[English] 日本語
- 3DEM data search -

-
Search query


Keywords
Database /
Q: What are the data sources of EM Navigator?
Data entries / weeks ago
Q: When the data are updated?
Author
Processing method
Display mode
Sort by
Num. of entries / page
Entry
Article
Sample
Experiment
Processing
Max number of data0 for all data
File format
  • CSV format (Comma-Separated Values, for Excel, etc.)
  • TSV format (Tab Separated Values, for Excel, etc.)
  • JSON format

Yorodumi Search

-
Search result

Showing 1 - 50 of 94 items for (author: yamaguchi & t)

EMDB-71386:
Structure of CloA apo
Method: single particle / : Yamaguchi S, Fernandez SG, Wassarman DR, Luder M, Schwede F, Kranzusch PJ

EMDB-71388:
Structure of CloA co-expressed with CloB
Method: single particle / : Yamaguchi S, Fernandez SG, Wassarman DR, Luder M, Schwede F, Kranzusch PJ

EMDB-71389:
Structure of CloA in complex with dGTP and p3diT
Method: single particle / : Yamaguchi S, Fernandez SG, Wassarman DR, Luder M, Schwede F, Kranzusch PJ

EMDB-71390:
Structure of CloA in complex with dGTP and dTTP
Method: single particle / : Yamaguchi S, Fernandez SG, Wassarman DR, Luder M, Schwede F, Kranzusch PJ

PDB-9p8s:
Structure of CloA apo
Method: single particle / : Yamaguchi S, Fernandez SG, Wassarman DR, Luder M, Schwede F, Kranzusch PJ

PDB-9p8t:
Structure of CloA co-expressed with CloB
Method: single particle / : Yamaguchi S, Fernandez SG, Wassarman DR, Luder M, Schwede F, Kranzusch PJ

PDB-9p8u:
Structure of CloA in complex with dGTP and p3diT
Method: single particle / : Yamaguchi S, Fernandez SG, Wassarman DR, Luder M, Schwede F, Kranzusch PJ

PDB-9p8v:
Structure of CloA in complex with dGTP and dTTP
Method: single particle / : Yamaguchi S, Fernandez SG, Wassarman DR, Luder M, Schwede F, Kranzusch PJ

EMDB-62659:
Cryo-EM structure of the LGI1 LRR-LGI1 EPTP-ADAM22 ECD complex
Method: single particle / : Yamaguchi T, Okatsu K, Kubota M, Mitsumori A, Yamagata A, Fukai S

EMDB-62668:
Cryo-EM structure of the 3:3 LGI1-ADAM22 complex
Method: single particle / : Yamaguchi T, Okatsu K, Kubota M, Mistumori A, Yamagata A, Fukai S

PDB-9kzc:
Cryo-EM structure of the LGI1 LRR-LGI1 EPTP-ADAM22 ECD complex
Method: single particle / : Yamaguchi T, Okatsu K, Kubota M, Mitsumori A, Yamagata A, Fukai S

PDB-9kzt:
Cryo-EM structure of the 3:3 LGI1-ADAM22 complex
Method: single particle / : Yamaguchi T, Okatsu K, Kubota M, Mistumori A, Yamagata A, Fukai S

EMDB-38604:
RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei
Method: single particle / : Kujirai T, Kato J, Yamamoto K, Hirai S, Negishi L, Ogasawara M, Takizawa Y, Kurumizaka H

EMDB-38607:
RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei
Method: single particle / : Kujirai T, Kato J, Yamamoto K, Hirai S, Negishi L, Ogasawara M, Takizawa Y, Kurumizaka H

EMDB-38624:
RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei
Method: single particle / : Kujirai T, Kato J, Yamamoto K, Hirai S, Negishi L, Ogasawara M, Takizawa Y, Kurumizaka H

EMDB-38717:
RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei
Method: single particle / : Kujirai T, Kato J, Yamamoto K, Hirai S, Negishi L, Ogasawara M, Takizawa Y, Kurumizaka H

PDB-8xrj:
RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei
Method: single particle / : Kujirai T, Kato J, Yamamoto K, Hirai S, Negishi L, Ogasawara M, Takizawa Y, Kurumizaka H

