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- PDB-9s13: Focused refinement of Rhodospirillum rubrum encapsulated ferritin... -

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Basic information

Entry
Database: PDB / ID: 9s13
TitleFocused refinement of Rhodospirillum rubrum encapsulated ferritin within the encapsulin nanocompartment
ComponentsEncapsulated ferritin-like protein
KeywordsOXIDOREDUCTASE / Encapsulin / nanocompartment / encapsulated ferritin / STRUCTURAL PROTEIN
Function / homology
Function and homology information


encapsulin nanocompartment / ferroxidase / ferroxidase activity / iron ion transport / metal ion binding
Similarity search - Function
Ferritin-like protein / : / EncFtn-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Encapsulated ferritin-like protein
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMcIver, Z. / McCorvie, T.J. / Basle, A. / Marles-Wright, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)2306768 United Kingdom
CitationJournal: To Be Published
Title: Single particle reconstruction of Rhodospirillum rubrum encapsulin:encapsulated ferritin complex
Authors: McIver, Z. / McCorvie, T.J. / Basle, A. / Marles-Wright, J.
History
DepositionJul 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Encapsulated ferritin-like protein
B: Encapsulated ferritin-like protein
C: Encapsulated ferritin-like protein
D: Encapsulated ferritin-like protein
E: Encapsulated ferritin-like protein
F: Encapsulated ferritin-like protein
G: Encapsulated ferritin-like protein
H: Encapsulated ferritin-like protein
I: Encapsulated ferritin-like protein
J: Encapsulated ferritin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,67620
Polymers152,11710
Non-polymers55810
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "J"
d_2ens_1chain "B"
d_3ens_1chain "H"
d_4ens_1chain "C"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "A"
d_9ens_1chain "I"
d_10ens_1chain "D"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 4 - 97 / Label seq-ID: 4 - 97

Dom-IDAuth asym-IDLabel asym-ID
d_1JJ
d_2BB
d_3HH
d_4CC
d_5EE
d_6FF
d_7GG
d_8AA
d_9II
d_10DD

NCS oper:
IDCodeMatrixVector
1given(0.80702568164316, -0.5905152149001, 0.0011533169039931), (-0.59051504086406, -0.80702646402713, -0.00052237264272838), (0.001239226256311, -0.00025948284062109, -0.99999919849315)169.13829784843, 518.62798435359, 432.36925407187
2given(-0.81034205013016, -0.58595557559241, -0.0013510081454112), (0.5859548523308, -0.81034317510133, 0.00092173569048529), (-0.0016348763972026, -4.4708589236138E-5, 0.99999866258926)518.57264742788, 264.58454789767, 0.33556092746721
3given(0.81033699404659, 0.58596257178466, 0.0013492764847314), (0.58596183492855, -0.8103381165279, 0.00093000493757846), (0.0016383182503085, 3.7007119253321E-5, -0.99999865727099)-85.996848245429, 264.580275521, 432.24141741343
4given(-0.99997419740601, 0.0040799513733538, -0.0059125729599914), (0.0040767242209484, 0.99999153457519, 0.00055776122613367), (0.0059147985462302, 0.00053364290505308, -0.99998236503621)433.0251148884, -0.87167766237982, 431.34320820243
5given(0.31392186084901, 0.94944747171636, 0.0016011659826175), (-0.94944835623592, 0.31392293063512, -0.00046093640087946), (-0.00094027761813359, -0.00137552639756, 0.9999986119016)-57.239743014499, 353.89034229749, 0.52147667427545
6given(-0.80661821087106, 0.59107180657202, 0.0010869070160229), (-0.59107278367991, -0.80661732113708, -0.0012089807775644), (0.00016212357328368, -0.0016176270673383, 0.99999867849844)262.71802188379, 518.81744146947, 0.39625302644413
7given(-0.31828802289116, -0.94797066103521, -0.0066603528820794), (-0.9479934590597, 0.318287865404, 0.0011118977451426), (0.001065863061208, 0.0066678747021993, -0.99997720143156)491.38588092834, 352.34001533879, 430.83326576486
8given(0.30835778092169, -0.95127045433446, 4.0686266356227E-5), (0.95127044760194, 0.30835777276784, -0.00013961682252896), (0.00012026743172401, 8.1755576382307E-5, 0.99999998942589)355.32282402945, -56.135422512099, -0.035429093368862
9given(-0.30835803617389, 0.95127037157108, -4.1206876202038E-5), (0.95127036486329, 0.30835802794517, -0.00013976630411448), (-0.00012024907296466, -8.2296943219613E-5, -0.99999998938369)77.253388600859, -56.135450652017, 432.61153142747

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Components

#1: Protein
Encapsulated ferritin-like protein / EncFtn


Mass: 15211.720 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: fer, Rru_A0973 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2RVS1, ferroxidase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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

Component
IDNameTypeEntity IDParent-IDSource
1Rhodospirillum rubrum encapsulated ferritinCOMPLEX#10RECOMBINANT
2Rhodospirillum rubrum encapsulated ferritinCOMPLEX#11RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
112.4 MDaNO
210.15 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Rhodospirillum rubrum (bacteria)1085
42Rhodospirillum rubrum (bacteria)1085
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli BL21(DE3) (bacteria)469008
42Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 8 / Details: 150 mM NaCl, 50 mM Tris-HCl, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium chlorideNaCl1
250 mMTrisC4H11NO31
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Complex of Rhodospirillum rubrum encapsulin and encapsulated ferritin
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K
Details: 4 uL of sample was applied to the grids, which were then blotted 100% humidity blot force 5 wait time 10 s blot time 3 seconds

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80 K
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 7994

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraX9.03model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC4.73D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 346315
Details: Particles from icosahedral reconstruction of Encapsulin:Encapsulated Ferritin complex
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272846 / Algorithm: FOURIER SPACE
Details: Final reconstruction performed by local refinement of aligned encapsulated ferritin decamers from custom symmetry expansion.
Num. of class averages: 14 / Symmetry type: POINT
Atomic model buildingB value: 146.6 / Protocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingDetails: model produced in ModelAngelo / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 62.14 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00267850
ELECTRON MICROSCOPYf_angle_d0.446110680
ELECTRON MICROSCOPYf_chiral_restr0.03531200
ELECTRON MICROSCOPYf_plane_restr0.00371390
ELECTRON MICROSCOPYf_dihedral_angle_d2.89581020
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2JJELECTRON MICROSCOPYNCS constraints3.4181789207066E-13
ens_1d_3JJELECTRON MICROSCOPYNCS constraints9.9318636058365E-11
ens_1d_4JJELECTRON MICROSCOPYNCS constraints2.6534727366913E-13
ens_1d_5JJELECTRON MICROSCOPYNCS constraints4.560537266484E-12
ens_1d_6JJELECTRON MICROSCOPYNCS constraints3.8909266690134E-13
ens_1d_7JJELECTRON MICROSCOPYNCS constraints6.8455486862809E-12
ens_1d_8JJELECTRON MICROSCOPYNCS constraints1.6549199504029E-11
ens_1d_9JJELECTRON MICROSCOPYNCS constraints7.2470178714539E-11
ens_1d_10JJELECTRON MICROSCOPYNCS constraints1.4453875588358E-10

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