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- PDB-9e08: Cryo-EM structure of MdoD from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 900000000
TitleCryo-EM structure of MdoD from Escherichia coli
ComponentsGlucans biosynthesis protein D
KeywordsSUGAR BINDING PROTEIN / MdoD / signal peptide / glucanase
Function / homology
Function and homology information


beta-glucan biosynthetic process / catalytic activity / outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
Glucan biosynthesis, MdoD / Glucan biosynthesis, periplasmic, MdoG C-terminal / Glucan biosynthesis protein MdoG/MdoD / Periplasmic glucan biosynthesis protein, MdoG / Glycoside hydrolase-type carbohydrate-binding / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Galactose mutarotase-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Glucans biosynthesis protein D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsDeme, J.C. / Bryant, O.J. / Berks, B.C. / Lea, S.M.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L000776/1 United Kingdom
Wellcome Trust107929/Z/15/Z United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To Be Published
Title: Structure of the twin-arginine protein translocation pathway core complex and the molecular basis for substrate recognition
Authors: Deme, J.C. / Bryant, O.J. / Berks, B.C. / Lea, S.M.
History
DepositionOct 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
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Revision 1.0Aug 27, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucans biosynthesis protein D
B: Glucans biosynthesis protein D


Theoretical massNumber of molelcules
Total (without water)125,8342
Polymers125,8342
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glucans biosynthesis protein D


Mass: 62916.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: opgD, mdoD, BGM66_002243, BJI68_05615, CTR35_003307, E4K51_22440, E6D34_24965, FOI11_006015, FOI11_12985, FWK02_00580, GNW61_13365, GP965_04670, GRW05_15845, HMV95_17475, IH772_11360, J0541_003971, P6223_003218
Production host: Escherichia coli (E. coli) / References: UniProt: A0A138L4Y6
Has protein modificationN

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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: MdoD dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 52.1 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 770564 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028552
ELECTRON MICROSCOPYf_angle_d0.39411608
ELECTRON MICROSCOPYf_dihedral_angle_d3.7941144
ELECTRON MICROSCOPYf_chiral_restr0.041178
ELECTRON MICROSCOPYf_plane_restr0.0031528

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