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Showing all 50 items for author: chiu, & w

PDB-5w0s:
GroEL using cryoEM
Method: single particle / : Roh SH, Chiu W

PDB-5ng5:
multi-drug efflux; membrane transport; RND superfamily; Drug resistance
Method: single particle / : Wang Z, Fan G, Hryc CF, Blaza JN, Serysheva II, Schmid MF, Chiu W, Luisi BF, Du D

PDB-5v5s:
multi-drug efflux; membrane transport; RND superfamily; Drug resistance
Method: single particle / : wang Z, fan G, Hryc CF, Blaza JN, Serysheva II, Schmid MF, Chiu W, Luisi BF, Du D

PDB-5uu5:
Bacteriophage P22 mature virion capsid protein
Method: single particle / : Hryc CF, Chen DH, Afonine PV, Jakana J, Wang Z, Haase-Pettingell C, Jiang W, Adams PD, King JA, Schmid MF, Chiu W

PDB-5gai:
Probabilistic Structural Models of Mature P22 Bacteriophage Portal, Hub, and Tailspike proteins
Method: single particle / : Pintilie G, Chen DH, Haase-Pettingell CA, King JA, Chiu W

PDB-3jav:
Structure of full-length IP3R1 channel in the apo-state determined by single particle cryo-EM
Method: single particle / : Fan G, Baker ML, Wang Z, Baker MR, Sinyagovskiy PA, Chiu W, Ludtke SJ, Serysheva II

PDB-3j7v:
Capsid Expansion Mechanism Of Bacteriophage T7 Revealed By Multi-State Atomic Models Derived From Cryo-EM Reconstructions
Method: single particle / : Guo F, Liu Z, Fang PA, Zhang Q, Wright ET, Wu W, Zhang C, Vago F, Ren Y, Jakata J, Chiu W, Serwer P, Jiang W

PDB-3j7w:
Capsid Expansion Mechanism Of Bacteriophage T7 Revealed By Multi-State Atomic Models Derived From Cryo-EM Reconstructions
Method: single particle / : Guo F, Liu Z, Fang PA, Zhang Q, Wright ET, Wu W, Zhang C, Vago F, Ren Y, Jakata J, Chiu W, Serwer P, Jiang W

PDB-3j7x:
Capsid Expansion Mechanism Of Bacteriophage T7 Revealed By Multi-State Atomic Models Derived From Cryo-EM Reconstructions
Method: single particle / : Guo F, Liu Z, Fang PA, Zhang Q, Wright ET, Wu W, Zhang C, Vago F, Ren Y, Jakata J, Chiu W, Serwer P, Jiang W

PDB-3j7l:
Full virus map of brome mosaic virus
Method: single particle / : Wang Z, Hryc C, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W

PDB-3j7m:
Virus model of brome mosaic virus (first half data set)
Method: single particle / : Wang Z, Hryc C, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W

PDB-3j7n:
Virus model of brome mosaic virus (second half data set)
Method: single particle / : Wang Z, Hryc C, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W

PDB-4bml:
C-alpha backbone trace of major capsid protein gp39 found in marine virus Syn5.
Method: single particle / : Gipson P, Baker ML, Raytcheva D, Haase-Pettingell C, Piret J, King J, Chiu W

PDB-4chv:
The electron crystallography structure of the cAMP-bound potassium channel MloK1
Method: electron crystallography / : Kowal J, Chami M, Baumgartner P, Arheit M, Chiu PL, Rangl M, Scheuring S, Schroeder GF, Nimigean CM, Stahlberg H

PDB-4chw:
The electron crystallography structure of the cAMP-free potassium channel MloK1
Method: electron crystallography / : Kowal J, Chami M, Baumgartner P, Arheit M, Chiu PL, Rangl M, Scheuring S, Schroeder GF, Nimigean CM, Stahlberg H

PDB-3j40:
Validated Near-Atomic Resolution Structure of Bacteriophage Epsilon15 Derived from Cryo-EM and Modeling
Method: single particle / : Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C, Afonine PV, Adams PD, King JA, Jiang W, Chiu W

PDB-3zpz:
Visualizing GroEL-ES in the Act of Encapsulating a Non-Native Substrate Protein
Method: single particle / : Chen DH, Madan D, Weaver J, Lin Z, Schroder GF, Chiu W, Rye HS

PDB-3zq0:
Visualizing GroEL-ES in the Act of Encapsulating a Non-Native Substrate Protein
Method: single particle / : Chen DH, Madan D, Weaver J, Lin Z, Schroder GF, Chiu W, Rye HS

PDB-3zq1:
Visualizing GroEL-ES in the Act of Encapsulating a Non-Native Substrate Protein
Method: single particle / : Chen DH, Madan D, Weaver J, Lin Z, Schroder GF, Chiu W, Rye HS

PDB-3j3x:
Independent reconstruction of Mm-cpn cryo-EM density map from half dataset in the closed state (training map)
Method: single particle / : DiMaio F, Zhang J, Chiu W, Baker D

PDB-3j32:
An asymmetric unit map from electron cryo-microscopy of Haliotis diversicolor molluscan hemocyanin isoform 1 (HdH1)
Method: single particle / : Zhang Q, Dai X, Cong Y, Zhang J, Chen DH, Dougherty M, Wang J, Ludtke S, Schmid MF, Chiu W

