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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Jakana, J."

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Search Summary

This query matches 24 Structures.

Refinements

Structure Determination Methodology

experimental (24)

Scientific Name of Source Organism

	Methanococcus maripaludis (9)
	Bos taurus (4)
	Brome mosaic virus (3)
	Lederbergvirus P22 (3)
	Barmah Forest virus (1)
	Mycobacterium tuberculosis (1)
	Salmonella phage epsilon15 (1)
	Singapore grouper iridovirus (1)
	Streptomyces californicus (1)
	Venezuelan equine encephalitis virus (strain TC-83) (1)

Taxonomy

	Archaea (9)
	Riboviria (5)
	Duplodnaviria (4)
	Eukaryota (4)
	Bacteria (1)
	Varidnaviria (1)

Experimental Method

ELECTRON MICROSCOPY (24)

Polymer Entity Type

	Protein (24)
	RNA (1)

Refinement Resolution (Å)

	3.0 - 3.5 (1)
	3.5 - 4.0 (4)
	4.0 - 4.5 (3)
	> 4.5 (16)

Release Date

	2010 - 2014 (21)
	2015 - 2019 (3)

Enzyme Classification Name

Hydrolases (2)

Membrane Protein Annotation

	OPM (2)
	PDBTM (2)

Symmetry Type

	Dihedral (10)
	Icosahedral (9)
	Cyclic (3)
	Asymmetric (2)

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1 to 24 of 24 Structures

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2XYY \| pdb_00002xyy	Download File View File

De Novo model of Bacteriophage P22 procapsid coat protein

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.

(2011) Proc Natl Acad Sci U S A 108: 1355

Released	2011-02-02
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Lederbergvirus P22
Macromolecule	COAT PROTEIN (protein)

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2XYZ \| pdb_00002xyz	Download File View File

De Novo model of Bacteriophage P22 virion coat protein

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.

(2011) Proc Natl Acad Sci U S A 108: 1355

Released	2011-02-02
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Lederbergvirus P22
Macromolecule	COAT PROTEIN (protein)

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2YEW \| pdb_00002yew	Download File View File

Modeling Barmah Forest virus structural proteins

Kostyuchenko, V.A., Jakana, J., Liu, X., Haddow, A.D., Aung, M., Weaver, S.C., Chiu, W., Lok, S.M.

(2011) J Virol 85: 9327

Released	2012-04-18
Method	ELECTRON MICROSCOPY 5 Å
Organisms	Barmah Forest virus
Macromolecule	CAPSID PROTEIN (protein) E1 ENVELOPE GLYCOPROTEIN (protein) E2 ENVELOPE GLYCOPROTEIN (protein)

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3IYF \| pdb_00003iyf	Download File View File

Atomic Model of the Lidless Mm-cpn in the Open State

Zhang, J., Baker, M.L., Schroeder, G., Douglas, N.R., Reissmann, S., Jakana, J., Dougherty, M., Fu, C.J., Levitt, M., Ludtke, S.J., Frydman, J., Chiu, W.

(2010) Nature 463: 379-383

Released	2010-02-02
Method	ELECTRON MICROSCOPY 8 Å
Organisms	Methanococcus maripaludis
Macromolecule	Chaperonin (protein)

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3IZH \| pdb_00003izh	Download File View File

Mm-cpn D386A with ATP

Douglas, N.R., Reissmann, S., Zhang, J., Chen, B., Jakana, J., Kumar, R., Chiu, W., Frydman, J.

(2011) Cell 144: 240-252

Released	2011-02-02
Method	ELECTRON MICROSCOPY 11 Å
Organisms	Methanococcus maripaludis
Macromolecule	Chaperonin (protein)

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3IZI \| pdb_00003izi	Download File View File

Mm-cpn rls with ATP

Douglas, N.R., Reissmann, S., Zhang, J., Chen, B., Jakana, J., Kumar, R., Chiu, W., Frydman, J.

(2011) Cell 144: 240-252

Released	2011-02-02
Method	ELECTRON MICROSCOPY 6.7 Å
Organisms	Methanococcus maripaludis
Macromolecule	Chaperonin (protein)

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3IZJ \| pdb_00003izj	Download File View File

Mm-cpn rls with ATP and AlFx

Douglas, N.R., Reissmann, S., Zhang, J., Chen, B., Jakana, J., Kumar, R., Chiu, W., Frydman, J.

