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- EMDB-62049: Cryo-EM structure of glomalin (a group I chaperonin) from Rhizoph... -

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Basic information

Entry
Database: EMDB / ID: EMD-62049
TitleCryo-EM structure of glomalin (a group I chaperonin) from Rhizophagus irregularis BGC BJ09
Map datamap
Sample
  • Complex: glomalin (a group I chaperonin) from Rhizophagus irregularis BGC BJ09
    • Protein or peptide: glomalin
Keywordsglomalin / Rhizophagus irregularis / hsp60 / CHAPERONE
Biological speciesRhizophagus irregularis (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsWang Y / Jia M / Tan W
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32061123007 China
National Natural Science Foundation of China (NSFC)41977023 China
CitationJournal: Soil Biol.Biochem. / Year: 2025
Title: Soil aggregates stability is evidently enhanced by super-binding of the N-terminal disordered tail of glomalin to soil minerals
Authors: Jia M / Wang Y / He J / Chou SH / Luo D / Fang L / Hou J / Fan Y / Zhang W / Chen H / Zhou D / Liu Y / Feng Y / Koopal L / Tan W
History
DepositionOct 21, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62049.png

Downloads & links

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Map

FileDownload / File: emd_62049.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.2976207 - 1.143285
Average (Standard dev.)-0.0011717296 (±0.041100617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62049_msk_1.map
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Additional map: map sharp

Fileemd_62049_additional_1.map
Annotationmap_sharp
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Half map: map half A

Fileemd_62049_half_map_1.map
Annotationmap_half_A
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Half map: map half B

Fileemd_62049_half_map_2.map
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Sample components

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Entire : glomalin (a group I chaperonin) from Rhizophagus irregularis BGC BJ09

EntireName: glomalin (a group I chaperonin) from Rhizophagus irregularis BGC BJ09
Components
  • Complex: glomalin (a group I chaperonin) from Rhizophagus irregularis BGC BJ09
    • Protein or peptide: glomalin

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Supramolecule #1: glomalin (a group I chaperonin) from Rhizophagus irregularis BGC BJ09

SupramoleculeName: glomalin (a group I chaperonin) from Rhizophagus irregularis BGC BJ09
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rhizophagus irregularis (fungus)

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Macromolecule #1: glomalin

MacromoleculeName: glomalin / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Rhizophagus irregularis (fungus)
Molecular weightTheoretical: 63.925082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHQRV SQFFNKAPHI TIPPSLSMVS RNSKRPFLSR FYATHKELKF GVEGRASLLK GVDILAKAVA VTLGPKGRNV LIEQPYGSP KITKDGVTVA KSISLKDKFE NLGARLVQDV ANKTNEVAGD GTTTATILTR AIFAEGVKNV AAGCNPMDLR R GVQMAVDS ...String:
MHHHHHHQRV SQFFNKAPHI TIPPSLSMVS RNSKRPFLSR FYATHKELKF GVEGRASLLK GVDILAKAVA VTLGPKGRNV LIEQPYGSP KITKDGVTVA KSISLKDKFE NLGARLVQDV ANKTNEVAGD GTTTATILTR AIFAEGVKNV AAGCNPMDLR R GVQMAVDS IVKFLREKSR VITTSEEIAQ VATISANGDT HVGKLIANAM EKVGKEGVIT VKEGKTIEDE LEITEGMRFD RG YISPYFI TDAKTQKVEF EKPLILLTEK KISILQDILP ALETSSTQRR PLLIIAEDID GEALAACILN KLRGNLQVAA VKA PGFGDN RKSILGDLAI LTGGTVFSDE LDIKLERATP DLFGSTGSVT ITKEDTILLN GEGSKDMINQ RCEQIRAAIN DSSV SDYER EKLQERLAKL SGGVAVIKVG GSSELEVGEK KDRFVDALNA TRAAVEEGTV PGGGVALLKS TKCLDKLTPG NFDQQ LGIN IIKSALQKPA KIIADNAGEE GAVIVGKILD NHTDDFNYGY DAAKSEYGDL VSRGIVDPLK VVRTALVDAS GVASLL TTT ECTITEAPEE NKTAGGMGRM GGMGGMGDMG MM

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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

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.9 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

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 411609
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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