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- PDB-7s5c: M. xanthus ferritin-like protein EncB -

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Basic information

Entry
Database: PDB / ID: 7s5c
TitleM. xanthus ferritin-like protein EncB
ComponentsEncB
KeywordsCYTOSOLIC PROTEIN / encapsulin / cargo protein / encapsulated ferritin / ferroxidase
Function / homology: / EncFtn-like / encapsulin nanocompartment / Ferritin-like superfamily / intracellular iron ion homeostasis / metal ion binding / : / Encapsulin nanocompartment cargo protein EncB
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsEren, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS) United States
CitationJournal: Structure / Year: 2022
Title: Structural characterization of the Myxococcus xanthus encapsulin and ferritin-like cargo system gives insight into its iron storage mechanism.
Authors: Elif Eren / Bing Wang / Dennis C Winkler / Norman R Watts / Alasdair C Steven / Paul T Wingfield /
Abstract: Encapsulins are bacterial organelle-like cages involved in various aspects of metabolism, especially protection from oxidative stress. They can serve as vehicles for a wide range of medical ...Encapsulins are bacterial organelle-like cages involved in various aspects of metabolism, especially protection from oxidative stress. They can serve as vehicles for a wide range of medical applications. Encapsulin shell proteins are structurally similar to HK97 bacteriophage capsid protein and their function depends on the encapsulated cargos. The Myxococcus xanthus encapsulin system comprises EncA and three cargos: EncB, EncC, and EncD. EncB and EncC are similar to bacterial ferritins that can oxidize Fe to less toxic Fe. We analyzed EncA, EncB, and EncC by cryo-EM and X-ray crystallography. Cryo-EM shows that EncA cages can have T = 3 and T = 1 symmetry and that EncA T = 1 has a unique protomer arrangement. Also, we define EncB and EncC binding sites on EncA. X-ray crystallography of EncB and EncC reveals conformational changes at the ferroxidase center and additional metal binding sites, suggesting a mechanism for Fe oxidation and storage within the encapsulin shell.
History
DepositionSep 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EncB
B: EncB
E: EncB
F: EncB
G: EncB
H: EncB
I: EncB
J: EncB
C: EncB
D: EncB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,32639
Polymers119,86410
Non-polymers1,46229
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25050 Å2
ΔGint-387 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.830, 68.360, 83.390
Angle α, β, γ (deg.)90.00, 103.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
EncB


Mass: 11986.373 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: MXAN_3557 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D6H3
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: Fe
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 20% PEG MME, 10% PEG 20000, 100 mM Tris-Bicine pH 8.5, 30 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→43.34 Å / Num. obs: 56065 / % possible obs: 95.4 % / Redundancy: 6.2 % / CC1/2: 1 / Rrim(I) all: 0.09 / Net I/σ(I): 12.8
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4286 / CC1/2: 0.59 / Rrim(I) all: 0.87 / % possible all: 71.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N5E

5n5e


Resolution: 1.86→43.34 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 1970 3.58 %
Rwork0.1886 --
obs0.1899 54977 93.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5117 0 29 340 5486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065192
X-RAY DIFFRACTIONf_angle_d0.7616999
X-RAY DIFFRACTIONf_dihedral_angle_d32.701702
X-RAY DIFFRACTIONf_chiral_restr0.041774
X-RAY DIFFRACTIONf_plane_restr0.006938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.910.33861010.30512631X-RAY DIFFRACTION65
1.91-1.960.36371160.27063042X-RAY DIFFRACTION76
1.96-2.020.27031320.24613513X-RAY DIFFRACTION87
2.02-2.080.26681440.22423859X-RAY DIFFRACTION96
2.08-2.160.24391440.19493894X-RAY DIFFRACTION97
2.16-2.240.24011460.18133958X-RAY DIFFRACTION98
2.24-2.340.23261460.18743968X-RAY DIFFRACTION98
2.34-2.470.2051450.17973970X-RAY DIFFRACTION98
2.47-2.620.24571470.1813954X-RAY DIFFRACTION98
2.62-2.820.22551500.20614028X-RAY DIFFRACTION100
2.82-3.110.22881500.19664049X-RAY DIFFRACTION100
3.11-3.560.21811480.1884017X-RAY DIFFRACTION99
3.56-4.480.19061490.15694019X-RAY DIFFRACTION99
4.48-43.340.21081520.18824105X-RAY DIFFRACTION99

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