9L2S | pdb_00009l2s

Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 2

PDB DOI: https://doi.org/10.2210/pdb9L2S/pdb
EM Map EMD-62779: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Latrodectus hesperus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-17 Released: 2025-12-24
Deposition Author(s): Zhang, Y.L., Dai, B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.08 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 2

Zhang, Y.L., Dai, B.

To be published.

Macromolecule Content

Total Structure Weight: 435.65 kDa
Atom Count: 1,119
Modeled Residue Count: 183
Deposited Residue Count: 5,085
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
silk-G6V	A [auth D] B [auth G] C [auth A] D [auth E] E [auth H] A [auth D], B [auth G], C [auth A], D [auth E], E [auth H], F [auth B], G [auth F], H [auth I], I [auth C]	565	Latrodectus hesperus	Mutation(s): 0
UniProt
Find proteins for A6YIY1 (Latrodectus hesperus) Explore A6YIY1 Go to UniProtKB: A6YIY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6YIY1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.08 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.15.2_3472

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	China	--

Revision History (Full details and data files)

Version 1.0: 2025-12-24
Type: Initial release

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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.