[English] 日本語
Yorodumi
- EMDB-16521: Cryo-EM structure of the Cibeles-Demetra 3:3 heterocomplex from G... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16521
TitleCryo-EM structure of the Cibeles-Demetra 3:3 heterocomplex from Galleria mellonella saliva
Map data
Sample
  • Complex: Cibeles-Demetra heterocomplex
    • Protein or peptide: Arylphorin
    • Protein or peptide: Demetra
  • Ligand: COPPER (II) ION
  • Ligand: water
KeywordsGalleria mellonella / Wax worm saliva / Plastic degradation / Polyethylene degradation / PEases / Hexamerin / Hemocyanin/phenoloxidase superfamily / Metal binding / Arylphorin / UNKNOWN FUNCTION
Function / homology
Function and homology information


nutrient reservoir activity / extracellular region
Similarity search - Function
Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / 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 ...Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / 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
Biological speciesGalleria mellonella (greater wax moth)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsSpinola-Amilibia M / Arias-Palomo E / Araujo-Bazan L / Berger JM
Funding support Germany, Belgium, Spain, 7 items
OrganizationGrant numberCountry
Roechling Stiftung Germany
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
Spanish National Research Council 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

-
Structure visualization

Supplemental images

emd_16521.png

Downloads & links

-
Map

FileDownload / File: emd_16521.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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81595 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.09567714 - 0.19876005
Average (Standard dev.)0.000106571584 (±0.00783634)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_16521_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_16521_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16521_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_16521_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cibeles-Demetra heterocomplex

EntireName: Cibeles-Demetra heterocomplex
Components
  • Complex: Cibeles-Demetra heterocomplex
    • Protein or peptide: Arylphorin
    • Protein or peptide: Demetra
  • Ligand: COPPER (II) ION
  • Ligand: water

-
Supramolecule #1: Cibeles-Demetra heterocomplex

SupramoleculeName: Cibeles-Demetra heterocomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Complex of two trimeric rings of Cibeles and Demetra
Source (natural)Organism: Galleria mellonella (greater wax moth)

-
Macromolecule #1: Arylphorin

MacromoleculeName: Arylphorin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Galleria mellonella (greater wax moth)
Molecular weightTheoretical: 83.778 KDa
SequenceString: MQTVLFLAAL VSLAAAGYPQ YHYDVETRKL DPSLLNIQTK VLSLLENWKQ VNPDDEYYKI GKEYNVEANM ESYTNREVVT EFLSLYKAG FIPKNEVFSI FYENQALEVI ALYRLFYYAK DFETFYKTAA FARVWLNEGQ FVYAFYLAVI HRADTRGIVL P APYEIWPE ...String:
MQTVLFLAAL VSLAAAGYPQ YHYDVETRKL DPSLLNIQTK VLSLLENWKQ VNPDDEYYKI GKEYNVEANM ESYTNREVVT EFLSLYKAG FIPKNEVFSI FYENQALEVI ALYRLFYYAK DFETFYKTAA FARVWLNEGQ FVYAFYLAVI HRADTRGIVL P APYEIWPE YFMNSDVLSK IYRIQMQKGL IIPEQGPYYG ILSKDNAYYF YANYSGPLTY EDNENLLSYF IEDIGWNSYY YY FHNRFPF WENGEQLIGP LKERRGEIYY YVYQKILARY YLERLANGLG EIPRFNWLDK YQTSYYPLLS SYQLPFAQRN DDY YLASGD NINDIQFIDT YEKTFLQLLQ KGQFKAYKQE VDLYNSKSIN FVGNYWQSNA DLYEKVPKRN YWRSYEATAR RVLG AAPRS SINYENMNIP TALDFYQTSL RDPAFYQLYA KILDYINEYK EYLEPYSQDV LHYVGVKIND VKVDKLVTYF EYFDW NATN AVYLSEQQLD TVSPSYIVRQ PRLNNKPFTV NIDIKSDVES EVVVKIFLGP KYDGNGLPIS LEDNWINFIE LDWFTH KLT SGQNKIARKS EEFFFFKDDS VSLFKIYELL SNGQVPSYMV DRYIYLPRRL ILPRGTQRGF PLQLFVVVYP YQAPVKE WE SMRQYIVDNK PFGYPFDRPV TLPYYFNQPN MYFKDVYVYQ EGEQYPYYNS YWSQNQVSNH

UniProtKB: Arylphorin

-
Macromolecule #2: Demetra

MacromoleculeName: Demetra / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Galleria mellonella (greater wax moth)
Molecular weightTheoretical: 83.310484 KDa
SequenceString: MKTVLVLAAL IGLVAAGYPL FNNNVKTKTL DPNLVNIQKK VLLLLENWKQ VDPDDEYYKI GKEYNIEANI ESYTNREVVT EFLSLYKTG FTAKNQIFSI YYENQALEVR ALYRLFYYAK DFETFYKTAA FARVWLNEGQ FIYAFYIAVI HRADTRGIVL P APYEIWPE ...String:
MKTVLVLAAL IGLVAAGYPL FNNNVKTKTL DPNLVNIQKK VLLLLENWKQ VDPDDEYYKI GKEYNIEANI ESYTNREVVT EFLSLYKTG FTAKNQIFSI YYENQALEVR ALYRLFYYAK DFETFYKTAA FARVWLNEGQ FIYAFYIAVI HRADTRGIVL P APYEIWPE YFVNSDVLAK INRIQMQKGL ILPETAQYYG VLAKDNAYYF YANYSGPWTY ENNENLLSYF IEDVAWNSYY YY FHSKLQF WEKGENAIGP FKERRGEIYY FIYQQILARY YLERLSNGLG EIPRFNWNDR LQAGYYPLLT THQIPFAQRN GDY YLANDD NIEDIQFVDS YEKTFLQFLQ KGQFKAYKQE VDLYNSKSVN FVGNYWQANV DLYEKVPQRN YLRSYEDAAR RILG AAPRN SYENLNVPTA LDFYQTSLRD PAFYQLYAKI LDFINQYKEY LEPYTQDVLH FVGVKINDVK VDKLVTYFEY FDWNA TNAV YLSEQQLDTG SPSYIVRQPR LNNQPFTVTI DIKSDVESEA VIKIFIGPKY DGNGYPIDLE NNWVNLVEID WFTHKL TSG QNKIERKSEN FFWFKEDSVS VSKIYELLNN GQVPRYMIEK FLLLPRRLLL PRGTEGGVPF QFFVFVYPYQ APYKEWE PM KEFVVDNKPF GYPFDRPVTE SYYFTQPNMY FKDVYIYQEG EEYPYYTSYW SQNQVPKH

-
Macromolecule #7: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION / Copper

-
Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 2107 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
50.0 mMNaClSodium chlorideSodium 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

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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

3wjm

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 6 / Avg.num./class: 47500 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 152240
DetailsSuper-resolution counting mode
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 45.533
Output model

PDB-8ca9:
Cryo-EM structure of the Cibeles-Demetra 3:3 heterocomplex from Galleria mellonella saliva

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more