8PO9 | pdb_00008po9

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 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8PO9

This is version 1.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 518.36 kDa 
  • Atom Count: 37,172 
  • Modeled Residue Count: 4,055 
  • Deposited Residue Count: 4,212 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD 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 GlycosylationD 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 GlycosylationD 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 GlycosylationD 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 GlycosylationD 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 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
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
  • Version 1.1: 2024-11-13
    Changes: Structure summary