8PO9

Polyethylene oxidation hexamerin PEase Cibeles (XP_026756460) from Galleria mellonella


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Plastic degradation by insect hexamerins: Near-atomic resolution structures of the polyethylene-degrading proteins from the wax worm saliva.

Spinola-Amilibia, M.Illanes-Vicioso, R.Ruiz-L Formula See Text Pez, E.Colomer-Vidal, P.Rodriguez, F.V.Peces Perez, R.Arias, C.F.Torroba, T.Sol Formula See Text, M.Arias-Palomo, E.Bertocchini, F.

(2023) Sci Adv 9: eadi6813-eadi6813

  • DOI: https://doi.org/10.1126/sciadv.adi6813
  • Primary Citation of Related Structures:  
    8CA9, 8CAD, 8CAN, 8PO9

  • PubMed Abstract: 

    Plastic waste management is a pressing ecological, social, and economic challenge. The saliva of the lepidopteran Galleria mellonella larvae is capable of oxidizing and depolymerizing polyethylene in hours at room temperature. Here, we analyze by cryo-electron microscopy (cryo-EM) G. mellonella 's saliva directly from the native source. The three-dimensional reconstructions reveal that the buccal secretion is mainly composed of four hexamerins belonging to the hemocyanin/phenoloxidase family, renamed Demetra, Cibeles, Ceres, and a previously unidentified factor termed Cora. Functional assays show that this factor, as its counterparts Demetra and Ceres, is also able to oxidize and degrade polyethylene. The cryo-EM data and the x-ray analysis from purified fractions show that they self-assemble primarily into three macromolecular complexes with striking structural differences that likely modulate their activity. Overall, these results establish the ground to further explore the hexamerins' functionalities, their role in vivo, and their eventual biotechnological application.


  • Organizational Affiliation

    Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arylphorin
A, B, C, D, E
A, B, C, D, E, F
702Galleria mellonellaMutation(s): 0 
UniProt
Find proteins for Q24995 (Galleria mellonella)
Explore Q24995 
Go to UniProtKB:  Q24995
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ24995
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, K, M, N, O
H, K, M, N, O, P, R
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, L
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68668TB
GlyCosmos:  G68668TB
GlyGen:  G68668TB
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Q
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
IA [auth B],
QB [auth E],
V [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
AC [auth F]
HB [auth D]
IB [auth D]
JA [auth B]
KA [auth B]
AC [auth F],
HB [auth D],
IB [auth D],
JA [auth B],
KA [auth B],
RB [auth E],
UA [auth C],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
GB [auth D],
ZB [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
LA [auth B]
MA [auth B]
SB [auth E]
AA [auth A],
BA [auth A],
LA [auth B],
MA [auth B],
SB [auth E],
VA [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLY
Query on GLY

Download Ideal Coordinates CCD File 
BC [auth F]
JB [auth D]
KB [auth D]
TB [auth E]
UB [auth E]
BC [auth F],
JB [auth D],
KB [auth D],
TB [auth E],
UB [auth E],
WA [auth C],
XA [auth C]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
CA [auth B]
LB [auth E]
NA [auth C]
S [auth A]
VB [auth F]
CA [auth B],
LB [auth E],
NA [auth C],
S [auth A],
VB [auth F],
YA [auth D]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AB [auth D]
BB [auth D]
CB [auth D]
DB [auth D]
EA [auth B]
AB [auth D],
BB [auth D],
CB [auth D],
DB [auth D],
EA [auth B],
EB [auth D],
FA [auth B],
FB [auth D],
GA [auth B],
HA [auth B],
NB [auth E],
OB [auth E],
PA [auth C],
PB [auth E],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
U [auth A],
XB [auth F],
YB [auth F],
ZA [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth B],
MB [auth E],
OA [auth C],
T [auth A],
WB [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.75α = 90
b = 196.58β = 90
c = 224.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2021-129038NB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release