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- EMDB-66973: High-resolution cryo-EM structure of Maltose Binding Protein -

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Basic information

Entry
Database: EMDB / ID: EMD-66973
TitleHigh-resolution cryo-EM structure of Maltose Binding Protein
Map data
Sample
  • Complex: High-resolution cryo-EM structure of Maltosee Binding Protein
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein
  • Ligand: water
Keywordssmall protein-ligand complex / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsPark K / Yoo Y / Jeon H / Choi K / Kwon E / Lim H / Kim DY / No KT
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: High-resolution cryo-EM structures of small protein-ligand complexes near the theoretical size limit.
Authors: Kunwoong Park / Youngki Yoo / Hyunbum Jeon / Kiju Choi / Hanseong Kim / Eunju Kwon / Hyun-Ho Lim / Dong Young Kim / Kyoung Tai No /
Abstract: Cryo-electron microscopy (cryo-EM) is a widely used technique for determining macromolecular structures at near-atomic resolution. The theoretical lower limit of particle sizes suitable for cryo-EM ...Cryo-electron microscopy (cryo-EM) is a widely used technique for determining macromolecular structures at near-atomic resolution. The theoretical lower limit of particle sizes suitable for cryo-EM structural analysis is estimated to be 38 kDa; typical constraints involve factors such as image contrast and particle alignment accuracy. In this study, we present cryo-EM structures of two protein-ligand complexes near this lower size threshold. First, the structure of the maltose-binding protein complexed with maltose, with a structurally ordered mass of 40.8 kDa, was determined at a resolution of 2.4 Å; both the maltose and water molecules were clearly identified in this structure. The second structure was the kinase domain of human PLK1 complexed with onvansertib, with a structurally ordered mass of 31.6 kDa, below the theoretical 38 kDa limit; this domain was determined at a resolution of 3.4 Å using a gold-supported grid in the presence of β-octyl-glucoside. The density map clearly shows the backbone of PLK1 secondary structure, and the onvansertib. These results demonstrate that cryo-EM can be effectively employed to determine structures of small proteins or domains, and to perform structure-based drug screening for small proteins, without requiring structural fiducials for particle alignment.
History
DepositionNov 6, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66973.png

Downloads & links

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Map

FileDownload / File: emd_66973.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 300 pix.
= 216.63 Å		0.72 Å/pix.
x 300 pix.
= 216.63 Å		0.72 Å/pix.
x 300 pix.
= 216.63 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7221 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.155
Minimum - Maximum-0.591605 - 0.80511945
Average (Standard dev.)-0.000022797934 (±0.016028965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 216.63 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66973_msk_1.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_66973_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66973_half_map_2.map
Projections & Slices
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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 : High-resolution cryo-EM structure of Maltosee Binding Protein

EntireName: High-resolution cryo-EM structure of Maltosee Binding Protein
Components
  • Complex: High-resolution cryo-EM structure of Maltosee Binding Protein
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein
  • Ligand: water

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Supramolecule #1: High-resolution cryo-EM structure of Maltosee Binding Protein

SupramoleculeName: High-resolution cryo-EM structure of Maltosee Binding Protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein / type: protein_or_peptide / ID: 1
Details: A313V substitution reflects the MBP sequence encoded in the pMAL-c5X expression vector backbone
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 43.81927 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY ...String:
MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NKGETAMTIN GPWAWSNIDT SK VNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPLGAVALKS YEEELVKDPR IAA TMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TNSSSNNNNN NNNNNLGIEG RISHMENLYF Q

UniProtKB: Maltose/maltodextrin-binding periplasmic protein

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 207 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.4 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8352733
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1fqc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 509884
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1fqc


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9xko:
High-resolution cryo-EM structure of Maltose Binding Protein

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