7S5C | pdb_00007s5c

M. xanthus ferritin-like protein EncB

  • Classification: CYTOSOLIC PROTEIN
  • Organism(s): Myxococcus xanthus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-09-10 Released: 2022-02-02 
  • Deposition Author(s): Eren, E.
  • Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7S5C

This is version 1.3 of the entry. See complete history

Literature

Structural characterization of the Myxococcus xanthus encapsulin and ferritin-like cargo system gives insight into its iron storage mechanism.

Eren, E.Wang, B.Winkler, D.C.Watts, N.R.Steven, A.C.Wingfield, P.T.

(2022) Structure 30: 551-563.e4

  • DOI: https://doi.org/10.1016/j.str.2022.01.008
  • Primary Citation Related Structures: 
    7S20, 7S21, 7S2T, 7S4Q, 7S5C, 7S5K, 7S8T

  • PubMed 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 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 +2 to less toxic Fe +3 . 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.


  • Organizational Affiliation
    • Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: elif.eren@nih.gov.

Macromolecule Content 

  • Total Structure Weight: 121.33 kDa 
  • Atom Count: 5,486 
  • Modeled Residue Count: 632 
  • Deposited Residue Count: 1,070 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
EncB107Myxococcus xanthusMutation(s): 0 
Gene Names: MXAN_3557
UniProt
Find proteins for Q1D6H3 (Myxococcus xanthus (strain DK1622))
Explore Q1D6H3 
Go to UniProtKB:  Q1D6H3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1D6H3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE

Query on FE



Download:Ideal Coordinates CCD File
AA [auth H]
CA [auth I]
DA [auth I]
FA [auth J]
IA [auth D]
AA [auth H],
CA [auth I],
DA [auth I],
FA [auth J],
IA [auth D],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
O [auth B],
Q [auth E],
R [auth E],
T [auth F],
U [auth F],
W [auth G],
X [auth G],
Z [auth H]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
BA [auth H]
EA [auth I]
GA [auth J]
HA [auth C]
MA [auth D]
BA [auth H],
EA [auth I],
GA [auth J],
HA [auth C],
MA [auth D],
N [auth A],
P [auth B],
S [auth E],
V [auth F],
Y [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.83α = 90
b = 68.36β = 103.62
c = 83.39γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2022-02-02 
  • Deposition Author(s): Eren, E.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2022-04-20
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description