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

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Basic information

Entry
Database: PDB / ID: 8zaj
TitleCryo-EM structure of a 55 kDa nucleoplasmin domain of AtFKBP53
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP53
KeywordsCHAPERONE / nucleoplasmin domain / chaperon
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å
AuthorsBharambe, N. / Saharan, K. / Vasudevan, D. / Basak, S.
Funding support Singapore, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP53
B: Peptidyl-prolyl cis-trans isomerase FKBP53
C: Peptidyl-prolyl cis-trans isomerase FKBP53
D: Peptidyl-prolyl cis-trans isomerase FKBP53
E: Peptidyl-prolyl cis-trans isomerase FKBP53


Theoretical massNumber of molelcules
Total (without water)60,5585
Polymers60,5585
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Peptidyl-prolyl cis-trans isomerase FKBP53 / PPIase FKBP53 / FK506-binding protein 53 / AtFKBP53 / Immunophilin FKBP53 / Rotamase


Mass: 12111.609 Da / Num. of mol.: 5 / Fragment: nucleoplasmin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FKBP53, At4g25340, T30C3_20 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93ZG9, peptidylprolyl isomerase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Peptidyl-prolyl cis-trans isomerase FKBP53 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.06 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris1
250 mMsodium chlorideNaCl1
31 mMbeta-mercaptoethanolME1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 270000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 8687
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPUimage acquisition
4cryoSPARC4.2.0CTF correction
7Coot0.9.8.1model fitting
9cryoSPARC4.2.0initial Euler assignment
10cryoSPARC4.4.1final Euler assignment
11cryoSPARC4.4.1classification
12cryoSPARC4.4.13D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1769357
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205874 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6J2Z

6j2z


Accession code: 6J2Z / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033695
ELECTRON MICROSCOPYf_angle_d0.5375005
ELECTRON MICROSCOPYf_dihedral_angle_d3.955480
ELECTRON MICROSCOPYf_chiral_restr0.046560
ELECTRON MICROSCOPYf_plane_restr0.006660

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