(2011) Cell 144: 240-252

Released	2011-02-02
Method	ELECTRON MICROSCOPY 6.9 Å
Organisms	Methanococcus maripaludis
Macromolecule	Chaperonin (protein)

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3IZK \| pdb_00003izk	Download File View File

Mm-cpn rls deltalid with ATP

Douglas, N.R., Reissmann, S., Zhang, J., Chen, B., Jakana, J., Kumar, R., Chiu, W., Frydman, J.

(2011) Cell 144: 240-252

Released	2011-02-02
Method	ELECTRON MICROSCOPY 4.9 Å
Organisms	Methanococcus maripaludis
Macromolecule	Chaperonin (protein)

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3IZL \| pdb_00003izl	Download File View File

Mm-cpn rls deltalid with ATP and AlFx

Douglas, N.R., Reissmann, S., Zhang, J., Chen, B., Jakana, J., Kumar, R., Chiu, W., Frydman, J.

(2011) Cell 144: 240-252

Released	2011-02-02
Method	ELECTRON MICROSCOPY 6.2 Å
Organisms	Methanococcus maripaludis
Macromolecule	Mm-cpn rls deltalid (protein)

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3IZM \| pdb_00003izm	Download File View File

Mm-cpn wildtype with ATP

Douglas, N.R., Reissmann, S., Zhang, J., Chen, B., Jakana, J., Kumar, R., Chiu, W., Frydman, J.

(2011) Cell 144: 240-252

Released	2011-02-02
Method	ELECTRON MICROSCOPY 7.2 Å
Organisms	Methanococcus maripaludis
Macromolecule	Chaperonin (protein)

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3IZN \| pdb_00003izn	Download File View File

Mm-cpn deltalid with ATP

Douglas, N.R., Reissmann, S., Zhang, J., Chen, B., Jakana, J., Kumar, R., Chiu, W., Frydman, J.

(2011) Cell 144: 240-252

Released	2011-02-02
Method	ELECTRON MICROSCOPY 6.4 Å
Organisms	Methanococcus maripaludis
Macromolecule	Chaperonin (protein)

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3J0C \| pdb_00003j0c	Download File View File

Models of E1, E2 and CP of Venezuelan Equine Encephalitis Virus TC-83 strain restrained by a near atomic resolution cryo-EM map

Zhang, R., Hryc, C.F., Cong, Y., Liu, X., Jakana, J., Gorchakov, R., Baker, M.L., Weaver, S.C., Chiu, W.

(2011) EMBO J 30: 3854-3863

Released	2011-08-24
Method	ELECTRON MICROSCOPY 4.8 Å
Organisms	Venezuelan equine encephalitis virus (strain TC-83)
Macromolecule	Capsid protein (protein) E1 envelope glycoprotein (protein) E2 envelope glycoprotein (protein)

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3J40 \| pdb_00003j40	Download File View File

Validated Near-Atomic Resolution Structure of Bacteriophage Epsilon15 Derived from Cryo-EM and Modeling

Baker, M.L., Hryc, C.F., Zhang, Q., Wu, W., Jakana, J., Haase-Pettingell, C., Afonine, P.V., Adams, P.D., King, J.A., Jiang, W., Chiu, W.

(2013) Proc Natl Acad Sci U S A 110: 12301-12306

Released	2013-07-10
Method	ELECTRON MICROSCOPY 4.5 Å
Organisms	Salmonella phage epsilon15
Macromolecule	gp10 (protein) gp7 (protein)

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3J7L \| pdb_00003j7l	Download File View File

Full virus map of brome mosaic virus

Wang, Z., Hryc, C., Bammes, B., Afonine, P.V., Jakana, J., Chen, D.H., Liu, X., Baker, M.L., Kao, C., Ludtke, S.J., Schmid, M.F., Adams, P.D., Chiu, W.

(2014) Nat Commun 5: 4808-4808

Released	2014-09-10
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Brome mosaic virus
Macromolecule	Capsid protein (protein)

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3J7M \| pdb_00003j7m	Download File View File

Virus model of brome mosaic virus (first half data set)

Wang, Z., Hryc, C., Bammes, B., Afonine, P.V., Jakana, J., Chen, D.H., Liu, X., Baker, M.L., Kao, C., Ludtke, S.J., Schmid, M.F., Adams, P.D., Chiu, W.

