9NEQ | pdb_00009neq

Cryo-EM of NBD-L4pY nanofibers at 1.25mM concentration

• PDB DOI: https://doi.org/10.2210/pdb9NEQ/pdb
• EM Map EMD-49330: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2025-02-20 Released: 2026-03-11 
• Deposition Author(s): Zia, A., Guo, J., Xu, B., Wang, F.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Cryo-EM of NBD-L4pY nanofibers at 1.25mM concentration

Zia, A., Guo, J., Xu, B., Wang, F.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 3.1 kDa 
• Atom Count: 164 
• Modeled Residue Count: 15 
• Deposited Residue Count: 18 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(UQ4)LLLL(PTR)	A, B, C	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UQ4 (Subject of Investigation/LOI)	D [auth B]	N-(7-nitro-2,1,3-benzoxadiazol-4-yl)-beta-alanine C9 H8 N4 O5 MWTXZSDNHVFODA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B, C	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2_3874

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-11 
Deposition Author(s): Zia, A., Guo, J., Xu, B., Wang, F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM138756
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA142746

Revision History  

• Version 1.0: 2026-03-11
  Type: Initial release