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- EMDB-10893: Structure of GldLM, the proton-powered motor that drives protein ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10893
TitleStructure of GldLM, the proton-powered motor that drives protein transport and gliding motility
Map datapost processed volume
Sample
  • Complex: GldLM
    • Protein or peptide: GldM
    • Protein or peptide: GldL
Keywordsmembrane protein complex ion-driven motor / MOTOR PROTEIN
Function / homology
Function and homology information


: / : / GldM second domain / GldM third domain / Gliding motility-associated protein GldM / Gliding motility-associated protein GldM, C-terminal / Gliding motility-associated protein GldM, N-terminal / GldM C-terminal domain / GldM N-terminal domain / Gliding motility-associated protein, GldL / GldL N-terminal domain
Similarity search - Domain/homology
Biological speciesFlavobacterium johnsoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHennell James R / Deme JC
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust107929/Z/15/Z United Kingdom
Wellcome Trust100298/Z/12/Z United Kingdom
Wellcome Trust201536/Z/16/Z United Kingdom
CitationJournal: Nat Microbiol / Year: 2020
Title: Structure of a proton-powered molecular motor that drives protein transport and gliding motility
Authors: Hennell James R / Deme JC / Kjaer A / Alcock F / Silale A / Lauber F / Bersk BC / Lea SM
History
DepositionApr 21, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0168
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0168
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ys8
  • Surface level: 0.0168
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10893.png

Downloads & links

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Map

FileDownload / File: emd_10893.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost processed volume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.432 Å		0.82 Å/pix.
x 256 pix.
= 210.432 Å		0.82 Å/pix.
x 256 pix.
= 210.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0168 / Movie #1: 0.0168
Minimum - Maximum-0.050958797 - 0.08905641
Average (Standard dev.)0.00020144464 (±0.002161142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.432 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z210.432210.432210.432
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0510.0890.000

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Supplemental data

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Mask #1

Fileemd_10893_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D refinement volume

Fileemd_10893_additional_1.map
Annotation3D refinement volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: RELION local resolution filtered volume

Fileemd_10893_additional_2.map
AnnotationRELION local resolution filtered volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_10893_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_10893_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GldLM

EntireName: GldLM
Components
  • Complex: GldLM
    • Protein or peptide: GldM
    • Protein or peptide: GldL

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Supramolecule #1: GldLM

SupramoleculeName: GldLM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)

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Macromolecule #1: GldM

MacromoleculeName: GldM / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 54.8565 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGGKLTPRQ KMINLMYLVF IAMLAMNVSK EVISAFGLMN EKFEAANTSS VTTNESLLTS LDQKAAEAKG EFAKAAETAH KVQAASKEF YDYIGTLKTQ AVKGFEVDKE TGKMPYEAMD RGDNIDDWFT GDGYTKKGNE IIAKIEKYKS DIKAALGTDK K YAGIISEV ...String:
MAGGKLTPRQ KMINLMYLVF IAMLAMNVSK EVISAFGLMN EKFEAANTSS VTTNESLLTS LDQKAAEAKG EFAKAAETAH KVQAASKEF YDYIGTLKTQ AVKGFEVDKE TGKMPYEAMD RGDNIDDWFT GDGYTKKGNE IIAKIEKYKS DIKAALGTDK K YAGIISEV EKKFDVSDVK NKEGIKEKYL AYHFKGFPAI ASAAKLSAWQ NDVKKTEADV YNSALGKAAV AAASYSNYQA IV VLDKNAY FQGEKVTGKV VLGRYDENTK PTSFQGPGQI VNGQAVISLT AGGVGEQDIN GQFTFLEDGK NIPLKFSGKY VVV PRPNSA TISADKMNVV YRGVVNPISV SFAGVDANKI VASAPGLSSA GKPGKYNMSP GQGTEATISV TGTLPNGDKV TDKK TFRIK GIPGPTGTIR GEMGVVKGPK SNLEIATIGA KLLDFDFEVG LDVVGFNMKI AGQPTVVVTG NKMNAQCKSV LARAG KGDQ VTISEIKTKL VGAGSYLLPR TAPVIYEIQ

UniProtKB: GldM

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Macromolecule #2: GldL

MacromoleculeName: GldL / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Molecular weightTheoretical: 22.786209 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALLSKKVMN FAYGMGAAVV IVGALFKITH FEIGPLTGTV MLSIGLLTEA LIFALSAFEP VEDELDWTLV YPELANGQAR KKEAKAETA TDAQGLLSQK LDAMLKEAKV DGELMASLGN SIKNFEGAAK AISPTVDSIA GQKKYAEEMS MAAAQMESLN S LYKVQLES ...String:
MALLSKKVMN FAYGMGAAVV IVGALFKITH FEIGPLTGTV MLSIGLLTEA LIFALSAFEP VEDELDWTLV YPELANGQAR KKEAKAETA TDAQGLLSQK LDAMLKEAKV DGELMASLGN SIKNFEGAAK AISPTVDSIA GQKKYAEEMS MAAAQMESLN S LYKVQLES ASRNAQANSE IAENAAKLKE QMASMTANIA SLNSVYGGML SAMSNKG

UniProtKB: GldL

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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: 7.5
Component:
ConcentrationName
20.0 mMHEPES
150.0 mMNaCl
0.02 %LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0003 µm / Nominal defocus min: 0.0001 µm / Nominal magnification: 165000
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: 3284887
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 119230
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SIMPLE (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6ys8:
Structure of GldLM, the proton-powered motor that drives protein transport and gliding motility

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