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Showing 1 - 50 of 52 items for author: i. & yu

PDB-5nd2:
Microtubule-bound MKLP2 motor domain in the presence of ADP
Method: single particle / : Atherton J, Yu IM, Cook A, Muretta JM, Joseph AP, Major J, Sourigues Y, Clause J, Topf M, Rosenfeld SS, Houdusse A, Moores CA

PDB-5nd3:
Microtubule-bound MKLP2 motor domain in the with no nucleotide
Method: single particle / : Atherton J, Yu IM, Cook A, Muretta JM, Joseph AP, Major J, Sourigues Y, Clause J, Topf M, Rosenfeld SS, Houdusse A, Moores CA

PDB-5nd4:
Microtubule-bound MKLP2 motor domain in the presence of ADP.AlFx
Method: single particle / : Atherton J, Yu IM, Cook A, Muretta JM, Joseph AP, Major J, Sourigues Y, Clause J, Topf M, Rosenfeld SS, Houdusse A, Moores CA

PDB-5nd7:
Microtubule-bound MKLP2 motor domain in the presence of AMPPNP
Method: single particle / : Atherton J, Yu IM, Cook A, Muretta JM, Joseph AP, Major J, Sourigues Y, Clause J, Topf M, Rosenfeld SS, Houdusse A, Moores CA

PDB-5nd8:
Hibernating ribosome from Staphylococcus aureus (Unrotated state)
Method: single particle / : Khusainov I, Vicens Q, Ayupov R, Usachev K, Myasnikov A, Simonetti A, Validov S, Kieffer B, Yusupova G, Yusupov M, Hashem Y

PDB-5nd9:
Hibernating ribosome from Staphylococcus aureus (Rotated state)
Method: single particle / : Khusainov I, Vicens Q, Ayupov R, Usachev K, Myasnikov A, Simonetti A, Validov S, Kieffer B, Yusupova G, Yusupov M, Hashem Y

PDB-5no3:
RsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly intermediate without uS3)
Method: single particle / : Lopez-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR

PDB-5no4:
RsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly intermediate with uS3)
Method: single particle / : Lopez-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR

PDB-5no2:
RsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly intermediate)
Method: single particle / : Lopez-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR

PDB-5wsn:
Structure of Japanese encephalitis virus
Method: single particle / : Wang X, Zhu L, Li S, Yuan S, Qin C, Fry EE, Stuart ID, Rao Z

PDB-5muu:
dsRNA bacteriophage phi6 nucleocapsid
Method: single particle / : Sun Z, El Omari K, Sun X, Ilca SL, Kotecha A, Stuart DI, Poranen MM, Huiskonen JT

PDB-5muv:
Atomic structure fitted into a localized reconstruction of bacteriophage phi6 packaging hexamer P4
Method: single particle / : Sun Z, El Omari K, Sun X, Ilca S, Kotecha A, Stuart DI, Poranen MM, Huiskonen JT

PDB-5muw:
Atomic structure of P4 packaging enzyme fitted into a localized reconstruction of bacteriophage phi6 vertex
Method: single particle / : Sun Z, El Omari K, Sun X, Ilca S, Kotecha A, Stuart DI, Poranen MM, Huiskonen JT

PDB-5jul:
Near atomic structure of the Dark apoptosome
Method: single particle / : Cheng TC, Akey IV, Yuan S, Yu Z, Ludtke SJ, Akey CW

PDB-5h3o:
Structure of a eukaryotic cyclic nucleotide-gated channel
Method: single particle / : Li M, Zhou X, Wang S, Michailidis I, Gong Y, Su D, Li H, Li X, Yang J

PDB-5wte:
Cryo-EM structure for Hepatitis A virus full particle
Method: single particle / : Wang X, Zhu L, Dang M, Hu Z, Gao Q, Yuan S, Sun Y, Zhang B, Ren J, Walter TS, Wang J, Fry EE, Stuart DI, Rao Z

PDB-5wtf:
Cryo-EM structure for Hepatitis A virus empty particle
Method: single particle / : Wang X, Zhu L, Dang M, Hu Z, Gao Q, Yuan S, Sun Y, Zhang B, Ren J, Walter TS, Wang J, Fry EE, Stuart DI, Rao Z

PDB-5wth:
Cryo-EM structure for Hepatitis A virus complexed with FAB
Method: single particle / : Wang X, Zhu L, Dang M, Hu Z, Gao Q, Yuan S, Sun Y, Zhang B, Ren J, Walter TS, Wang J, Fry EE, Stuart DI, Rao Z

PDB-5li0:
70S ribosome from Staphylococcus aureus
Method: single particle / : Khusainov I, Vicens Q, Bochler A, Grosse F, Myasnikov A, Menetret JF, Chicher J, Marzi S, Romby P, Yusupova G, Yusupov M, Hashem Y

PDB-5juy:
Active human apoptosome with procaspase-9
Method: single particle / : Cheng TC, Hong C, Akey IV, Yuan S, Akey CW

PDB-5gka:
cryo-EM structure of human Aichi virus
Method: single particle / : Zhu L, Wang XX, Ren JS, Tuthill TJ, Fry EE, Rao ZH, Stuart DI

