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- EMDB-30939: Lamprey serum virus-like lectin-LSVL -

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Basic information

Entry
Database: EMDB / ID: EMD-30939
TitleLamprey serum virus-like lectin-LSVL
Map data
Sample
  • Tissue: lamprey serum virus-like lectin-LSVL
    • Protein or peptide: Serum lectin
  • Ligand: CALCIUM ION
KeywordsLamprey / serum / LSVL / innate immunity / ANTIMICROBIAL PROTEIN / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


oligosaccharide binding / extracellular space / metal ion binding
Similarity search - Function
Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesLethenteron camtschaticum (Arctic lamprey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsPeng Y
CitationJournal: To Be Published
Title: Structure of lamprey serum virus-like lectin with high binding capacity, involved in initiation and regulation of innate immunity
Authors: Qingwei L / Peng Y
History
DepositionFeb 1, 2021-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_30939.png

Downloads & links

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Map

FileDownload / File: emd_30939.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 256 pix.
= 334.474 Å		1.31 Å/pix.
x 256 pix.
= 334.474 Å		1.31 Å/pix.
x 256 pix.
= 334.474 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0521
Minimum - Maximum-0.09379877 - 0.20229246
Average (Standard dev.)0.001149745 (±0.008649251)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 334.47424 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : lamprey serum virus-like lectin-LSVL

EntireName: lamprey serum virus-like lectin-LSVL
Components
  • Tissue: lamprey serum virus-like lectin-LSVL
    • Protein or peptide: Serum lectin
  • Ligand: CALCIUM ION

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Supramolecule #1: lamprey serum virus-like lectin-LSVL

SupramoleculeName: lamprey serum virus-like lectin-LSVL / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Lethenteron camtschaticum (Arctic lamprey)

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Macromolecule #1: Serum lectin

MacromoleculeName: Serum lectin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lethenteron camtschaticum (Arctic lamprey)
Molecular weightTheoretical: 36.481047 KDa
SequenceString: MEASRLLLLL LLPLLLLFCN SVAAACSCTD SCSDAKESES KCGCKHEEET KQLPRSCKEI KLKTKTKEDG VYCLQTKSGQ FYQAFCDMN TNGGGWTLVA SVHENNIAAK CAIGDRWSSQ LGSNPAVGFV DGDRSWANLN TFGRVESATD DDYKNPGYFD V DAEDISVW ...String:
MEASRLLLLL LLPLLLLFCN SVAAACSCTD SCSDAKESES KCGCKHEEET KQLPRSCKEI KLKTKTKEDG VYCLQTKSGQ FYQAFCDMN TNGGGWTLVA SVHENNIAAK CAIGDRWSSQ LGSNPAVGFV DGDRSWANLN TFGRVESATD DDYKNPGYFD V DAEDISVW HVPNGTPLAQ WKISSIFRYH TATEFLTPLG GNLYFLYKIF YPLVYGSGTC PASNGPAIPI VYDFGNTISV AS QVCPACL GGTLQGYVHL RVFNNERAPF ALCSGLRVLD NCNTEHYCIG GAGYVPEQTP RQCGDFSAFD WSGIGTHVEW SAS KSLLEA AVFIFYR

UniProtKB: Serum lectin

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration2 mg/mL
BufferpH: 7
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 225296
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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