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- PDB-7stw: Structure of DPSL (DNA Protection in Starved Cells - Like) from P... -

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Basic information

Entry
Database: PDB / ID: 7stw
TitleStructure of DPSL (DNA Protection in Starved Cells - Like) from Pyrococcus furiosus
ComponentsDNA protection during starvation protein
KeywordsMETAL BINDING PROTEIN / DPS-like protein
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / nucleoid / ferroxidase activity / ferric iron binding / intracellular iron ion homeostasis / heme binding / DNA binding / cytosol
Similarity search - Function
: / DPS-like protein, ferritin-like diiron-binding domain / DNA-binding protein from starved cells-like / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA protection during starvation protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsGauvin, C.C. / Waghwani, H.K. / Douglas, T. / Lawrence, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DBI-1828765 United States
CitationJournal: To be published
Title: Structure of DPSL (DNA Protection in Starved Cells - Like) from Pyrococcus furiosus
Authors: Ramsay, B. / Wiedenheft, B. / Allen, M. / Gauss, G.H. / Lawrence, C.M. / Young, M. / Douglas, T.
History
DepositionNov 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-25437
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  • Superimposition on EM map
  • EMDB-25437
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,10236
Polymers256,64712
Non-polymers1,45524
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "F"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "H"
d_7ens_1chain "G"
d_8ens_1chain "A"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "L"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILELYSD1 - 170
d_12ens_1ZNZNE
d_21ens_1ILELYSP1 - 170
d_22ens_1ZNZNQ
d_31ens_1ILELYSG1 - 170
d_32ens_1ZNZNH
d_41ens_1ILELYSJ1 - 170
d_42ens_1ZNZNK
d_51ens_1ILELYSM1 - 170
d_52ens_1ZNZNN
d_61ens_1ILELYSV1 - 170
d_62ens_1ZNZNW
d_71ens_1ILELYSS1 - 170
d_72ens_1ZNZNT
d_81ens_1ILELYSA1 - 170
d_82ens_1ZNZNB
d_91ens_1ILELYSY1 - 170
d_92ens_1ZNZNZ
d_101ens_1ILELYSBA1 - 170
d_102ens_1ZNZNCA
d_111ens_1ILELYSEA1 - 170
d_112ens_1ZNZNFA
d_121ens_1ILELYSHA1 - 170
d_122ens_1ZNZNIA

NCS oper:
IDCodeMatrixVector
1given(-0.499950604097, 0.866053747602, -0.000547474251086), (-0.866053920637, -0.499950506779, 0.000311963349761), (-3.533001103E-6, 0.00063010848677, 0.999999801475)30.4547846468, 118.930210333, -0.034753321575
2given(0.501211654206, 0.865320378216, 0.00274239524558), (0.289894027846, -0.170897068412, 0.941677038388), (0.815320998324, -0.471184502134, -0.336506812176)-19.3859804661, 0.717602688048, 46.5322302714
3given(0.495511844739, 0.287031146194, 0.819805545747), (0.868599001567, -0.161628228724, -0.468414442728), (-0.00194581613279, 0.944187183134, -0.32940366878)-28.1601073092, 37.7548748936, 15.0890605664
4given(0.494060683763, -0.869421467296, 0.00321760238952), (-0.293432542124, -0.163261102561, 0.94193585536), (-0.818413944152, -0.466317622009, -0.335777443289)69.0669616554, 29.110088312, 127.077794736
5given(0.504576232092, -0.284016423637, -0.815314354782), (-0.863365995138, -0.167527854759, -0.475955435224), (-0.00140870428786, 0.944070489415, -0.329740695953)77.2028356493, 124.465169991, 15.1050192436
6given(0.00020001346429, -0.580380706491, 0.814345255729), (-0.579357532652, -0.663818517942, -0.472958586555), (0.815073499357, -0.471702460001, -0.336380706753)40.6694954676, 135.365071886, 46.517743837
7given(0.00749058597946, 0.575991708618, -0.817421214996), (0.574107956461, -0.671774507566, -0.468101554487), (-0.818745348353, -0.465781668368, -0.335713407481)58.4080097652, 78.4703677088, 127.148061945
8given(-0.500651145091, 0.293572700177, 0.814348513003), (-0.281398345374, 0.834451652306, -0.473820019822), (-0.818635084846, -0.466374859607, -0.335158303173)20.9786322009, 44.5538147999, 127.12532238
9given(-0.500090293775, -0.865973262978, 7.6676682144E-5), (0.865973144846, -0.500090174725, 0.000574063463621), (-0.000458778355378, 0.00035348351374, 0.999999832286)118.251527405, 33.1163379928, 0.0466748729279
10given(-0.502347804846, -0.284442224073, -0.816541060897), (0.289683843145, 0.834405245286, -0.468882882669), (0.81469623418, -0.472081039445, -0.3367633267)127.204293196, 15.9468919858, 46.5654008121
11given(-0.999983063318, -0.00340881481185, -0.00471731477626), (-0.00557775743422, 0.329873080097, 0.944008813333), (-0.00166183607037, 0.944019136993, -0.329886506684)99.633224099, -10.1603877992, 15.1153702418

