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- PDB-7e1e: Lamprey serum virus-like lectin-LSVL -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7e1e
TitleLamprey serum virus-like lectin-LSVL
ComponentsSerum lectin
KeywordsSUGAR BINDING PROTEIN / Lamprey / serum / LSVL / innate immunity / ANTIMICROBIAL 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)
MethodELECTRON MICROSCOPY / single 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, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Data processing / Category: em_3d_reconstruction / Item: _em_3d_reconstruction.resolution
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum lectin
B: Serum lectin
C: Serum lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6849
Polymers109,4433
Non-polymers2406
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Serum lectin / lamprey serum virus-like lectin


Mass: 36481.047 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Lethenteron camtschaticum (Arctic lamprey)
References: UniProt: Q98TC9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: lamprey serum virus-like lectin-LSVL / Type: TISSUE / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Lethenteron camtschaticum (Arctic lamprey)
Buffer solutionpH: 7
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN / Humidity: 100 %

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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
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225296 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076669
ELECTRON MICROSCOPYf_angle_d0.7759084
ELECTRON MICROSCOPYf_dihedral_angle_d18.5193813
ELECTRON MICROSCOPYf_chiral_restr0.05957
ELECTRON MICROSCOPYf_plane_restr0.0071188

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