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- PDB-4pt2: Myxococcus xanthus encapsulin protein (EncA) -

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Basic information

Entry
Database: PDB / ID: 4pt2
TitleMyxococcus xanthus encapsulin protein (EncA)
ComponentsEncapsulin protein
KeywordsVIRUS LIKE PARTICLE / HK97 fold / Shell protein
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / encapsulin nanocompartment / iron ion transport / intracellular iron ion homeostasis / Type 1 encapsulin shell protein EncA
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsFontana, J. / Aksyuk, A.A. / Steven, A.C. / Hoiczyk, E.
CitationJournal: EMBO J / Year: 2014
Title: A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress.
Authors: Colleen A McHugh / Juan Fontana / Daniel Nemecek / Naiqian Cheng / Anastasia A Aksyuk / J Bernard Heymann / Dennis C Winkler / Alan S Lam / Joseph S Wall / Alasdair C Steven / Egbert Hoiczyk /
Abstract: Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound ...Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound nanocompartments. Encapsulins constitute a class of nanocompartments widespread in bacteria and archaea whose functions have hitherto been unclear. Here, we characterize the encapsulin nanocompartment from Myxococcus xanthus, which consists of a shell protein (EncA, 32.5 kDa) and three internal proteins (EncB, 17 kDa; EncC, 13 kDa; EncD, 11 kDa). Using cryo-electron microscopy, we determined that EncA self-assembles into an icosahedral shell 32 nm in diameter (26 nm internal diameter), built from 180 subunits with the fold first observed in bacteriophage HK97 capsid. The internal proteins, of which EncB and EncC have ferritin-like domains, attach to its inner surface. Native nanocompartments have dense iron-rich cores. Functionally, they resemble ferritins, cage-like iron storage proteins, but with a massively greater capacity (~30,000 iron atoms versus ~3,000 in ferritin). Physiological data reveal that few nanocompartments are assembled during vegetative growth, but they increase fivefold upon starvation, protecting cells from oxidative stress through iron sequestration.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.3May 8, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-5917
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  • Superimposition on EM map
  • EMDB-5917
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Structure viewerMolecule:
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Assembly

Deposited unit
P: Encapsulin protein
A: Encapsulin protein
B: Encapsulin protein


Theoretical massNumber of molelcules
Total (without water)95,0763
Polymers95,0763
Non-polymers00
Water0
1
P: Encapsulin protein
A: Encapsulin protein
B: Encapsulin protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,704,556180
Polymers5,704,556180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
P: Encapsulin protein
A: Encapsulin protein
B: Encapsulin protein
x 5


  • icosahedral pentamer
  • 475 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)475,38015
Polymers475,38015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
P: Encapsulin protein
A: Encapsulin protein
B: Encapsulin protein
x 6


  • icosahedral 23 hexamer
  • 570 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)570,45618
Polymers570,45618
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Encapsulin protein / / EncA


Mass: 31691.977 Da / Num. of mol.: 3 / Fragment: UNP residues 8-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Strain: DK 1622 / Gene: MXAN_3556 / Plasmid: pET12a-3556 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q1D6H4

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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: Encapsulin protein (EncA) from Myxococcus xanthus / Type: COMPLEX
Buffer solutionName: 10 mM Tris, 10 mM MgCl2 / pH: 7.6 / Details: 10 mM Tris, 10 mM MgCl2
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh carbon grid with thin carbon support
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE / Temp: 83 K / Details: Plunged into liquid ethane (LEICA KF80)

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Dec 3, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 57620 X / Nominal defocus max: 1650 nm / Nominal defocus min: 600 nm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Polara cartridge-loading system
Image recordingElectron dose: 15 e/Å2
Image scansNum. digital images: 157

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
EM softwareName: Bsoft / Category: 3D reconstruction
CTF correctionDetails: Each micrograph
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: reference based / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14000 / Nominal pixel size: 1.102 Å / Actual pixel size: 1.102 Å
Details: Final map was calculated dividing particles into two independent data sets
Symmetry type: POINT
RefinementResolution: 4.6→771.4 Å / SU ML: 1.04 / σ(F): 0 / Phase error: 43.52 / Stereochemistry target values: MLHL
Details: Homology model of PDB entry 3DKT (I-TASSER), flexible fitting using MDFF and manual re-building using COOT, refined using structure factors derived from EMD-5917
RfactorNum. reflection% reflection
Rwork0.3489 --
obs0.3489 9859810 99.83 %
all-9859810 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.6→771.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6462 0 0 0 6462
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006395640
ELECTRON MICROSCOPYf_angle_d1.758536760
ELECTRON MICROSCOPYf_dihedral_angle_d18.807145800
ELECTRON MICROSCOPYf_chiral_restr0.06359760
ELECTRON MICROSCOPYf_plane_restr0.00670560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.6-4.71510.50161430.5055705705ELECTRON MICROSCOPY100
4.7151-4.84260.46291430.4851704782ELECTRON MICROSCOPY100
4.8426-4.98510.49481430.4819706995ELECTRON MICROSCOPY100
4.9851-5.1460.43691430.4563703960ELECTRON MICROSCOPY100
5.146-5.330.41281420.4322704720ELECTRON MICROSCOPY100
5.33-5.54340.44531440.4301705819ELECTRON MICROSCOPY100
5.5434-5.79570.44111420.4013705292ELECTRON MICROSCOPY100
5.7957-6.10130.42421430.4323705593ELECTRON MICROSCOPY100
6.1013-6.48360.41411430.392705092ELECTRON MICROSCOPY100
6.4836-6.98430.35941430.3629705117ELECTRON MICROSCOPY100
6.9843-7.68720.30541420.307705243ELECTRON MICROSCOPY100
7.6872-8.79960.31371430.293706205ELECTRON MICROSCOPY100
8.7996-11.08680.25321430.2476701578ELECTRON MICROSCOPY100
11.0868-782.48010.25061400.2398691712ELECTRON MICROSCOPY98

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