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- EMDB-50433: Cryo-EM structure of Lysozyme homo-dimer assembled by homo Di-Glu... -

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Basic information

Entry
Database: EMDB / ID: EMD-50433
TitleCryo-EM structure of Lysozyme homo-dimer assembled by homo Di-Gluebody - Local refinement
Map dataLysozyme:homoDiGb local refinement
Sample
  • Complex: Lysozyme homo-dimer assembled by homo Di-Gluebody GbLysozyme - one copy
    • Protein or peptide: anti-Lysozyme Gluebody
    • Protein or peptide: Lysozyme C
  • Ligand: GLYCEROL
KeywordsGluebody / Nanobody / cryo-EM SPA / small protein / PROTEIN BINDING
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsYi G / Ye M / Mamalis D / Carrique L / Fairhead M / Li H / Duerr K / Zhang P / Sauer DB / von Delft F ...Yi G / Ye M / Mamalis D / Carrique L / Fairhead M / Li H / Duerr K / Zhang P / Sauer DB / von Delft F / Davis BG / Gilbert RJC
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: To Be Published
Title: Di-Gluebodies: Covalently-rigidified, modular protein assemblies enable simultaneous determination of high-resolution, low-size, cryo-EM structures
Authors: Yi G / Ye M / Mamalis D / Carrique L / Fairhead M / Li H / Duerr K / Zhang P / Sauer DB / von Delft F / Davis BG / Gilbert RJC
History
DepositionMay 26, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50433.png

Downloads & links

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Map

FileDownload / File: emd_50433.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLysozyme:homoDiGb local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.518521 - 2.0506275
Average (Standard dev.)-0.000075123266 (±0.014983202)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 292.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A

Fileemd_50433_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_50433_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lysozyme homo-dimer assembled by homo Di-Gluebody GbLysozyme - on...

EntireName: Lysozyme homo-dimer assembled by homo Di-Gluebody GbLysozyme - one copy
Components
  • Complex: Lysozyme homo-dimer assembled by homo Di-Gluebody GbLysozyme - one copy
    • Protein or peptide: anti-Lysozyme Gluebody
    • Protein or peptide: Lysozyme C
  • Ligand: GLYCEROL

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Supramolecule #1: Lysozyme homo-dimer assembled by homo Di-Gluebody GbLysozyme - on...

SupramoleculeName: Lysozyme homo-dimer assembled by homo Di-Gluebody GbLysozyme - one copy
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 57 KDa

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Macromolecule #1: anti-Lysozyme Gluebody

MacromoleculeName: anti-Lysozyme Gluebody / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.863432 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SDVQLVENGG GCVKAGGSLR LSCAASGSTD SIEYMTWFRQ APGKAREGVA ALYTHTGNTY YTDSVKGRFT ISQDKAKNMA YLRMDSVKS EDTAIYTCGA TRKAVPVRFA LDQSSYDYWG QGTQVMVSS

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Macromolecule #2: Lysozyme C

MacromoleculeName: Lysozyme C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: lysozyme
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 14.33116 KDa
SequenceString:
KVFGRCELAA AMKRHGLDNY RGYSLGNWVC AAKFESNFNT QATNRNTDGS TDYGILQINS RWWCNDGRTP GSRNLCNIPC SALLSSDIT ASVNCAKKIV SDGNGMNAWV AWRNRCKGTD VQAWIRGCRL

UniProtKB: Lysozyme C

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Macromolecule #3: GLYCEROL

MacromoleculeName: GLYCEROL / type: ligand / ID: 3 / Number of copies: 1 / Formula: GOL
Molecular weightTheoretical: 92.094 Da
Chemical component information

ChemComp-GOL:
GLYCEROL

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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:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 7 / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 233961
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 8 / Avg.num./class: 33720 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6bj2


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-9fgy:
Cryo-EM structure of Lysozyme homo-dimer assembled by homo Di-Gluebody - Local refinement

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