PDB-2yew:
Modeling Barmah Forest virus structural proteins
Method: single particle / : Kostyuchenko VA, Jakana J, Liu X, Haddow AD, Aung M, Weaver SC, Chiu W, Lok SM

PDB-4a0o:
Symmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state
Method: single particle / : Cong Y, Schroder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SL, Frydman J, Chiu W

PDB-4a0v:
model refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP
Method: single particle / : Cong Y, Schroder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SL, Frydman J, Chiu W

PDB-4a0w:
model built against symmetry-free cryo-EM map of TRiC-ADP-AlFx
Method: single particle / : Cong Y, Schroder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SL, Frydman J, Chiu W

PDB-4a13:
model refined against symmetry-free cryo-EM map of TRiC-ADP
Method: single particle / : Cong Y, Schroder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SL, Frydman J, Chiu W

PDB-3j0c:
Models of E1, E2 and CP of Venezuelan Equine Encephalitis Virus TC-83 strain restrained by a near atomic resolution cryo-EM map
Method: single particle / : Zhang R, Hryc CF, Cong Y, Liu X, Jakana J, Gorchakov R, Baker ML, Weaver SC, Chiu W

PDB-3j0g:
Homology model of E3 protein of Venezuelan Equine Encephalitis Virus TC-83 strain fitted with a cryo-EM map
Method: single particle / : Zhang R, Hryc CF, Chiu W

PDB-3j02:
Lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state
Method: single particle / : Zhang J, Ma B, DiMaio F, Douglas NR, Joachimiak L, Baker D, Frydman J, Levitt M, Chiu W

PDB-3j03:
Lidless Mm-cpn in the closed state with ATP/AlFx
Method: single particle / : Zhang J, Ma B, DiMaio F, Douglas NR, Joachimiak L, Baker D, Frydman J, Levitt M, Chiu W

PDB-2xyy:
De Novo model of Bacteriophage P22 procapsid coat protein
Method: single particle / : Chen DH, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W, Baker D, King JA, Chiu W

PDB-2xyz:
De Novo model of Bacteriophage P22 virion coat protein
Method: single particle / : Chen DH, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W, Baker D, King JA, Chiu W

PDB-3izh:
Mm-cpn D386A with ATP
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izi:
Mm-cpn rls with ATP
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izj:
Mm-cpn rls with ATP and AlFx
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izk:
Mm-cpn rls deltalid with ATP
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izl:
Mm-cpn rls deltalid with ATP and AlFx
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izm:
Mm-cpn wildtype with ATP
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izn:
Mm-cpn deltalid with ATP
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-2xd8:
Capsid structure of the infectious Prochlorococcus Cyanophage P-SSP7
Method: single particle / : Liu X, Zhang Q, Murata K, Baker ML, Sullivan MB, Fu C, Dougherty M, Schmid MF, Osburne MS, Chisholm SW, Chiu W

PDB-3iyg:
Ca model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map
Method: single particle / : Cong Y, Baker ML, Ludtke SJ, Frydman J, Chiu W

PDB-3ktt:
Atomic model of bovine TRiC CCT2(beta) subunit derived from a 4.0 Angstrom cryo-EM map
Method: single particle / : Cong Y, Baker ML, Ludtke SJ, Frydman J, Chiu W

PDB-3los:
Atomic Model of Mm-cpn in the Closed State
Method: single particle / : Zhang J, Baker ML, Schroeder G, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W

PDB-3iyf:
Atomic Model of the Lidless Mm-cpn in the Open State
Method: single particle / : Zhang J, Baker ML, Schroeder G, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W

PDB-3ixv:
Scorpion Hemocyanin resting state pseudo atomic model built based on cryo-EM density map
Method: single particle / : Cong Y, Zhang Q, Woolford D, Schweikardt T, Khant H, Ludtke S, Chiu W, Decker H

PDB-3ixw:
Scorpion Hemocyanin activated state pseudo atomic model built based on cryo-EM density map
Method: single particle / : Cong Y, Zhang Q, Woolford D, Schweikardt T, Khant H, Ludtke S, Chiu W, Decker H

PDB-3b63:
Actin filament model in the extended form of acromsomal bundle in the Limulus sperm
Method: electron crystallography / : Cong Y, Topf M, Sali A, Matsudaira P, Dougherty M, Chiu W, Schmid MF

PDB-3c9v:
C7 Symmetrized Structure of Unliganded GroEL at 4.7 Angstrom Resolution from CryoEM
Method: single particle / : Ludtke SJ, Baker ML, Chen DH, Song JL, Chuang D, Chiu W

PDB-3cau:
D7 symmetrized structure of unliganded GroEL at 4.2 Angstrom resolution by cryoEM
Method: single particle / : Ludtke SJ, Baker ML, Chen DH, Song JL, Chuang D, Chiu W

PDB-3b5u:
Actin filament model from extended form of acromsomal bundle in the Limulus sperm
Method: electron crystallography / : Cong Y, Topf M, Sali A, Matsudaira P, Dougherty M, Chiu W, Schmid MF

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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New EM Navigator & Yorodumi

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