[English] 日本語
Yorodumi
- EMDB-39765: Homomeric 35mer of the Vibrio flagellar MS-ring protein FliF with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39765
TitleHomomeric 35mer of the Vibrio flagellar MS-ring protein FliF without symmetry imposition
Map data
Sample
  • Complex: Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus
    • Protein or peptide: FliFG fusion protein
KeywordsComplex / Rotor / MOTOR PROTEIN
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsTakekawa N / Nishikino T / Kishikawa J / Hirose M / Kato T / Imada K / Homma M
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H00393 Japan
Japan Society for the Promotion of Science (JSPS)21H01772 Japan
Japan Society for the Promotion of Science (JSPS)22K18943 Japan
Japan Society for the Promotion of Science (JSPS)20H03220 Japan
CitationJournal: To Be Published
Title: Structural analysis of S-ring composed of FliFG fusion proteins in marine Vibrio polar flagellar motors
Authors: Takekawa N / Nishikino T / Kishikawa J / Hirose M / Kinoshita M / Kojima S / Minamino T / Uchihashi T / Kato T / Imada K / Homma M
History
DepositionApr 17, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_39765.png

Downloads & links

-
Map

FileDownload / File: emd_39765.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 600 pix.
= 684. Å		1.14 Å/pix.
x 600 pix.
= 684. Å		1.14 Å/pix.
x 600 pix.
= 684. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.246
Minimum - Maximum-0.5758347 - 1.1125981
Average (Standard dev.)-0.0005394753 (±0.039683726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 684.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_39765_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_39765_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_39765_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus

EntireName: Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus
Components
  • Complex: Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus
    • Protein or peptide: FliFG fusion protein

-
Supramolecule #1: Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus

SupramoleculeName: Homomeric 35mer of FliFG fusion protein of Vibrio alginolyticus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: 138-2
Molecular weightTheoretical: 104 kDa/nm

-
Macromolecule #1: FliFG fusion protein

MacromoleculeName: FliFG fusion protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MNHKVHHHHH HIEGRHMADK STDLTVTEGG SDGALVASSD VDVESQNPDL EERSASKFDM AVGDLDLLRQ VVLVLSISIC VALIVMLFFW VKEPEMRPLG AYETEELIPV LDYLDQQKIN YKLDGNTISV ESSEYNSIKL GMVRSGVNQA TEAGDDILLQ DMGFGVSQRL ...String:
MNHKVHHHHH HIEGRHMADK STDLTVTEGG SDGALVASSD VDVESQNPDL EERSASKFDM AVGDLDLLRQ VVLVLSISIC VALIVMLFFW VKEPEMRPLG AYETEELIPV LDYLDQQKIN YKLDGNTISV ESSEYNSIKL GMVRSGVNQA TEAGDDILLQ DMGFGVSQRL EQERLKLSRE RQLAQAIEEM KQVRKARVLL ALPKHSVFVR HNQEASASVF LTLSTGTNLK QQEVDSIVDM VASAVPGMKT SRITVTDQHG RLLSSGSQDP ASAARRKEQE LERSQEQALR EKIDSVLLPI LGYGNYTAQV DIQMDFSAVE QTRKRFDPNT PATRSEYALE DYNNGNMVAG IPGALSNQPP ADASIPQDVA QMKDGSVMGQ GSVRKESTRN FELDTTISHE RKQTGTVARQ TVSVAIKDRR QVNPDTGEVT YTPMSESEIN AIRQVLIGTV GFDQGRGDLL NVLSVKFAEP EAEQLEEPPI WEHPNFSDWV RWFASALVII VVVLVLVRPA MKKLLNPTSD DEDEMYGPDG LPIGADGETS LIGSDIESSE LFEFGSSIDL PNLHKDEDVL KAVRALVANE PELAAQVVKN WMNDMANDIV PQDDNAAGMP VELDVSTITG EEKAAILLLS LNEQDAAGII RHLEPKQVQR VGSAMAKAKD LSQDKVSAVH RAFLEDIQKY TNIGMGSEDF MRNALVAALG EDKANNLVDQ ILLGTGSKGL DSLKWMDPRQ VASIIVNEHP QIQTIVLSYL EADQSAEILS QFPERVRLDL MMRIANLEEV QPSALAELNE IMEKQFAGQA GAQAAKISGL KAAAEIMNYL DNNVEGLLME QIRDQDEDMA TQIQDLMFVF ENLVEVDDQG IQKLLRDVPQ DVLQKALKGA DDSLREKVFK NMSKRAAEMM RDDIEAMPPV RVADVEAAQK EILAIARRMA DAGELMLSGG ADEFL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris-HCl
100.0 mMKClpotassium chloride
0.0025 %(w/v)C47H88O22LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 6372 / Average exposure time: 7.3 sec. / Average electron dose: 49.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2059366
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 184915
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
About Yorodumi

-
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

-
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

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more