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- PDB-6zgl: Structure of DPS determined by movement-free cryoEM with zero dos... -

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Basic information

Entry
Database: PDB / ID: 6zgl
TitleStructure of DPS determined by movement-free cryoEM with zero dose extrapolation
ComponentsDNA protection during starvation protein
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis / DNA binding ...DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis / DNA binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
DNA protection during starvation protein, gammaproteobacteria / Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
DNA protection during starvation protein / DNA protection during starvation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsNaydenova, K. / Russo, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC UP 120117 United Kingdom
CitationJournal: Science / Year: 2020
Title: Cryo-EM with sub-1 Å specimen movement.
Authors: Katerina Naydenova / Peipei Jia / Christopher J Russo /
Abstract: Most information loss in cryogenic electron microscopy (cryo-EM) stems from particle movement during imaging, which remains poorly understood. We show that this movement is caused by buckling and ...Most information loss in cryogenic electron microscopy (cryo-EM) stems from particle movement during imaging, which remains poorly understood. We show that this movement is caused by buckling and subsequent deformation of the suspended ice, with a threshold that depends directly on the shape of the frozen water layer set by the support foil. We describe a specimen support design that eliminates buckling and reduces electron beam-induced particle movement to less than 1 angstrom. The design allows precise foil tracking during imaging with high-speed detectors, thereby lessening demands on cryostage precision and stability. It includes a maximal density of holes, which increases throughput in automated cryo-EM without degrading data quality. Movement-free imaging allows extrapolation to a three-dimensional map of the specimen at zero electron exposure, before the onset of radiation damage.
History
DepositionJun 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high / _refine.ls_d_res_low

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Assembly

Deposited unit
A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
G: DNA protection during starvation protein
H: DNA protection during starvation protein
I: DNA protection during starvation protein
J: DNA protection during starvation protein
K: DNA protection during starvation protein
L: DNA protection during starvation protein


Theoretical massNumber of molelcules
Total (without water)224,64412
Polymers224,64412
Non-polymers00
Water17,366964
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area43700 Å2
ΔGint-126 kcal/mol
Surface area53270 Å2

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Components

#1: Protein
DNA protection during starvation protein


Mass: 18720.295 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A073HPB2, UniProt: P0ABT2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / Source method: isolated from a natural source / Formula: H2O

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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: DNA protection during starvation protein (DPS) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 35 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0256 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionResolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 275623 / Symmetry type: POINT
RefinementResolution: 1.9→1.9 Å / Cor.coef. Fo:Fc: 0.764 / ESU R: 0.168
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.32924 --
obs0.32924 284873 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.636 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0.01 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Total: 15616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0180.01314868
ELECTRON MICROSCOPYr_bond_other_d0.0360.01714028
ELECTRON MICROSCOPYr_angle_refined_deg1.9371.6320148
ELECTRON MICROSCOPYr_angle_other_deg2.3881.58432424
ELECTRON MICROSCOPYr_dihedral_angle_1_deg3.47851836
ELECTRON MICROSCOPYr_dihedral_angle_2_deg37.87523.188828
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.204152676
ELECTRON MICROSCOPYr_dihedral_angle_4_deg20.2391596
ELECTRON MICROSCOPYr_chiral_restr0.1170.22040
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0216680
ELECTRON MICROSCOPYr_gen_planes_other0.0260.023000
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.3891.6477380
ELECTRON MICROSCOPYr_mcbond_other2.3751.6467379
ELECTRON MICROSCOPYr_mcangle_it3.5342.4659204
ELECTRON MICROSCOPYr_mcangle_other3.5382.4669205
ELECTRON MICROSCOPYr_scbond_it5.7082.3457488
ELECTRON MICROSCOPYr_scbond_other5.7012.3437485
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other9.163.20510943
ELECTRON MICROSCOPYr_long_range_B_refined15.43721.35718681
ELECTRON MICROSCOPYr_long_range_B_other15.43921.36118682
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.597 21106 -
obs--100 %

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