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- EMDB-39764: Homomeric 34mer of the Vibrio flagellar MS-ring protein FliF with... -

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Basic information

Entry
Database: EMDB / ID: EMD-39764
TitleHomomeric 34mer of the Vibrio flagellar MS-ring protein FliF without symmetry imposition
Map data
Sample
  • Complex: Homomeric 34mer 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: 4.28 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

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Structure visualization

Supplemental images

emd_39764.png

Downloads & links

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Map

FileDownload / File: emd_39764.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.183
Minimum - Maximum-0.35066298 - 0.74201226
Average (Standard dev.)-0.0004927221 (±0.029361652)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_39764_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_39764_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39764_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Homomeric 34mer of FliFG fusion protein of Vibrio alginolyticus

EntireName: Homomeric 34mer of FliFG fusion protein of Vibrio alginolyticus
Components
  • Complex: Homomeric 34mer of FliFG fusion protein of Vibrio alginolyticus
    • Protein or peptide: FliFG fusion protein

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Supramolecule #1: Homomeric 34mer of FliFG fusion protein of Vibrio alginolyticus

SupramoleculeName: Homomeric 34mer 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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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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

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Image processing

Particle selectionNumber selected: 2059366
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 43546
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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