4pt2

From Proteopedia

(Difference between revisions)

Revision as of 07:29, 8 February 2023

Myxococcus xanthus encapsulin protein (EncA)

4pt2, resolution 4.60Å

Structural highlights

4pt2 is a 3 chain structure with sequence from Myxococcus xanthus DK 1622. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENCAP_MYXXD Shell component of a type 1, iron-storage encapsulin nanocompartment. Encapsulin nanocompartments are 32 nm in diameter with an iron- and phosphorus-rich core (4Fe:1P) about 24 nm in diameter. Upon expression in E.coli most particles are 32 nm, 20% are 18 nm. The core is filled with an average of 14 dense granules, 5-6 nm in diameter that are not evenly distributed. Each nanocompartment is estimated to hold 30,000-35,000 Fe atoms (PubMed:25024436, PubMed:31194509). The minor proteins EncB, EncC and EncD probably lie against the interior face of the nanocompartment (Probable).^[1] ^[2] ^[3]

Publication Abstract from PubMed

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.

A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress.,McHugh CA, Fontana J, Nemecek D, Cheng N, Aksyuk AA, Heymann JB, Winkler DC, Lam AS, Wall JS, Steven AC, Hoiczyk E EMBO J. 2014 Jul 14. pii: e201488566. PMID:25024436^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ McHugh CA, Fontana J, Nemecek D, Cheng N, Aksyuk AA, Heymann JB, Winkler DC, Lam AS, Wall JS, Steven AC, Hoiczyk E. A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. EMBO J. 2014 Jul 14. pii: e201488566. PMID:25024436 doi:http://dx.doi.org/10.15252/embj.201488566
↑ Sigmund F, Pettinger S, Kube M, Schneider F, Schifferer M, Schneider S, Efremova MV, Pujol-Martí J, Aichler M, Walch A, Misgeld T, Dietz H, Westmeyer GG. Iron-Sequestering Nanocompartments as Multiplexed Electron Microscopy Gene Reporters. ACS Nano. 2019 Jul 23;13(7):8114-8123. PMID:31194509 doi:10.1021/acsnano.9b03140
↑ McHugh CA, Fontana J, Nemecek D, Cheng N, Aksyuk AA, Heymann JB, Winkler DC, Lam AS, Wall JS, Steven AC, Hoiczyk E. A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. EMBO J. 2014 Jul 14. pii: e201488566. PMID:25024436 doi:http://dx.doi.org/10.15252/embj.201488566
↑ McHugh CA, Fontana J, Nemecek D, Cheng N, Aksyuk AA, Heymann JB, Winkler DC, Lam AS, Wall JS, Steven AC, Hoiczyk E. A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. EMBO J. 2014 Jul 14. pii: e201488566. PMID:25024436 doi:http://dx.doi.org/10.15252/embj.201488566

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4pt2"

@@ Line 3: / Line 3: @@
 <SX load='4pt2' size='340' side='right' viewer='molstar' caption='[[4pt2]], [[Resolution|resolution]] 4.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4pt2]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Myxxd Myxxd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PT2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4PT2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4pt2]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Myxococcus_xanthus_DK_1622 Myxococcus xanthus DK 1622]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PT2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PT2 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MXAN_3556 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246197 MYXXD])</td></tr>
+</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4pt2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pt2 OCA], [https://pdbe.org/4pt2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pt2 RCSB], [https://www.ebi.ac.uk/pdbsum/4pt2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pt2 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4pt2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pt2 OCA], [http://pdbe.org/4pt2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pt2 RCSB], [http://www.ebi.ac.uk/pdbsum/4pt2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pt2 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ENCAP_MYXXD ENCAP_MYXXD] Shell component of a type 1, iron-storage encapsulin nanocompartment. Encapsulin nanocompartments are 32 nm in diameter with an iron- and phosphorus-rich core (4Fe:1P) about 24 nm in diameter. Upon expression in E.coli most particles are 32 nm, 20% are 18 nm. The core is filled with an average of 14 dense granules, 5-6 nm in diameter that are not evenly distributed. Each nanocompartment is estimated to hold 30,000-35,000 Fe atoms (PubMed:25024436, PubMed:31194509). The minor proteins EncB, EncC and EncD probably lie against the interior face of the nanocompartment (Probable).<ref>PMID:25024436</ref> <ref>PMID:31194509</ref> <ref>PMID:25024436</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 </SX>
 [[Category: Large Structures]]
-[[Category: Myxxd]]
+[[Category: Myxococcus xanthus DK 1622]]
-[[Category: Aksyuk, A A]]
+[[Category: Aksyuk AA]]
-[[Category: Fontana, J]]
+[[Category: Fontana J]]
-[[Category: Hoiczyk, E]]
+[[Category: Hoiczyk E]]
-[[Category: Steven, A C]]
+[[Category: Steven AC]]
-[[Category: Hk97 fold]]
-[[Category: Shell protein]]
-[[Category: Virus like particle]]

4pt2

From Proteopedia

Revision as of 07:29, 8 February 2023

Myxococcus xanthus encapsulin protein (EncA)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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