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- PDB-7s8t: M. xanthus ferritin-like protein EncC -

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Basic information

Entry
Database: PDB / ID: 7s8t
TitleM. xanthus ferritin-like protein EncC
ComponentsEncC
KeywordsCYTOSOLIC PROTEIN / encapsulin / cargo protein / encapsulated ferritin / ferroxidase
Function / homologyEncFtn-like / : / encapsulin nanocompartment / Ferritin-like superfamily / : / Demethoxyubiquinone hydroxylase family protein
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 19, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)154,09317
Polymers153,70210
Non-polymers3917
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29970 Å2
ΔGint-267 kcal/mol
Surface area36030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.703, 47.797, 135.330
Angle α, β, γ (deg.)90.000, 90.130, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 23 through 25 or (resid 26...
21(chain B and (resid 23 through 28 or (resid 29...
31(chain C and (resid 23 through 25 or (resid 26...
41(chain D and (resid 23 through 25 or (resid 26...
51(chain E and (resid 23 through 25 or (resid 26...
61(chain F and (resid 23 through 25 or (resid 26...
71(chain G and (resid 23 through 25 or (resid 26...
81(chain H and (resid 23 through 25 or (resid 26...
91(chain I and (resid 23 through 25 or (resid 26...
101(chain J and (resid 23 through 25 or (resid 26...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain A and (resid 23 through 25 or (resid 26...AA23 - 2523 - 25
12GLUGLUGLUGLU(chain A and (resid 23 through 25 or (resid 26...AA2626
13PROPROILEILE(chain A and (resid 23 through 25 or (resid 26...AA19 - 10019 - 100
14PROPROILEILE(chain A and (resid 23 through 25 or (resid 26...AA19 - 10019 - 100
15PROPROILEILE(chain A and (resid 23 through 25 or (resid 26...AA19 - 10019 - 100
16PROPROILEILE(chain A and (resid 23 through 25 or (resid 26...AA19 - 10019 - 100
21THRTHRALAALA(chain B and (resid 23 through 28 or (resid 29...BB23 - 2823 - 28
22ARGARGARGARG(chain B and (resid 23 through 28 or (resid 29...BB2929
23LYSLYSILEILE(chain B and (resid 23 through 28 or (resid 29...BB21 - 10021 - 100
24LYSLYSILEILE(chain B and (resid 23 through 28 or (resid 29...BB21 - 10021 - 100
25LYSLYSILEILE(chain B and (resid 23 through 28 or (resid 29...BB21 - 10021 - 100
26LYSLYSILEILE(chain B and (resid 23 through 28 or (resid 29...BB21 - 10021 - 100
31THRTHRTHRTHR(chain C and (resid 23 through 25 or (resid 26...CC23 - 2523 - 25
32GLUGLUGLUGLU(chain C and (resid 23 through 25 or (resid 26...CC2626
33LYSLYSILEILE(chain C and (resid 23 through 25 or (resid 26...CC21 - 10021 - 100
34LYSLYSILEILE(chain C and (resid 23 through 25 or (resid 26...CC21 - 10021 - 100
35LYSLYSILEILE(chain C and (resid 23 through 25 or (resid 26...CC21 - 10021 - 100
36LYSLYSILEILE(chain C and (resid 23 through 25 or (resid 26...CC21 - 10021 - 100
41THRTHRTHRTHR(chain D and (resid 23 through 25 or (resid 26...DD23 - 2523 - 25
42GLUGLUGLUGLU(chain D and (resid 23 through 25 or (resid 26...DD2626
43LYSLYSILEILE(chain D and (resid 23 through 25 or (resid 26...DD21 - 10021 - 100
44LYSLYSILEILE(chain D and (resid 23 through 25 or (resid 26...DD21 - 10021 - 100
45LYSLYSILEILE(chain D and (resid 23 through 25 or (resid 26...DD21 - 10021 - 100
46LYSLYSILEILE(chain D and (resid 23 through 25 or (resid 26...DD21 - 10021 - 100
51THRTHRTHRTHR(chain E and (resid 23 through 25 or (resid 26...EE23 - 2523 - 25
52GLUGLUGLUGLU(chain E and (resid 23 through 25 or (resid 26...EE2626
53THRTHRILEILE(chain E and (resid 23 through 25 or (resid 26...EE23 - 10023 - 100
54THRTHRILEILE(chain E and (resid 23 through 25 or (resid 26...EE23 - 10023 - 100
55THRTHRILEILE(chain E and (resid 23 through 25 or (resid 26...EE23 - 10023 - 100
56THRTHRILEILE(chain E and (resid 23 through 25 or (resid 26...EE23 - 10023 - 100
61THRTHRTHRTHR(chain F and (resid 23 through 25 or (resid 26...FF23 - 2523 - 25
62GLUGLUGLUGLU(chain F and (resid 23 through 25 or (resid 26...FF2626
63LYSLYSILEILE(chain F and (resid 23 through 25 or (resid 26...FF21 - 10021 - 100
64LYSLYSILEILE(chain F and (resid 23 through 25 or (resid 26...FF21 - 10021 - 100
65LYSLYSILEILE(chain F and (resid 23 through 25 or (resid 26...FF21 - 10021 - 100
66LYSLYSILEILE(chain F and (resid 23 through 25 or (resid 26...FF21 - 10021 - 100
71THRTHRTHRTHR(chain G and (resid 23 through 25 or (resid 26...GG23 - 2523 - 25
72GLUGLUGLUGLU(chain G and (resid 23 through 25 or (resid 26...GG2626
73LYSLYSILEILE(chain G and (resid 23 through 25 or (resid 26...GG21 - 10021 - 100
74LYSLYSILEILE(chain G and (resid 23 through 25 or (resid 26...GG21 - 10021 - 100
75LYSLYSILEILE(chain G and (resid 23 through 25 or (resid 26...GG21 - 10021 - 100
76LYSLYSILEILE(chain G and (resid 23 through 25 or (resid 26...GG21 - 10021 - 100
81THRTHRTHRTHR(chain H and (resid 23 through 25 or (resid 26...HH23 - 2523 - 25
82GLUGLUGLUGLU(chain H and (resid 23 through 25 or (resid 26...HH2626
83THRTHRILEILE(chain H and (resid 23 through 25 or (resid 26...HH23 - 10023 - 100
84THRTHRILEILE(chain H and (resid 23 through 25 or (resid 26...HH23 - 10023 - 100
85THRTHRILEILE(chain H and (resid 23 through 25 or (resid 26...HH23 - 10023 - 100
86THRTHRILEILE(chain H and (resid 23 through 25 or (resid 26...HH23 - 10023 - 100
91THRTHRTHRTHR(chain I and (resid 23 through 25 or (resid 26...II23 - 2523 - 25
92GLUGLUGLUGLU(chain I and (resid 23 through 25 or (resid 26...II2626
93METMETILEILE(chain I and (resid 23 through 25 or (resid 26...II22 - 10022 - 100
94METMETILEILE(chain I and (resid 23 through 25 or (resid 26...II22 - 10022 - 100
95METMETILEILE(chain I and (resid 23 through 25 or (resid 26...II22 - 10022 - 100
96METMETILEILE(chain I and (resid 23 through 25 or (resid 26...II22 - 10022 - 100
101THRTHRTHRTHR(chain J and (resid 23 through 25 or (resid 26...JJ23 - 2523 - 25
102GLUGLUGLUGLU(chain J and (resid 23 through 25 or (resid 26...JJ2626
103VALVALILEILE(chain J and (resid 23 through 25 or (resid 26...JJ18 - 10018 - 100
104VALVALILEILE(chain J and (resid 23 through 25 or (resid 26...JJ18 - 10018 - 100
105VALVALILEILE(chain J and (resid 23 through 25 or (resid 26...JJ18 - 10018 - 100
106VALVALILEILE(chain J and (resid 23 through 25 or (resid 26...JJ18 - 10018 - 100

