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- PDB-9k47: Cryo-EM structure of glomalin (a group I chaperonin) from Rhizoph... -

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Basic information

Entry
Database: PDB / ID: 9k47
TitleCryo-EM structure of glomalin (a group I chaperonin) from Rhizophagus irregularis BGC BJ09
Componentsglomalin
KeywordsCHAPERONE / glomalin / Rhizophagus irregularis / hsp60
Biological speciesRhizophagus irregularis (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsWang, Y. / Jia, M. / Tan, W.
Funding support China, 2items
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, S.H. / 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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glomalin
B: glomalin
C: glomalin
D: glomalin
E: glomalin
F: glomalin
G: glomalin
H: glomalin
I: glomalin
J: glomalin
K: glomalin
L: glomalin
M: glomalin
N: glomalin


Theoretical massNumber of molelcules
Total (without water)894,95114
Polymers894,95114
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
glomalin


Mass: 63925.082 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizophagus irregularis (fungus) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: glomalin (a group I chaperonin) from Rhizophagus irregularis BGC BJ09
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Rhizophagus irregularis (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 900 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.20.1_4487:model refinement
3EPUimage acquisition
13cryoSPARC4.33D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 411609 / Symmetry type: POINT

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