(2014) Nat Commun 5: 4808-4808

Released	2014-09-10
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Brome mosaic virus
Macromolecule	Capsid protein (protein)

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3J7N \| pdb_00003j7n	Download File View File

Virus model of brome mosaic virus (second half data set)

Wang, Z., Hryc, C., Bammes, B., Afonine, P.V., Jakana, J., Chen, D.H., Liu, X., Baker, M.L., Kao, C., Ludtke, S.J., Schmid, M.F., Adams, P.D., Chiu, W.

(2014) Nat Commun 5: 4808-4808

Released	2014-09-10
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Brome mosaic virus
Macromolecule	Capsid protein (protein)

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3LOS \| pdb_00003los	Download File View File

Atomic Model of Mm-cpn in the Closed State

Zhang, J., Baker, M.L., Schroeder, G., Douglas, N.R., Reissmann, S., Jakana, J., Dougherty, M., Fu, C.J., Levitt, M., Ludtke, S.J., Frydman, J., Chiu, W.

(2010) Nature 463: 379-383

Released	2010-03-16
Method	ELECTRON MICROSCOPY 4.3 Å
Organisms	Methanococcus maripaludis
Macromolecule	Chaperonin (protein)

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4A0O \| pdb_00004a0o	Download File View File

Symmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state

Cong, Y., Schroder, G.F., Meyer, A.S., Jakana, J., Ma, B., Dougherty, M.T., Schmid, M.F., Reissmann, S., Levitt, M., Ludtke, S.L., Frydman, J., Chiu, W.

(2012) EMBO J 31: 720

Released	2012-02-15
Method	ELECTRON MICROSCOPY 10.5 Å
Organisms	Bos taurus
Macromolecule	T-COMPLEX PROTEIN 1 SUBUNIT BETA (protein)

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4A0V \| pdb_00004a0v	Download File View File

model refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP

Cong, Y., Schroder, G.F., Meyer, A.S., Jakana, J., Ma, B., Dougherty, M.T., Schmid, M.F., Reissmann, S., Levitt, M., Ludtke, S.L., Frydman, J., Chiu, W.

(2012) EMBO J 31: 720

Released	2012-02-15
Method	ELECTRON MICROSCOPY 10.7 Å
Organisms	Bos taurus
Macromolecule	T-COMPLEX PROTEIN 1 SUBUNIT BETA (protein)

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4A0W \| pdb_00004a0w	Download File View File

model built against symmetry-free cryo-EM map of TRiC-ADP-AlFx

Cong, Y., Schroder, G.F., Meyer, A.S., Jakana, J., Ma, B., Dougherty, M.T., Schmid, M.F., Reissmann, S., Levitt, M., Ludtke, S.L., Frydman, J., Chiu, W.

(2012) EMBO J 31: 720

Released	2012-02-15
Method	ELECTRON MICROSCOPY 13.9 Å
Organisms	Bos taurus
Macromolecule	T-COMPLEX PROTEIN 1 SUBUNIT BETA (protein)

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4A13 \| pdb_00004a13	Download File View File

model refined against symmetry-free cryo-EM map of TRiC-ADP

Cong, Y., Schroder, G.F., Meyer, A.S., Jakana, J., Ma, B., Dougherty, M.T., Schmid, M.F., Reissmann, S., Levitt, M., Ludtke, S.L., Frydman, J., Chiu, W.

(2012) EMBO J 31: 720

Released	2012-02-15
Method	ELECTRON MICROSCOPY 11.3 Å
Organisms	Bos taurus
Macromolecule	T-COMPLEX PROTEIN 1 SUBUNIT BETA (protein)

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5UU5 \| pdb_00005uu5	Download File View File

Bacteriophage P22 mature virion capsid protein

Hryc, C.F., Chen, D.-H., Afonine, P.V., Jakana, J., Wang, Z., Haase-Pettingell, C., Jiang, W., Adams, P.D., King, J.A., Schmid, M.F., Chiu, W.

(2017) Proc Natl Acad Sci U S A 114: 3103-3108

Released	2017-03-15
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Lederbergvirus P22
Macromolecule	Major capsid protein (protein)

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5V93 \| pdb_00005v93	Download File View File

Cryo-EM structure of the 70S ribosome from Mycobacterium tuberculosis bound with Capreomycin

Yang, K., Chang, J.-Y., Cui, Z., Li, X., Meng, R., Duan, L., Thongchol, J., Jakana, J., Huwe, C., Sacchettini, J., Zhang, J.

(2017) Nucleic Acids Res 45: 10884-10894

Released	2017-09-20
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Mycobacterium tuberculosis Streptomyces californicus
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 3