9C1U | pdb_00009c1u

Cryo-EM Structure of a Tm1C Fibril

• PDB DOI: https://doi.org/10.2210/pdb9C1U/pdb
• EM Map EMD-45130: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-29 Released: 2024-10-09 
• Deposition Author(s): Fonda, B.D., Kato, M., Li, Y., Murray, D.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.31 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Literature

Cryo-EM and solid state NMR together provide a more comprehensive structural investigation of protein fibrils.

Fonda, B.D., Kato, M., Li, Y., Murray, D.T.

(2024) Protein Sci 33: e5168-e5168

• PubMed: 39276003 
• DOI: https://doi.org/10.1002/pro.5168
• Primary Citation Related Structures: 
  9C1U


• PubMed Abstract: 
  

  The tropomyosin 1 isoform I/C C-terminal domain (Tm1-LC) fibril structure is studied jointly with cryogenic electron microscopy (cryo-EM) and solid state nuclear magnetic resonance (NMR). This study demonstrates the complementary nature of these two structural biology techniques. Chemical shift assignments from solid state NMR are used to determine the secondary structure at the level of individual amino acids, which is faithfully seen in cryo-EM reconstructions. Additionally, solid state NMR demonstrates that the region not observed in the reconstructed cryo-EM density is primarily in a highly mobile random coil conformation rather than adopting multiple rigid conformations. Overall, this study illustrates the benefit of investigations combining cryo-EM and solid state NMR to investigate protein fibril structure.

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Organizational Affiliation: 
• Department of Chemistry, University of California, Davis, California, USA.
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 89.05 kDa 
• Atom Count: 2,376 
• Modeled Residue Count: 312 
• Deposited Residue Count: 852 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tropomyosin 1 I/C	A, B, C, D, E, F, G, H, I, J, K, L	71	Drosophila melanogaster	Mutation(s): 0  Gene Names:  Tm1, 1305/10, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, chr3R:11122272..11122408, cTM, cTmII, Dm Tm1, Dm TmH33, Dm TmH34, Dmel\CG4898, DmTm1, l(3)02299, l(3)S130510, l(3)s2958, mTmII, PmI, region 3, TM, TM1, TmH, TmH-33, TmH-34, TmH33, TmH34, TMII, Tmr33, Tmr34, TnH, TnH-33, TnH-34, tropomyosin, CG4898, Dmel_CG4898,
UniProt
Find proteins for Q8IG84 (Drosophila melanogaster) Explore Q8IG84  Go to UniProtKB:  Q8IG84

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.31 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Fonda, B.D., Kato, M., Li, Y., Murray, D.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35142892
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP220582

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release