PDB-5it7:
Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2
Method: single particle / : Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernandez IS

PDB-5it9:
Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES.
Method: single particle / : Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernandez IS

PDB-5ivw:
Human core TFIIH bound to DNA within the PIC
Method: single particle / : He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E

PDB-5iy6:
Human holo-PIC in the closed state
Method: single particle / : He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E

PDB-5iy7:
Human holo-PIC in the open state
Method: single particle / : He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E

PDB-5iy8:
Human holo-PIC in the initial transcribing state
Method: single particle / : He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E

PDB-5iy9:
Human holo-PIC in the initial transcribing state (no IIS)
Method: single particle / : He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E

PDB-5iya:
Human core-PIC in the closed state
Method: single particle / : He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E

PDB-5iyb:
Human core-PIC in the open state
Method: single particle / : He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E

PDB-5iyc:
Human core-PIC in the initial transcribing state
Method: single particle / : He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E

PDB-5iyd:
Human core-PIC in the initial transcribing state (no IIS)
Method: single particle / : He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E

PDB-5iqr:
Structure of RelA bound to the 70S ribosome
Method: single particle / : Brown A, Fernandez IS, Gordiyenko Y, Ramakrishnan V

PDB-5fj5:
Structure of the in vitro assembled bacteriophage phi6 polymerase complex
Method: single particle / : Ilca S, Kotecha A, Sun X, Poranen MP, Stuart DI, Huiskonen JT

PDB-5fj6:
Structure of the P2 polymerase inside in vitro assembled bacteriophage phi6 polymerase complex
Method: single particle / : Ilca S, Kotecha A, Sun X, Poranen MP, Stuart DI, Huiskonen JT

PDB-5fj7:
Structure of the P2 polymerase inside in vitro assembled bacteriophage phi6 polymerase complex, with P1 included
Method: single particle / : Ilca S, Kotecha A, Sun X, Poranen MP, Stuart DI, Huiskonen JT

PDB-3j6p:
Pseudo-atomic model of dynein microtubule binding domain-tubulin complex based on a cryoEM map
Method: helical / : Uchimura S, Fujii T, Takazaki H, Ayukawa R, Nishikawa Y, Minoura I, Hachikubo Y, Kurisu G, Sutoh K, Kon T, Namba K, Muto E

PDB-4d3e:
Tetramer of IpaD, modified from 2J0O, fitted into negative stain electron microscopy reconstruction of the wild type tip complex from the type III secretion system of Shigella flexneri
Method: single particle / : Cheung M, Shen DK, Makino F, Kato T, Roehrich D, Martinez-Argudo I, Walker ML, Murillo I, Liu X, Pain M, Brown J, Frazer G, Mantell J, Mina P, Todd T, Sessions RB, Namba K, Blocker AJ

PDB-4uxo:
Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins
Method: single particle / : Atherton J, Farabella I, Yu IM, Rosenfeld SS, Houdusse A, Topf M, Moores C

PDB-4uxp:
Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins
Method: single particle / : Atherton J, Farabella I, Yu IM, Rosenfeld SS, Houdusse A, Topf M, Moores C

PDB-4uxr:
Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins
Method: single particle / : Atherton J, Farabella I, Yu IM, Rosenfeld SS, Houdusse A, Topf M, Moores C

PDB-4uxs:
Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins
Method: single particle / : Atherton J, Farabella I, Yu IM, Rosenfeld SS, Houdusse A, Topf M, Moores C

PDB-4uxt:
Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins
Method: single particle / : Atherton J, Farabella I, Yu IM, Rosenfeld SS, Houdusse A, Topf M, Moores C

PDB-4uxy:
Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins
Method: single particle / : Atherton J, Farabella I, Yu IM, Rosenfeld SS, Houdusse A, Topf M, Moores C

PDB-4uy0:
Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins
Method: single particle / : Atherton J, Farabella I, Yu IM, Rosenfeld SS, Houdusse A, Topf M, Moores C

PDB-4d2q:
Negative-stain electron microscopy of E. coli ClpB mutant E432A (BAP form bound to ClpP)
Method: single particle / : Carroni M, Kummer E, Oguchi Y, Clare DK, Wendler P, Sinning I, Kopp J, Mogk A, Bukau B, Saibil HR

PDB-4d2u:
Negative-stain electron microscopy of E. coli ClpB (BAP form bound to ClpP)
Method: single particle / : Carroni M, Kummer E, Oguchi Y, Clare DK, Wendler P, Sinning I, Kopp J, Mogk A, Bukau B, Saibil HR

PDB-4d2x:
Negative-stain electron microscopy of E. coli ClpB of Y503D hyperactive mutant (BAP form bound to ClpP)
Method: single particle / : Carroni M, Kummer E, Oguchi Y, Clare DK, Wendler P, Sinning I, Kopp J, Mogk A, Bukau B, Saibil HR

PDB-3j5m:
Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs
Method: single particle / : Lyumkis D, Julien JP, Wilson IA, Ward AB

PDB-3izx:
3.1 Angstrom cryoEM structure of cytoplasmic polyhedrosis virus
Method: single particle / : Yu X, Ge P, Jiang J, Atanasov I, Zhou ZH

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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).
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