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Components

#1: Protein
EncC / Ferritin / Demethoxyubiquinone hydroxylase family protein


Mass: 15370.245 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: BHS06_21005, HK404_00050, I5Q59_22090 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y6CD88
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
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, 5 mM iron 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 EIGER 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: 2.49→37.77 Å / Num. obs: 32526 / % possible obs: 96.4 % / Redundancy: 6.6 % / CC1/2: 1 / Rrim(I) all: 0.16 / Net I/σ(I): 12.5
Reflection shellResolution: 2.49→2.58 Å / Mean I/σ(I) obs: 6.7 / Num. unique obs: 3099 / CC1/2: 0.5 / Rrim(I) all: 0.54 / % possible all: 92.9

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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: 2.49→37.77 Å / Cross valid method: THROUGHOUT / σ(F): 122.73 / Phase error: 38.68 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3395 2042 6.28 %
Rwork0.3248 30532 -
obs0.3341 32526 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.88 Å2 / Biso mean: 57.3928 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.49→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6341 0 7 86 6434
Biso mean--58.7 48.65 -
Num. residues----800
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2280X-RAY DIFFRACTION10.018TORSIONAL
12B2280X-RAY DIFFRACTION10.018TORSIONAL
13C2280X-RAY DIFFRACTION10.018TORSIONAL
14D2280X-RAY DIFFRACTION10.018TORSIONAL
15E2280X-RAY DIFFRACTION10.018TORSIONAL
16F2280X-RAY DIFFRACTION10.018TORSIONAL
17G2280X-RAY DIFFRACTION10.018TORSIONAL
18H2280X-RAY DIFFRACTION10.018TORSIONAL
19I2280X-RAY DIFFRACTION10.018TORSIONAL
110J2280X-RAY DIFFRACTION10.018TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.49-2.560.37681360.34792050218686
2.56-2.630.36211440.34312135227991
2.63-2.70.38421450.352189233490
2.7-2.790.36961280.36292055218385
2.79-2.890.41521390.36222197233693
2.89-3.010.42641450.36552231237693
3.01-3.140.36361440.36262198234293
3.14-3.310.33691450.38532205235093
3.31-3.510.40271480.35332234238293
3.52-3.790.37111440.33262213235792
3.79-4.170.33011380.30672083222186
4.17-4.770.30841450.2992233237891
4.77-60.34181460.35672277242392
6-37.770.33841470.3032232237989

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