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- EMDB-56794: GFP bound to distal DARPin (AHIR dodecamer scaffold system from s... -

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Basic information

Entry
Database: EMDB / ID: EMD-56794
TitleGFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 4500 micrographs)
Map data
Sample
  • Complex: GFP bound to DARPin on an AHIR dodecamer scaffold system.
    • Complex: DARPin
      • Protein or peptide: DARPin
    • Complex: Green fluorescent protein
      • Protein or peptide: Green fluorescent protein
KeywordsGFP / DARPin / scaffold / FLUORESCENT PROTEIN
Biological speciessynthetic construct (others) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsFerreira DSM / Noble M / Rowland RJ / Fairhead M / Gittins O / von Delft F / Endicott J / Martin M / Pike ACW / Sauer DB / Dlamini LS
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T003677/1 United Kingdom
CitationJournal: To Be Published
Title: An engineered symmetrical scaffold system enables high resolution imaging of small cargo proteins by cryo-electron microscopy
Authors: Ferreira DSM / Noble M / Rowland RJ / Gittins O / Martin M / Endicott J / Fairhead M / von Delft F / Pike ACW / Sauer DB / Dlamini LS
History
DepositionFeb 17, 2026-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56794.png

Downloads & links

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Map

FileDownload / File: emd_56794.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 288 pix.
= 404.554 Å		1.4 Å/pix.
x 288 pix.
= 404.554 Å		1.4 Å/pix.
x 288 pix.
= 404.554 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.662
Minimum - Maximum-2.6765652 - 3.9969287
Average (Standard dev.)0.0013586424 (±0.038817767)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 404.55362 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56794_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_56794_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56794_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56794_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GFP bound to DARPin on an AHIR dodecamer scaffold system.

EntireName: GFP bound to DARPin on an AHIR dodecamer scaffold system.
Components
  • Complex: GFP bound to DARPin on an AHIR dodecamer scaffold system.
    • Complex: DARPin
      • Protein or peptide: DARPin
    • Complex: Green fluorescent protein
      • Protein or peptide: Green fluorescent protein

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Supramolecule #1: GFP bound to DARPin on an AHIR dodecamer scaffold system.

SupramoleculeName: GFP bound to DARPin on an AHIR dodecamer scaffold system.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.4 KDa

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Supramolecule #2: DARPin

SupramoleculeName: DARPin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #3: Green fluorescent protein

SupramoleculeName: Green fluorescent protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: DARPin

MacromoleculeName: DARPin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
SequenceString:
MSDLGKKLLE AARAGQDDEV RILMANGADV NAADDVGVTP LHLAAQRGHL EIVEVLLKYG ADVNAADLWG QTPLHLAATA GHLEIVEVLL KNGADVNARD NIGHTPLHLA AWAGHLEIVE VLLKYGADVN AQDKFGKTPK DLARDNGNEW IRELLEKAER KLK

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Macromolecule #2: Green fluorescent protein

MacromoleculeName: Green fluorescent protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
SequenceString: KGEELFTGVV PILVELDGDV NGHKFSVRGE GEGDATNGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKRHD FFKSAMPEGY VQERTISFKD DGTYKTRAEV KFEGDTLVNR IELKGIDFKE DGNILGHKLE YNFNSHNVYI TADKQKNGIK ANFKIRHNVE ...String:
KGEELFTGVV PILVELDGDV NGHKFSVRGE GEGDATNGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKRHD FFKSAMPEGY VQERTISFKD DGTYKTRAEV KFEGDTLVNR IELKGIDFKE DGNILGHKLE YNFNSHNVYI TADKQKNGIK ANFKIRHNVE DGSVQLADHY QQNTPIGDGP VLLPDNHYLS TQSALSKDPN EKRDHMVLLE FVTAAGI

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.5 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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 308062
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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