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- EMDB-56750: MBP bound to distal DARPin (AHIR dodecamer scaffold system) -

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Basic information

Entry
Database: EMDB / ID: EMD-56750
TitleMBP bound to distal DARPin (AHIR dodecamer scaffold system)
Map data
Sample
  • Complex: MBP bound to DARPin on an AHIR dodecamer scaffold system.
    • Complex: DARPin
      • Complex: MBP
        • Protein or peptide: Maltose-binding periplasmic protein,PigG
      • Protein or peptide: DARPin
  • Ligand: ETHANOL
KeywordsMBP / DARPin / scaffold / SUGAR BINDING PROTEIN
Function / homologyMaltose-binding periplasmic protein,PigG
Function and homology information
Biological speciessynthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFerreira DSM / Noble M / Rowland RJ / Fairhead M / Gittins O / von Delft F / Endicott J / Pike ACW / Sauer DB / Martin M / 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 13, 2026-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56750.png

Downloads & links

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Map

FileDownload / File: emd_56750.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 448 pix.
= 371.392 Å		0.83 Å/pix.
x 448 pix.
= 371.392 Å		0.83 Å/pix.
x 448 pix.
= 371.392 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0812
Minimum - Maximum-0.32324588 - 0.50187314
Average (Standard dev.)0.0003071531 (±0.0059844363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 371.392 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56750_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: Unsharpened map.

Fileemd_56750_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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Additional map: Local resolution.

Fileemd_56750_additional_2.map
AnnotationLocal resolution.
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56750_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_56750_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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

EntireName: MBP bound to DARPin on an AHIR dodecamer scaffold system.
Components
  • Complex: MBP bound to DARPin on an AHIR dodecamer scaffold system.
    • Complex: DARPin
      • Complex: MBP
        • Protein or peptide: Maltose-binding periplasmic protein,PigG
      • Protein or peptide: DARPin
  • Ligand: ETHANOL

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

SupramoleculeName: MBP bound to DARPin on an AHIR dodecamer scaffold system.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 40.6 KDa

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Supramolecule #2: DARPin

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

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Supramolecule #3: MBP

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

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Macromolecule #1: Maltose-binding periplasmic protein,PigG

MacromoleculeName: Maltose-binding periplasmic protein,PigG / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.675906 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: KIEEGKLVIW INGDKGYNGL AEVGKKFEKD TGIKVTVEHP DKLEEKFPQV AATGDGPDII FWAHDRFGGY AQSGLLAEIT PAAAFQDKL YPFTWDAVRY NGKLIAYPIA VEALSLIYNK DLLPNPPKTW EEIPALDKEL KAKGKSALMF NLQEPYFTWP L IAADGGYA ...String:
KIEEGKLVIW INGDKGYNGL AEVGKKFEKD TGIKVTVEHP DKLEEKFPQV AATGDGPDII FWAHDRFGGY AQSGLLAEIT PAAAFQDKL YPFTWDAVRY NGKLIAYPIA VEALSLIYNK DLLPNPPKTW EEIPALDKEL KAKGKSALMF NLQEPYFTWP L IAADGGYA FKYENGKYDI KDVGVDNAGA KAGLTFLVDL IKNKHMNADT DYSIAEAAFN KGETAMTING PWAWSNIDTS AV NYGVTVL PTFKGQPSKP FVGVLSAGIN AASPNKELAK EFLENYLLTD EGLEAVNKDK PLGAVALKSY EEELAKDPRI AAT MENAQK GEIMPNIPQM SAFWYAVRTA VINAASGRQT VDAALAAAQT NGSHHAH

UniProtKB: Maltose-binding periplasmic protein,PigG

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Macromolecule #2: DARPin

MacromoleculeName: DARPin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 17.173264 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
DLGRKLLEAA RAGQDDEVRI LMANGADVNA ADNTGTTPLH LAAYSGHLEI VEVLLKHGAD VDASDVFGYT PLHLAAYWGH LEIVEVLLK NGADVNAMDS DGMTPLHLAA KWGYLEIVEV LLKHGADVNA QDKFGKTPKD LARDNGNQWI YELLEAAGRA

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Macromolecule #3: ETHANOL

MacromoleculeName: ETHANOL / type: ligand / ID: 3 / Number of copies: 1 / Formula: EOH
Molecular weightTheoretical: 46.068 Da
Chemical component information

ChemComp-EOH:
ETHANOL

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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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 180813
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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