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- EMDB-39878: Cryo-EM structure of a 55 kDa nucleoplasmin domain of AtFKBP53 -

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Basic information

Entry
Database: EMDB / ID: EMD-39878
TitleCryo-EM structure of a 55 kDa nucleoplasmin domain of AtFKBP53
Map datasharpened final refinement map
Sample
  • Complex: Peptidyl-prolyl cis-trans isomerase FKBP53
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP53
Keywordsnucleoplasmin domain / chaperon / CHAPERONE
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / nucleosome assembly / histone binding / nucleolus / nucleus
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase Fpr3/Fpr4-like / Nucleoplasmin-like domain / Nucleoplasmin-like domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP53
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsBharambe N / Saharan K / Vasudevan D / Basak S
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Other privateNRF Singapore
CitationJournal: J Struct Biol / Year: 2025
Title: 2.0 Å cryo-EM structure of the 55 kDa nucleoplasmin domain of AtFKBP53.
Authors: Nikhil Bharambe / Ketul Saharan / Dileep Vasudevan / Sandip Basak /
Abstract: The knowledge of three-dimensional structures of biological macromolecules is crucial for understanding the molecular mechanisms underlying disease pathology and for devising drugs targeting specific ...The knowledge of three-dimensional structures of biological macromolecules is crucial for understanding the molecular mechanisms underlying disease pathology and for devising drugs targeting specific molecules. Single particle cryo-electron microscopy (Cryo-EM) has become indispensable for this purpose, particularly for large macromolecules and their complexes. However, its effectiveness has been limited in achieving near-atomic resolution for smaller macromolecules. This study presents the Cryo-EM structure of a 55 kDa pentameric AtFKBP53 nucleoplasmin domain at 2.0 Å nominal resolution. Our approach involves selecting the optimal grid for data collection and precise alignment of small particles to enhance the resolution of the final 3D reconstructed map. In this study, we systematically processed cryo-EM dataset of a small molecule to improve alignment, and this data processing strategy can be used as a guidance to process the cryo-EM data of other small molecules.
History
DepositionApr 25, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39878.png

Downloads & links

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Map

FileDownload / File: emd_39878.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened final refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.46 Å/pix.
x 300 pix.
= 138. Å		0.46 Å/pix.
x 300 pix.
= 138. Å		0.46 Å/pix.
x 300 pix.
= 138. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.46 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0447
Minimum - Maximum-0.2128477 - 0.3423327
Average (Standard dev.)-0.00014780267 (±0.009548178)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 138.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39878_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_39878_msk_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened final refinement map

Fileemd_39878_additional_1.map
Annotationunsharpened final refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_39878_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_39878_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Peptidyl-prolyl cis-trans isomerase FKBP53

EntireName: Peptidyl-prolyl cis-trans isomerase FKBP53
Components
  • Complex: Peptidyl-prolyl cis-trans isomerase FKBP53
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP53

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Supramolecule #1: Peptidyl-prolyl cis-trans isomerase FKBP53

SupramoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP53 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 60 KDa

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Macromolecule #1: Peptidyl-prolyl cis-trans isomerase FKBP53

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP53 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 12.111609 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGFWGLEVKP GKPQAYNPKN EQGKIHVTQA TLGTGLSKEK SVIQCSIGDK APIALCSLLP NKIECCPLNL EFDDDDEPVE FTVTGDRSI HLSGFLEYYQ DLEHHHHHH

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP53

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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: 7.5
Component:
ConcentrationNameFormula
50.0 mMTris
50.0 mMsodium chlorideNaCl
1.0 mMbeta-mercaptoethanolME
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Number real images: 8687 / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 270000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1769357
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6j2z

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 205874
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6j2z


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

PDB-8zaj:
Cryo-EM structure of a 55 kDa nucleoplasmin domain of AtFKBP53

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