[English] 日本語
Yorodumi
- PDB-5wk6: Cryo-EM structure of P. aeruginosa flagellar filaments G420A -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5wk6
TitleCryo-EM structure of P. aeruginosa flagellar filaments G420A
DescriptorB-type flagellin
KeywordsPROTEIN FIBRIL / bacteria flagella / helical polymers / cryo-EM
Specimen sourcePseudomonas aeruginosa (strain atcc 15692 / dsm 22644 / cip 104116 / jcm 14847 / lmg 12228 / 1c / prs 101 / pao1) / bacteria
MethodElectron microscopy (4.3 Å resolution / Filament / Helical)
AuthorsWang, F. / Postel, S. / Sundberg, E.J. / Egelman, E.H.
CitationNat Commun, 2017, 8, 960-960

Nat Commun, 2017, 8, 960-960 Yorodumi Papers
A structural model of flagellar filament switching across multiple bacterial species.
Fengbin Wang / Andrew M Burrage / Sandra Postel / Reece E Clark / Albina Orlova / Eric J Sundberg / Daniel B Kearns / Edward H Egelman

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 24, 2017 / Release: Oct 25, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 25, 2017Structure modelrepositoryInitial release
1.1Nov 1, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8856
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: B-type flagellin
B: B-type flagellin
C: B-type flagellin
D: B-type flagellin
E: B-type flagellin
F: B-type flagellin
G: B-type flagellin
H: B-type flagellin
I: B-type flagellin
J: B-type flagellin
K: B-type flagellin
L: B-type flagellin
M: B-type flagellin
N: B-type flagellin
O: B-type flagellin
P: B-type flagellin
Q: B-type flagellin
R: B-type flagellin
S: B-type flagellin
T: B-type flagellin
U: B-type flagellin
V: B-type flagellin
W: B-type flagellin
X: B-type flagellin
Y: B-type flagellin
Z: B-type flagellin
a: B-type flagellin
b: B-type flagellin
c: B-type flagellin
d: B-type flagellin
e: B-type flagellin
f: B-type flagellin
g: B-type flagellin
h: B-type flagellin
i: B-type flagellin
j: B-type flagellin
k: B-type flagellin
l: B-type flagellin
m: B-type flagellin
n: B-type flagellin
o: B-type flagellin


Theoretical massNumber of molelcules
Total (without water)2,020,84441
Polyers2,020,84441
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)275580
ΔGint (kcal/M)-870
Surface area (Å2)372730

-
Components

#1: Polypeptide(L) ...
B-type flagellin


Mass: 49288.883 Da / Num. of mol.: 41 / Mutation: G420A
Source: (gene. exp.) Pseudomonas aeruginosa (strain atcc 15692 / dsm 22644 / cip 104116 / jcm 14847 / lmg 12228 / 1c / prs 101 / pao1) / bacteria
References: UniProt: P72151

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: HELICAL

-
Sample preparation

ComponentName: Pseudomonas aeruginosa flagella filament / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1
Source (recombinant)Organism: Pseudomonas aeruginosa PAO1
Buffer solutionDetails: PBS / pH: 7.4
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: negative stain
VitrificationCryogen name: ETHANE / Humidity: 90 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 2 sec. / Electron dose: 20 e/Å2
Details: Images were stored containing seven parts, where each part represented a set of frames corresponding to a dose of ~20 electrons per Angstrom^2. The full dose image stack was used for the estimation of the CTF as well as for boxing filaments. Only the first two parts were used for the reconstruction (~5 electrons per Angstrom^2).
Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 7

-
Processing

SoftwareName: PHENIX / Version: dev_2439: / Classification: refinement
EM software
IDNameCategoryImage processing IDImaging IDFitting ID
1EMAN2PARTICLE SELECTION1
2EPUIMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
7RosettaMODEL FITTING1
9SPIDERINITIAL EULER ASSIGNMENT1
10SPIDERFINAL EULER ASSIGNMENT1
11SPIDERCLASSIFICATION1
12SPIDERRECONSTRUCTION1
13PHENIXMODEL REFINEMENT1
14CootMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.27 deg. / Axial rise/subunit: 4.73 Å / Axial symmetry: C1
3D reconstructionResolution: 4.3 Å / Resolution method: OTHER / Number of particles: 17450 / Algorithm: BACK PROJECTION / Details: model-map FSC 0.38 cut-off / Symmetry type: HELICAL
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010161352
ELECTRON MICROSCOPYf_angle_d1.357289902
ELECTRON MICROSCOPYf_dihedral_angle_d6.96882332
ELECTRON MICROSCOPYf_chiral_restr0.05513735
ELECTRON MICROSCOPYf_plane_restr0.00627902

+
About Yorodumi

-
News

-
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

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

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

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

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

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more