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- EMDB-45130: Cryo-EM Structure of a Tm1C Fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-45130
TitleCryo-EM Structure of a Tm1C Fibril
Map dataEM density map of the class A structure from Relion post-processing, using a 10% central Z length mask.
Sample
  • Organelle or cellular component: Tropomyosin 1 I/C C-terminal Domain
    • Protein or peptide: Tropomyosin 1 I/C
KeywordsPROTEIN FIBRIL
Function / homologyTropomyosin / Tropomyosin / GH09289p
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
Methodhelical reconstruction / cryo EM / Resolution: 2.31 Å
AuthorsFonda BD / Kato M / Li Y / Murray DT
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35142892 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP220582 United States
CitationJournal: Protein Sci / Year: 2024
Title: Cryo-EM and solid state NMR together provide a more comprehensive structural investigation of protein fibrils.
Authors: Blake D Fonda / Masato Kato / Yang Li / Dylan T Murray /
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 ...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.
History
DepositionMay 29, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45130.png

Downloads & links

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Map

FileDownload / File: emd_45130.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM density map of the class A structure from Relion post-processing, using a 10% central Z length mask.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0107
Minimum - Maximum-0.03662399 - 0.073487535
Average (Standard dev.)0.000013676496 (±0.00090352166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45130_msk_1.map
Projections & Slices
AxesZYX

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Mask #2

Fileemd_45130_msk_2.map
Projections & Slices
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Additional map: EM density map of the class A structure...

Fileemd_45130_additional_1.map
AnnotationEM density map of the class A structure from Relion post-processing, using a 20% central Z length mask. This map is used for model building and refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The first unfiltered half map used in Relion post-processing.

Fileemd_45130_half_map_1.map
AnnotationThe first unfiltered half map used in Relion post-processing.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The second unfiltered half map used in Relion post-processing.

Fileemd_45130_half_map_2.map
AnnotationThe second unfiltered half map used in Relion post-processing.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tropomyosin 1 I/C C-terminal Domain

EntireName: Tropomyosin 1 I/C C-terminal Domain
Components
  • Organelle or cellular component: Tropomyosin 1 I/C C-terminal Domain
    • Protein or peptide: Tropomyosin 1 I/C

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Supramolecule #1: Tropomyosin 1 I/C C-terminal Domain

SupramoleculeName: Tropomyosin 1 I/C C-terminal Domain / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 7.41557 kDa/nm

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Macromolecule #1: Tropomyosin 1 I/C

MacromoleculeName: Tropomyosin 1 I/C / type: protein_or_peptide / ID: 1 / Details: SY-tagged Tm1 I/C alternative isoform / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 7.420535 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SYSSIKLSNN NNNSNSNNIE ISKSESCNAS DIGGTNNNNA SRTIASAAVG EETSTLSSTS HEHNNNPNND T

UniProtKB: GH09289p

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMTris-HCl
200.0 mMsodium chloride
0.5 mMethylenediaminetetraacetic acid
0.1 mMphenylmethylsulfonyl fluoride
20.0 mMB-mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.69 Å
Applied symmetry - Helical parameters - Δ&Phi: 2.58 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 17145
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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