[English] 日本語
EMN search
- 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 68 items for (author: gabriel & waksman)

EMDB-17863:
2.7 A cryo-EM structure of in vitro assembled type 1 pilus rod
Method: helical / : Hospenthal M, Zyla D, Glockshuber R, Waksman G

EMDB-17878:
2.5 A cryo-EM structure of the in vitro FimD-catalyzed assembly of type 1 pilus rod
Method: helical / : Zyla D, Hospenthal M, Glockshuber R, Waksman G

PDB-8psv:
2.7 A cryo-EM structure of in vitro assembled type 1 pilus rod
Method: helical / : Hospenthal M, Zyla D, Glockshuber R, Waksman G

PDB-8ptu:
2.5 A cryo-EM structure of the in vitro FimD-catalyzed assembly of type 1 pilus rod
Method: helical / : Zyla D, Hospenthal M, Glockshuber R, Waksman G

EMDB-12707:
O-Layer C14 at 2.58A - Local refinement with C14 symmetry of the O-layer of the outer membrane core complex from the fully-assembled R388 type IV secretion system.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

EMDB-12708:
I-Layer C16 at 3.08A - Local refinement with C16 symmetry of I-layer of the outer membrane core complex from the fully-assembled R388 type IV secretion system.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

EMDB-12709:
Stalk C1 at 3.71A - Local refinement without symmetry of the Stalk complex from the fully-assembled R388 type IV secretion system.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

EMDB-12715:
IMC-Arches C6 at 8.33A - Refinement with C6 symmetry of the Inner Membrane Complex (IMC) with the Arches from the fully-assembled R388 type IV secretion system.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

EMDB-12716:
Trimer of dimers TrwK/VirB4unbound C1 at 4.14A - Refinement without symmetry of TrwK/VirB4unbound trimer of dimers complex (with Hcp1) from the R388 type IV secretion system.
Method: single particle / : Vadakkepat AK, Mace K, Lukoyanova N, Waksman G

EMDB-12717:
Dimer TrwK/VirB4unbound C1 at 3.49A - Local refinement without symmetry of the TrwK/VirB4unbound dimer complex from the R388 type IV secretion system.
Method: single particle / : Vadakkepat AK, Mace K, Lukoyanova N, Waksman G

EMDB-12933:
IMC protomer C1 at 3.75A - Local refinement without symmetry of the inner membrane complex (IMC) protomer from the fully-assembled R388 type IV secretion system.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

EMDB-13765:
OMCC C1 at 3.28A - Refinement without symmetry of the outer membrane core complex (O- and I-layer) from the fully-assembled R388 type IV secretion system.
Method: single particle / : Mace K, Vadakkepat AK, Waksman G, Lukoyanova N

EMDB-13766:
Ab Initio model for IMC-Arches-Stalk from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Method: single particle / : Mace K, Vadakkepat AK, Waksman G, Lukoyanova N

EMDB-13767:
IMC-Arches-Stalk C1 at 6.18A - Refinement of the IMC, Arches and Stalk complex without symmetry from the fully-assembled R388 type IV secretion system.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

EMDB-13768:
Stalk C5 at 3.28A - Local refinement with C5 symmetry of the Stalk complex from the fully-assembled R388 type IV secretion system.
Method: single particle / : Mace K, Vadakkepat AK, Waksman G, Lukoyanova N

PDB-7o3j:
O-layer structure (TrwH/VirB7, TrwF/VirB9CTD, TrwE/VirB10CTD) of the outer membrane core complex from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

PDB-7o3t:
I-layer structure (TrwF/VirB9NTD, TrwE/VirB10NTD) of the outer membrane core complex from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

PDB-7o3v:
Stalk complex structure (TrwJ/VirB5-TrwI/VirB6) from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

PDB-7o41:
Hexameric composite model of the Inner Membrane Complex (IMC) with the Arches from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

PDB-7o42:
TrwK/VirB4unbound trimer of dimers complex (with Hcp1) from the R388 type IV secretion system determined by cryo-EM.
Method: single particle / : Vadakkepat AK, Mace K, Lukoyanova N, Waksman G

PDB-7o43:
TrwK/VirB4unbound dimer complex from R388 type IV secretion system determined by cryo-EM.
Method: single particle / : Vadakkepat AK, Mace K, Lukoyanova N, Waksman G

PDB-7oiu:
Inner Membrane Complex (IMC) protomer structure (TrwM/VirB3, TrwK/VirB4, TrwG/VirB8tails) from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

PDB-7q1v:
Arches protomer (trimer of TrwG/VirB8peri) structure from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Method: single particle / : Mace K, Vadakkepat AK, Lukoyanova N, Waksman G

EMDB-13083:
L. pneumophila Type IV Coupling Complex (T4CC) with density for DotY N-terminal and middle domains
Method: single particle / : Mace K, Meir A, Lukoyanova N, Waksman G

