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- PDB-6ys8: Structure of GldLM, the proton-powered motor that drives protein ... -

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Basic information

Entry
Database: PDB / ID: 6ys8
TitleStructure of GldLM, the proton-powered motor that drives protein transport and gliding motility
Components
  • GldL
  • GldM
KeywordsMOTOR PROTEIN / membrane protein complex ion-driven motor
Function / homology
Function and homology information


Gliding motility-associated protein, GldL / : / GldL N-terminal domain / : / : / 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 ...Gliding motility-associated protein, GldL / : / GldL N-terminal domain / : / : / 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
Similarity search - Domain/homology
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHennell James, R. / Deme, J.C. / Lea, S.M.
Funding support United Kingdom, 3items
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, J.C. / Kjaer, A. / Alcock, F. / Silale, A. / Lauber, F. / Bersk, B.C. / Lea, S.M.
History
DepositionApr 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: GldM
B: GldM
G: GldL
F: GldL
E: GldL
D: GldL
C: GldL


Theoretical massNumber of molelcules
Total (without water)223,6447
Polymers223,6447
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS in addition to structure
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15540 Å2
ΔGint-139 kcal/mol
Surface area34370 Å2
MethodPISA

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Components

#1: Protein GldM


Mass: 54856.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: gldM / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EGM3
#2: Protein
GldL / Protein involved in gliding motility GldL


Mass: 22786.209 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: gldL, SAMN05444388_10142 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EGM4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GldLM / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Flavobacterium johnsoniae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
2150 mMNaCl1
30.02 %LMNG1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 0.3 nm / Nominal defocus min: 0.1 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4SIMPLE3CTF correction
9SIMPLE3initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3284887
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119230 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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