015-10-14
Method:ELECTRON MICROSCOPY
Cite:EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.
Nat.Methods, 12, 2015
3JCL
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CRYO-ELECTRON MICROSCOPY STRUCTURE OF A CORONAVIRUS SPIKE GLYCOPROTEIN TRIMER
Descriptor:Spike glycoprotein
Authors:Walls, A.C., Tortorici, M.A., Bosch, B.J., Frenz, B., Rottier, P.J.M., DiMaio, F., Rey, F.A., Veesler, D.
Deposit date:2015-12-21
Release date:2016-02-03
Modification date:2016-03-09
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer.
Nature, 531, 2016
3NNG
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CRYSTAL STRUCTURE OF THE F5/8 TYPE C DOMAIN OF Q5LFR2_BACFN PROTEIN FROM BACTEROIDES FRAGILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BFR258E
Descriptor:uncharacterized protein
Authors:Vorobiev, S., Su, M., Dimaio, F., Baker, D., Seetharaman, J., Janjua, J., Xiao, R., Ciccosanti, C., Foote, E.L., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)
Deposit date:2010-06-23
Release date:2010-08-18
Method:X-RAY DIFFRACTION (2.177 Å)
Cite:Crystal structure of the F5/8 type C domain of Q5LFR2_BACFN protein from Bacteroides fragilis.
To be Published
4EQF
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TRIP8B-1A#206-567 INTERACTING WITH THE CARBOXY-TERMINAL SEVEN RESIDUES OF HCN2
Descriptor:PEX5-related protein, Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2
Authors:Bankston, J.R., Camp, S.S., Dimaio, F., Lewis, A.S., Chetkovich, D.M., Zagotta, W.N.
Deposit date:2012-04-18
Release date:2012-05-30
Method:X-RAY DIFFRACTION (3 Å)
Cite:Structure and stoichiometry of an accessory subunit TRIP8b interaction with hyperpolarization-activated cyclic nucleotide-gated channels.
Proc.Natl.Acad.Sci.USA, 109, 2012
4TQL
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COMPUTATIONALLY DESIGNED THREE HELIX BUNDLE
Descriptor:Three helix bundle
Authors:Nannenga, B.L., Oberdorfer, G., DiMaio, F., Baker, D., Gonen, T.
Deposit date:2014-06-11
Release date:2014-10-15
Modification date:2015-08-26
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:High thermodynamic stability of parametrically designed helical bundles.
Science, 346, 2014
5EC0
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CRYSTAL STRUCTURE OF ACTIN-LIKE PROTEIN ALP7A
Descriptor:Alp7A
Authors:Petek, N.A., Kraemer, J.A., Mullins, R.D., Agard, D.A., DiMaio, F., Baker, D.
Deposit date:2015-10-20
Release date:2016-11-02
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structure and function of Alp7A reveal both conserved and unique features of plasmid segregation.
To Be Published
5FLU
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STRUCTURE OF A CHAPERONE-USHER PILUS REVEALS THE MOLECULAR BASIS OF ROD UNCOILIN
Descriptor:PAP FIMBRIAL MAJOR PILIN PROTEIN
Authors:Hospenthal, M.K., Redzej, A., Dodson, K., Ukleja, M., Frenz, B., Hultgren, S.J., DiMaio, F., Egelman, E.H., Waksman, G.
Deposit date:2015-10-28
Release date:2016-01-13
Modification date:2016-01-27
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling.
Cell(Cambridge,Mass.), 164, 2016
5J0H
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DE NOVO DESIGN OF PROTEIN HOMO-OLIGOMERS WITH MODULAR HYDROGEN BOND NETWORK-MEDIATED SPECIFICITY
Descriptor:Design construct 2L6HC3_13
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
Method:X-RAY DIFFRACTION (1.64 Å)
Cite:De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.
Science, 352, 2016
5J0I
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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
Modification date:2016-07-20
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
5J0J
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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
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
5J0K
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DE NOVO DESIGN OF PROTEIN HOMO-OLIGOMERS WITH MODULAR HYDROGEN BOND NETWORK-MEDIATED SPECIFICITY
Descriptor:designed protein 2L4HC2_23
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
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.
Science, 352, 2016
5J0L
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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
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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