7E1E | pdb_00007e1e

Lamprey serum virus-like lectin-LSVL

PDB DOI: https://doi.org/10.2210/pdb7E1E/pdb
EM Map EMD-30939: EMDB EMDataResource

Classification: SUGAR BINDING PROTEIN
Organism(s): Lethenteron camtschaticum
Mutation(s): No

Deposited: 2021-02-01 Released: 2022-10-19
Deposition Author(s): Peng, Y.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.34 Å
Aggregation State: 3D ARRAY
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7E1E

This is version 1.3 of the entry. See complete history.

Literature

Structure of lamprey serum virus-like lectin with high binding capacity, involved in initiation and regulation of innate immunity

Qingwei, L., Peng, Y.

To be published.

Macromolecule Content

Total Structure Weight: 109.68 kDa
Atom Count: 6,489
Modeled Residue Count: 837
Deposited Residue Count: 999
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serum lectin	A, B, C	333	Lethenteron camtschaticum	Mutation(s): 0
UniProt
Find proteins for Q98TC9 (Lethenteron camtschaticum) Explore Q98TC9 Go to UniProtKB: Q98TC9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q98TC9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C]	D [auth A] E [auth A] F [auth B] G [auth B] H [auth C] D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.34 Å
Aggregation State: 3D ARRAY
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

Deposition Data

Released Date: 2022-10-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-10-19
Type: Initial release
Version 1.1: 2022-11-02
Changes: Data processing
Version 1.2: 2024-10-23
Changes: Data collection, Structure summary
Version 1.3: 2025-06-18
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.