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- EMDB-74011: Human TTR-C10A at pH 7.4 -

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Basic information

Entry
Database: EMDB / ID: EMD-74011
TitleHuman TTR-C10A at pH 7.4
Map data
Sample
  • Complex: TTR homotetramer
    • Protein or peptide: Transthyretin
Keywordsthyroxine transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen ...Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / : / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRafiq M / Schaefer JH / Lander GC
Funding support United States, Germany, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS095892 United States
German Research Foundation (DFG)556478029 Germany
CitationJournal: bioRxiv / Year: 2026
Title: DM: a simple solution to suppress air-water interface interactions in cryo-EM.
Authors: Maria Rafiq / Jan-Hannes Schäfer / Hamidreza Rahmani / Shaochen You / Michael Bollong / Danielle Grotjahn / R Luke Wiseman / Gabriel C Lander /
Abstract: The air-water interface (AWI) remains the primary barrier to routine high-resolution cryo-EM structure determination, driving protein adsorption, structural denaturation, and restricted particle ...The air-water interface (AWI) remains the primary barrier to routine high-resolution cryo-EM structure determination, driving protein adsorption, structural denaturation, and restricted particle orientations during vitrification. Here, we describe a simple and broadly applicable strategy to mitigate these effects using the mild non-ionic detergent n-decyl-β-D-maltopyranoside (DM). Addition of DM at low millimolar concentrations immediately prior to vitrification consistently suppresses AWI-driven artifacts, resulting in improved angular sampling, reduced structural damage, and enhanced reconstruction quality across diverse macromolecular systems. Using this approach, we obtained a high-resolution reconstruction of the 65 kDa Nucleophosmin 1 pentamer, a target previously limited by severe preferred orientation issues. We further show that DM promotes isotropic particle distributions for high-resolution reconstruction of hemagglutinin, transthyretin, as well as suppressing denaturation of aldolase while stabilizing its C-terminus. Our results indicate that DM effectively passivates deleterious air-water interface interactions without compromising particle integrity. These results establish DM as an effective additive for improving the robustness of single-particle cryo-EM sample preparation.
History
DepositionNov 21, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74011.png

Downloads & links

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Map

FileDownload / File: emd_74011.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 256 pix.
= 189.44 Å		0.74 Å/pix.
x 256 pix.
= 189.44 Å		0.74 Å/pix.
x 256 pix.
= 189.44 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.0481133 - 1.3466752
Average (Standard dev.)0.00017764553 (±0.033009004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 189.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74011_msk_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_74011_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_74011_half_map_2.map
Projections & Slices
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Sample components

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Entire : TTR homotetramer

EntireName: TTR homotetramer
Components
  • Complex: TTR homotetramer
    • Protein or peptide: Transthyretin

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Supramolecule #1: TTR homotetramer

SupramoleculeName: TTR homotetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transthyretin

MacromoleculeName: Transthyretin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.705373 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHGPT GTGESKAPLM VKVLDAVRGS PAINVAVHVF RKAADDTWEP FASGKTSESG ELHGLTTEEE FVEGIYKVEI DTKSYWKAL GISPFHEHAE VVFTANDSGP RRYTIAALLS PYSYSTTAVV TNPKE

UniProtKB: Transthyretin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 388411
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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