[English] 日本語
Yorodumi
- EMDB-16524: Cryo-EM structure of the Ceres homohexamer from Galleria mellonel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16524
TitleCryo-EM structure of the Ceres homohexamer from Galleria mellonella saliva
Map data
Sample
  • Complex: Ceres homocomplex
    • Protein or peptide: acidic juvenile hormone-suppressible protein 1
  • Ligand: COPPER (II) 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


nutrient reservoir activity
Similarity search - Function
Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, C-terminal domain superfamily / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin ...Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, C-terminal domain superfamily / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin / Di-copper centre-containing domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Acidic juvenile hormone-suppressible protein 1
Similarity search - Component
Biological speciesGalleria mellonella (greater wax moth)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 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-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16524.png

Downloads & links

-
Map

FileDownload / File: emd_16524.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: 0.02
Minimum - Maximum-0.066315725 - 0.12082624
Average (Standard dev.)0.00012347379 (±0.0052694906)
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_16524_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_16524_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_16524_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16524_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ceres homocomplex

EntireName: Ceres homocomplex
Components
  • Complex: Ceres homocomplex
    • Protein or peptide: acidic juvenile hormone-suppressible protein 1
  • Ligand: COPPER (II) ION
  • Ligand: water

-
Supramolecule #1: Ceres homocomplex

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

-
Macromolecule #1: acidic juvenile hormone-suppressible protein 1

MacromoleculeName: acidic 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: 81.674148 KDa
SequenceString: MGRLVLCVLA LLVGGGISDP VKKLQRTVDQ TVLDRQYKLL TLFFHPHEPI HIKEQQEIAA SWDLEKNIGL YENATAVHLT IQMLHNNYQ VPRGVPFTVL ESVHRFEISV YYSLLYSAKT YDTFYKTAVF LRQHVNENLF VNVLSVVILH RSDTQDIRIP P IYDVFPSY ...String:
MGRLVLCVLA LLVGGGISDP VKKLQRTVDQ TVLDRQYKLL TLFFHPHEPI HIKEQQEIAA SWDLEKNIGL YENATAVHLT IQMLHNNYQ VPRGVPFTVL ESVHRFEISV YYSLLYSAKT YDTFYKTAVF LRQHVNENLF VNVLSVVILH RSDTQDIRIP P IYDVFPSY FHNGEIMTTA QRITTHGQRM LEHYPSTYVW ENNVVIRHNE TAWPYYCNTE SMPVSYFTHD VTLNALYYNI KL AYPIWLR SDACAIKEKR GELFFFWNKQ LLARYYMERL SVGLGEIPEL GLNEVEEGYV SGLLYHNGIP YPVRPNHLVL NHQ TWHAEA IEEIEVYENR IRDMIDQGFY ITNTGEHVSI NSPDSIDVLG RLIEANVDSP NVQYYKDFIS IWKKVLGNSL VHES VAFNG IPLVVPSVLE QYQTALRDPA YYMIMKRVLK LFNLWHEHLP HYTTKELSVP SVKIEKVEVD KLLTYFEYTN FNVTN HLHL NEIECNNVIN TKSVLVQRTR LNHKVFTVRV NVKSGVAKHV TVRFFLAPKY DSVGNEIPLN VNTQNFLLID IFNYEL KEG DNLITRVSSD NLLVTDEIDS ASVLFNKVDS ALQGHGQYML NMKQNILKTP RHLLLPKGRV GGMPFVLMVY ISEYHAP ND VHRGTVETST IDNTIRLTSD TLGFPVDRPL FPWMLTGVEN IFLQDVQIYH KPTTEVTGVP VYVE

UniProtKB: Acidic juvenile hormone-suppressible protein 1

-
Macromolecule #4: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 766 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
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 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
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

+
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 reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 18461
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: 2 / Avg.num./class: 21000 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 59.283
Output model

PDB-8cad:
Cryo-EM structure of the Ceres homohexamer 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