PDB-8xrm:
RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei
Method: single particle / : Kujirai T, Kato J, Yamamoto K, Hirai S, Negishi L, Ogasawara M, Takizawa Y, Kurumizaka H

PDB-8xso:
RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei
Method: single particle / : Kujirai T, Kato J, Yamamoto K, Hirai S, Negishi L, Ogasawara M, Takizawa Y, Kurumizaka H

PDB-8xvs:
RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei
Method: single particle / : Kujirai T, Kato J, Yamamoto K, Hirai S, Negishi L, Ogasawara M, Takizawa Y, Kurumizaka H

EMDB-61204:
Cryo-EM Structure of calcium sensing receptor in complex gamma-glutamyl-valyl-glycine as a kokumi substance
Method: single particle / : Yamaguchi H, Kitajima S, Suzuki H, Suzuki S, Nishikawa K, Maruyama Y, Kamegawa A, Kazutoshi T, Tagami U, Kuroda M, Fujiyoshi Y, Sugiki M

PDB-9j7i:
Cryo-EM Structure of calcium sensing receptor in complex gamma-glutamyl-valyl-glycine as a kokumi substance
Method: single particle / : Yamaguchi H, Kitajima S, Suzuki H, Suzuki S, Nishikawa K, Maruyama Y, Kamegawa A, Kazutoshi T, Tagami U, Kuroda M, Fujiyoshi Y, Sugiki M

EMDB-36635:
Structure of arginine oxidase from Pseudomonas sp. TRU 7192
Method: single particle / : Yamaguchi H, Numoto N, Suzuki H, Nishikawa K, Kamegawa A, Takahashi K, Sugiki M, Fujiyoshi Y

PDB-8jt7:
Structure of arginine oxidase from Pseudomonas sp. TRU 7192
Method: single particle / : Yamaguchi H, Numoto N, Suzuki H, Nishikawa K, Kamegawa A, Takahashi K, Sugiki M, Fujiyoshi Y

EMDB-34791:
Doublet microtubule of zebrafish sperm axoneme, WT
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-34792:
Radial spoke 1 of zebrafish sperm axoneme, WT
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-34793:
Radial spoke 2 of zebrafish sperm axoneme, WT
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-34794:
Radial spoke 3 of zebrafish sperm axoneme, WT
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-34795:
Doublet microtubule of zebrafish sperm axoneme, calaxin-/-, OAD+ class
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-34796:
Doublet microtubule of zebrafish sperm axoneme, calaxin-/-, OAD- class
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-34797:
Doublet microtubule of zebrafish sperm axoneme, armc4-/-
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-34798:
Outer arm dynein of zebrafish sperm axoneme, WT
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-34799:
Outer arm dynein of zebrafish sperm axoneme, WT, refined focusing on the docking complex
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-34800:
Outer arm dynein of zebrafish sperm axoneme, WT, 1 mM calcium condition, refined focusing on the docking complex
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-34801:
Outer arm dynein of zebrafish sperm axoneme, calaxin-/-, refined focusing on the docking complex
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-34802:
Outer arm dynein of zebrafish sperm axoneme, calaxin-/-, incubated with recombinant Calaxin protein, refined focusing on the docking complex
Method: subtomogram averaging / : Yamaguchi H, Kikkawa M

EMDB-33200:
Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form)
Method: single particle / : Onoda H, Kikuchi A, Kori S, Yoshimi S, Yamagata A, Arita K

EMDB-33201:
Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form)
Method: single particle / : Onoda H, Kikuchi A, Kori S, Yoshimi S, Yamagata A, Arita K

EMDB-33298:
Cryo-EM map of apo-DNMT1 (aa:351-1616)
Method: single particle / : Onoda H, Kikuchi A, Kori S, Yoshimi S, Yamagata A, Matsuzawa S, Arita K

EMDB-33299:
Cryo-EM map of DNMT1 (aa:351-1616) in complex with ubiquitinated H3
Method: single particle / : Onoda H, Kikuchi A, Kori S, Yoshimi S, Yamagata A, Arita K