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Components

#1: Protein
DNA protection during starvation protein


Mass: 21387.254 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: dps, PF1193 / Plasmid: pET-30a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8U1L3, Oxidoreductases; Oxidizing metal ions
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: Dodecameric assembly of DPS-like protein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.25632 MDa / Experimental value: NO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET-30a(+)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1120 mMSodium chlorideNaCl1
220 mMTris(HOCH2)3CNH21
SpecimenConc.: 2 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 R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: Blot force 5 Blot time 4

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Details: Beam tilt was performed with a 3x3 matrix with corners omitted.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2200 nm / Cs: 2.62 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 77 K
Image recordingAverage exposure time: 7 sec. / Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1574 / Details: Images were dose-fractionated to have 50 frames

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.2particle selectionManual picking to generate templates, which were then fed into template picker
2SerialEM3.8.8image acquisition
4cryoSPARC3.2CTF correction
7UCSF Chimera1.15model fittingFitmap was used
9cryoSPARC3.2initial Euler assignmentAb-initio
10cryoSPARC3.2final Euler assignment
11cryoSPARC3.2classification
12cryoSPARC3.23D reconstruction
13PHENIX1.19model refinementReal space refine was primarily used
Image processingDetails: Images were gain normalized in SerialEM
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1812595
SymmetryPoint symmetry: T (tetrahedral)
3D reconstructionResolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 436835 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Details: Workflow involved generating a homology model from 2CLB structure from S. solfataricus with the Pf sequence, using Swiss Model. Then, that homology model was fit to the map density initially ...Details: Workflow involved generating a homology model from 2CLB structure from S. solfataricus with the Pf sequence, using Swiss Model. Then, that homology model was fit to the map density initially in Chimera using fitmap. After that, it was initially refined with rigid body real-space refinement in Phenix, tuned in coot, and subsequently finished refining with flexible fitting and enforced tetrahedral symmetry.
Atomic model buildingPDB-ID: 2CLB

2clb


Accession code: 2CLB / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 9.58 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002316920
ELECTRON MICROSCOPYf_angle_d0.434822920
ELECTRON MICROSCOPYf_chiral_restr0.03532508
ELECTRON MICROSCOPYf_plane_restr0.00352976
ELECTRON MICROSCOPYf_dihedral_angle_d3.66582280
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DELECTRON MICROSCOPYNCS constraints0.000707573323418
ens_1d_3DELECTRON MICROSCOPYNCS constraints0.000715509361007
ens_1d_4DELECTRON MICROSCOPYNCS constraints0.000707451121711
ens_1d_5DELECTRON MICROSCOPYNCS constraints0.000702437523294
ens_1d_6DELECTRON MICROSCOPYNCS constraints0.00070358533864
ens_1d_7DELECTRON MICROSCOPYNCS constraints0.000711894385023
ens_1d_8DELECTRON MICROSCOPYNCS constraints0.000710472292236
ens_1d_9DELECTRON MICROSCOPYNCS constraints0.00070436925189
ens_1d_10DELECTRON MICROSCOPYNCS constraints0.000714233457333
ens_1d_11DELECTRON MICROSCOPYNCS constraints0.000705747481605
ens_1d_12DELECTRON MICROSCOPYNCS constraints0.000700461978145

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