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- EMDB-16531: Cryo-EM structure of the Cora homohexamer from Galleria mellonell... -

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Basic information

Entry
Database: EMDB / ID: EMD-16531
TitleCryo-EM structure of the Cora homohexamer from Galleria mellonella saliva
Map data
Sample
  • Complex: Cora homocomplex
    • Protein or peptide: basic juvenile hormone-suppressible protein 1
  • Ligand: TRYPTOPHAN
  • Ligand: COPPER (II) ION
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsGalleria mellonella / Wax worm saliva / Plastic degradation / Polyethylene degradation / PEases / Hexamerin / Hemocyanin/phenoloxidase superfamily / Metal binding / UNKNOWN FUNCTION
Function / homology
Function and homology information


Arthropod hemocyanins / insect LSPs signature 1. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin ...Arthropod hemocyanins / insect LSPs signature 1. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin / Di-copper centre-containing domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Basic juvenile hormone-suppressible protein 1
Similarity search - Component
Biological speciesGalleria mellonella (greater wax moth)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.93 Å
AuthorsSpinola-Amilibia M / Arias-Palomo E / Araujo-Bazan L / Berger JM
Funding support Germany, Spain, Belgium, 7 items
OrganizationGrant numberCountry
Roechling Stiftung Germany
Spanish National Research Council Spain
NATO Science for Peace and Security ProgramSPS G5536 Belgium
Junta de Castilla y Leon, Consejeria de Educacion y Cultura y Fondo Social EuropeoBU263P18 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-111215RB-100 Spain
Generalitat de Catalunya2017 SGR 1192 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-120275GB-I00 Spain
CitationJournal: Sci Adv / Year: 2023
Title: Plastic degradation by insect hexamerins: Near-atomic resolution structures of the polyethylene-degrading proteins from the wax worm saliva.
Authors: Mercedes Spínola-Amilibia / Ramiro Illanes-Vicioso / Elena Ruiz-López / Pere Colomer-Vidal / Francisco Rodriguez-Ventura / Rosa Peces Pérez / Clemente F Arias / Tomas Torroba / Maria ...Authors: Mercedes Spínola-Amilibia / Ramiro Illanes-Vicioso / Elena Ruiz-López / Pere Colomer-Vidal / Francisco Rodriguez-Ventura / Rosa Peces Pérez / Clemente F Arias / Tomas Torroba / Maria Solà / Ernesto Arias-Palomo / Federica Bertocchini /
Abstract: Plastic waste management is a pressing ecological, social, and economic challenge. The saliva of the lepidopteran larvae is capable of oxidizing and depolymerizing polyethylene in hours at room ...Plastic waste management is a pressing ecological, social, and economic challenge. The saliva of the lepidopteran larvae is capable of oxidizing and depolymerizing polyethylene in hours at room temperature. Here, we analyze by cryo-electron microscopy (cryo-EM) '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.
History
DepositionJan 24, 2023-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16531.png

Downloads & links

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Map

FileDownload / File: emd_16531.map.gz / Format: CCP4 / Size: 199.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 374 pix.
= 305.165 Å		0.82 Å/pix.
x 374 pix.
= 305.165 Å		0.82 Å/pix.
x 374 pix.
= 305.165 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81595 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.17071283 - 0.28437942
Average (Standard dev.)0.000075937416 (±0.01032626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions374374374
Spacing374374374
CellA=B=C: 305.16528 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16531_msk_1.map
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Additional map: #1

Fileemd_16531_additional_1.map
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Half map: #2

Fileemd_16531_half_map_1.map
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Half map: #1

Fileemd_16531_half_map_2.map
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Sample components

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Entire : Cora homocomplex

EntireName: Cora homocomplex
Components
  • Complex: Cora homocomplex
    • Protein or peptide: basic juvenile hormone-suppressible protein 1
  • Ligand: TRYPTOPHAN
  • Ligand: COPPER (II) ION
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: Cora homocomplex

SupramoleculeName: Cora homocomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Homohexamer
Source (natural)Organism: Galleria mellonella (greater wax moth)

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Macromolecule #1: basic juvenile hormone-suppressible protein 1

MacromoleculeName: basic juvenile hormone-suppressible protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Galleria mellonella (greater wax moth)
Molecular weightTheoretical: 88.394211 KDa
SequenceString: MVVTMRLVVA AVLLAAVAAS VVHDELKNIV ITKEPMKNMD MKSKEMCILK LMNHILQPTM YEDVREVAKA WVLEENEDKY MKMEAVKEF INTYKMGMLP RGEVFVHMDH KHVEEAVKVF KLLYFANDFD VFLKTACWLR ERINGGMFVY ALTAAIFHRS D CSGIKIPA ...String:
MVVTMRLVVA AVLLAAVAAS VVHDELKNIV ITKEPMKNMD MKSKEMCILK LMNHILQPTM YEDVREVAKA WVLEENEDKY MKMEAVKEF INTYKMGMLP RGEVFVHMDH KHVEEAVKVF KLLYFANDFD VFLKTACWLR ERINGGMFVY ALTAAIFHRS D CSGIKIPA PYEIYPYLFV DSNILHKAFM MKMSKAAMDP VMKNYYGIKV KDNSMVIIDW RKGLRHTMSE FDRTSYFTED ID LNTYLYY MHMSYPYWMN EDMYRVNKER RGEAMWYGYQ QLQARLRLER LSHHMCDLKP LDLDGTLDEG YWPKILLHTG DEM PVRYNK MKLTNENNIK YRLLLEDNKR LIRDGIKKGH MAMHDGTTVS LKKPDDIENL CRIVLGGFVS KDDHKGKSSI WRNL AKTML SYGTYNMGKY TYIPTAADMY STALRDPGMW KMLKLISEYF IMFKEMLPKY TREELDFPGV KIEQVTTDKL VTFMD EYDV DITNAVYLDH DEMQKHRSDM MYVARMHRLN HQPFKITIDV ASDKAVECVV RVFLGPKLDC MGRFTSVNDK RNDMVE IDS FLYKLETGKN TIVRDSLEMN NVIKERPWSR NNWAMDPSGG QKAQDNWWYK SRIGFPHRLL LPMGSHGGMP YQMFVIV TP VRAGMSLPSI DMNTAKERKA CRWTVCMDTM PLGFPFDRPI DETNFYTKNM KFHDVMVYTK DLAMSNMVKD VDMSEMVM K RDDLTYLDKD MLVKRSYKSV MMMSGDDMTH M

UniProtKB: Basic juvenile hormone-suppressible protein 1

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Macromolecule #2: TRYPTOPHAN

MacromoleculeName: TRYPTOPHAN / type: ligand / ID: 2 / Number of copies: 6 / Formula: TRP
Molecular weightTheoretical: 204.225 Da
Chemical component information

ChemComp-TRP:
TRYPTOPHAN

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Macromolecule #3: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 3170 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
50.0 mMNaClSodium chloride
0.5 %GlycerolGlycerol
0.015 %NP-40Nonidet P-40
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 2 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 6386 / Average exposure time: 5.5 sec. / Average electron dose: 58.3 e/Å2
Details: Images were collected in super-resolution mode (pixel size of 0.543 angstrom)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.1 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsSuper-resolution counting mode
Particle selectionNumber selected: 1826686 / Details: Autopicking from relion_3.1 with two templates
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3wjm

Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 1.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 258795
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 251000 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 39.074
Output model

PDB-8can:
Cryo-EM structure of the Cora homohexamer from Galleria mellonella saliva

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