EMDB-13858:
L. pneumophila Type IV Coupling Complex (T4CC) computed from WT particles where DotY/Z is missing (referred to as T4CCWTminusYZ at 6.3A)
Method: single particle / : Mace K, Meir A, Lukoyanova N, Waksman G

EMDB-13859:
L. pneumophila Type IV Coupling Complex (T4CC) computed from a sample where dotY/Z genes were deleted (referred to as T4CCdeltaDotYZ at 15A)
Method: single particle / : Mace K, Meir A, Lukoyanova N, Waksman G

PDB-7ovb:
L. pneumophila Type IV Coupling Complex (T4CC) with density for DotY N-terminal and middle domains
Method: single particle / : Mace K, Meir A, Lukoyanova N, Waksman G

EMDB-10721:
2.85 A cryo-EM structure of the in vivo assembled type 1 pilus rod
Method: helical / : Zyla D, Hospenthal M

PDB-6y7s:
2.85 A cryo-EM structure of the in vivo assembled type 1 pilus rod
Method: helical / : Zyla D, Hospenthal M, Waksman G, Glockshuber R

EMDB-10350:
Type IV Coupling Complex (T4CC) from L. pneumophila.
Method: single particle / : Mace K, Meir A, Lukoyanova N, Waksman G

PDB-6sz9:
Type IV Coupling Complex (T4CC) from L. pneumophila.
Method: single particle / : Mace K, Meir A, Lukoyanova N, Waksman G

EMDB-4510:
Cryo em structure of the Listeria stressosome
Method: single particle / : Williams AH, Redzej A

EMDB-4508:
Cryo em structure of the Listeria stressosome
Method: single particle / : Williams AH, Redzej A, Waksman G, Cossart P

PDB-6qcm:
Cryo em structure of the Listeria stressosome
Method: single particle / : Williams AH, Redzej A, Waksman G, Cossart P

EMDB-0089:
Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri
Method: single particle / : Costa TRD, Sgro GG, Farah CS, Waksman G

PDB-6gyb:
Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri
Method: single particle / : Sgro GG, Costa TRD, Farah CS, Waksman G

EMDB-3585:
Structure of the VirD4 bound to a Type IV secretion system
Method: single particle / : Redzej A, Ukleja M

EMDB-3809:
The Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod
Method: helical / : Hospenthal MK, Costa TRD, Redzej A, Waksman G

PDB-5oh0:
The Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod
Method: helical / : Hospenthal MK, Costa TRD, Redzej A, Waksman G

EMDB-3725:
Negative-stain EM structure of the A. tumefaciens outer-membrane core complex
Method: single particle / : Costa TRD, Orlova EV, Waksman G

EMDB-3601:
Cryo EM structure of the conjugative relaxase TraI of the F/R1 plasmid system
Method: single particle / : Zanetti G, Ilangovan A, Waksman G

PDB-5n8o:
Cryo EM structure of the conjugative relaxase TraI of the F/R1 plasmid system
Method: single particle / : Ilangovan A, Zanetti G, Waksman G

PDB-5ler:
Structure of the bacterial sex F pilus (13.2 Angstrom rise)
Method: helical / : Costa TRD, Ilangovan I, Ukleja M, Redzej A, Santini JM, Smith TK, Egelman EH, Waksman G

PDB-5lfb:
Structure of the bacterial sex F pilus (12.5 Angstrom rise)
Method: helical / : Costa TRD, Ilangovan I, Ukleja M, Redzej A, Santini JM, Smith TK, Egelman EH, Waksman G

PDB-5leg:
Structure of the bacterial sex F pilus (pED208)
Method: helical / : Costa TRD, Ilangovan I, Ukleja M, Redzej A, Santini JM, Smith TK, Egelman EH, Waksman G

EMDB-4042:
Cryo-EM structure of the bacterial sex F pilus (pED208)
Method: helical / : Costa TRD, Ilangovan I, Ukleja M, Redzej A, Santini JM, Smith TK, Egelman EH, Waksman G

EMDB-4044:
Cryo-EM structure of the bacterial sex F pilus (13.2 Angstrom rise)
Method: helical / : Costa TRD, Ilangovan I, Ukleja M, Redzej A, Santini JM, Smith TK, Egelman EH, Waksman G

EMDB-4046:
Cryo-EM structure of the bacterial sex F pilus (12.5 Angstrom rise)
Method: helical / : Costa TRD, Ilangovan I, Ukleja M, Redzej A, Santini JM, Smith TK, Egelman EH, Waksman G

EMDB-3222:
Structure of a Chaperone-Usher pilus reveals the molecular basis of rod uncoilin
Method: helical / : Hospenthal MK, Redzej A, Dodson K, Ukleja M, Frenz B, Hultgren SJ, DiMaio F, Egelman EH, Waksman G

PDB-5flu:
Structure of a Chaperone-Usher pilus reveals the molecular basis of rod uncoilin
Method: helical / : Hospenthal MK, Redzej A, Dodson K, Ukleja M, Frenz B, Hultgren SJ, DiMaio F, Egelman EH, Waksman G

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