PDB-7xi9:
Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form)
Method: single particle / : Onoda H, Kikuchi A, Kori S, Yoshimi S, Yamagata A, Arita K

PDB-7xib:
Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form)
Method: single particle / : Onoda H, Kikuchi A, Kori S, Yoshimi S, Yamagata A, Arita K

EMDB-32078:
Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P86
Method: single particle / : Maeda R, Fujita J

EMDB-32079:
Cryo-EM structure of the SARS-CoV-2 spike protein (3-up RBD) bound to neutralizing nanobodies P86
Method: single particle / : Maeda R, Fujita J, Konishi Y, Kazuma Y, Yamazaki H, Anzai I, Yamaguchi K, Kasai K, Nagata K, Yamaoka Y, Miyakawa K, Ryo A, Shirakawa K, Makino F, Matsuura Y, Inoue T, Imura A, Namba K, Takaori-Kondo A

EMDB-32080:
Cryo-EM structure of the SARS-CoV-2 spike protein (1-up RBD) bound to neutralizing nanobodies P17
Method: single particle / : Maeda R, Fujita J, Konishi Y, Kazuma Y, Yamazaki H, Anzai I, Yamaguchi K, Kasai K, Nagata K, Yamaoka Y, Miyakawa K, Ryo A, Shirakawa K, Makino F, Matsuura Y, Inoue T, Imura A, Namba K, Takaori-Kondo A

EMDB-32081:
Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P17
Method: single particle / : Maeda R, Fujita J, Konishi Y, Kazuma Y, Yamazaki H, Anzai I, Yamaguchi K, Kasai K, Nagata K, Yamaoka Y, Miyakawa K, Ryo A, Shirakawa K, Makino F, Matsuura Y, Inoue T, Imura A, Namba K, Takaori-Kondo A

PDB-7vq0:
Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P86
Method: single particle / : Maeda R, Fujita J, Konishi Y, Kazuma Y, Yamazaki H, Anzai I, Yamaguchi K, Kasai K, Nagata K, Yamaoka Y, Miyakawa K, Ryo A, Shirakawa K, Makino F, Matsuura Y, Inoue T, Imura A, Namba K, Takaori-Kondo A

EMDB-31741:
Structure of the Dicer-2-R2D2 heterodimer
Method: single particle / : Yamaguchi S, Nishizawa T, Kusakizako T, Yamashita K, Tomita A, Hirano H, Nishimasu H, Nureki O

EMDB-31742:
Structure of the Dicer-2-R2D2 heterodimer bound to small RNA duplex
Method: single particle / : Yamaguchi S, Nishizawa T, Kusakizako T, Yamashita K, Tomita A, Hirano H, Nishimasu H, Nureki O

PDB-7v6b:
Structure of the Dicer-2-R2D2 heterodimer
Method: single particle / : Yamaguchi S, Nishizawa T, Kusakizako T, Yamashita K, Tomita A, Hirano H, Nishimasu H, Nureki O

Pages:

+
About EMN search

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Oct 5, 2021. Nobel Prize for mechanically activated and temperature-gated ion channels

Nobel Prize for mechanically activated and temperature-gated ion channels

  • The Nobel Prize in Physiology or Medicine 2021 was awarded jointly to David Julius and Ardem Patapoutian "for their discoveries of receptors for temperature and touch."
  • EM Navigator can help to find cryo-EM structure data by both pioneers.

External links:The Nobel Prize in Physiology or Medicine 2021 - NobelPrize.org / Structure data by Ardem Patapoutian / Structure data by David Julius

+
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jul 5, 2019. Downlodablable text data

Downlodablable text data

Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.

PageDataFormat
EMN Searchsearch resultCSV, TSV, or JSON
EMN statisticsdata tableCSV or TSV

Related info.:EMN Search / EMN Statistics

-
EMN Search

3DEM data search

Advanced data search for EMDB and EM data in PDB widh various search and display options

Related info.:EMDB / PDB / EM Navigator / Q: What are the data sources of EM Navigator? / Yorodumi Search / Jul 5, 2019. Downlodablable text data

Read more