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- EMDB-83142: Cryo-EM structure of GroEL on a NHS(5K)-functionalized graphene grid -

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Basic information

Entry
Database: EMDB / ID: EMD-83142
TitleCryo-EM structure of GroEL on a NHS(5K)-functionalized graphene grid
Map data
Sample
  • Complex: Escherichia coli GroEL
KeywordsGroEL / functionalized grid / NHS esster / PEG chain / STRUCTURAL PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.12 Å
AuthorsYarimizu S / Inoue T / Asahara H
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K05606 Japan
New Energy and Industrial Technology Development Organization (NEDO)24000999-0 Japan
Japan Agency for Medical Research and Development (AMED)JP26ama121054 Japan
Japan Agency for Medical Research and Development (AMED)JP26ama121003 Japan
CitationJournal: Langmuir / Year: 2026
Title: Silane-Coupled Photo-Oxidized Graphene Grids for Controlling Protein-Surface Interactions in Cryo-EM Sample Preparation.
Authors: Yarimizu S / Inoue T / Asahara H
History
DepositionAug 22, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_83142.png

Downloads & links

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Map

FileDownload / File: emd_83142.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 480 pix.
= 417.6 Å		0.87 Å/pix.
x 480 pix.
= 417.6 Å		0.87 Å/pix.
x 480 pix.
= 417.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
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Contour LevelBy AUTHOR: 0.0505
Minimum - Maximum-0.073664166 - 0.2315789
Average (Standard dev.)-0.00013501043 (±0.0065248683)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 417.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_83142_msk_1.map
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Mask #2

Fileemd_83142_msk_2.map
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Mask #3

Fileemd_83142_msk_3.map
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Half map: #1

Fileemd_83142_half_map_1.map
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Half map: #2

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Sample components

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Entire : Escherichia coli GroEL

EntireName: Escherichia coli GroEL
Components
  • Complex: Escherichia coli GroEL

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Supramolecule #1: Escherichia coli GroEL

SupramoleculeName: Escherichia coli GroEL / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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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

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMHEPES
50.0 mMsodium chlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4275 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 124538
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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