9K47 | pdb_00009k47

Cryo-EM structure of glomalin (a group I chaperonin) from Rhizophagus irregularis BGC BJ09

PDB DOI: https://doi.org/10.2210/pdb9K47/pdb
EM Map EMD-62049: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Rhizophagus irregularis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-21 Released: 2025-08-13
Deposition Author(s): Wang, Y., Jia, M., Tan, W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9K47

This is version 1.0 of the entry. See complete history.

Literature

Soil aggregates stability is evidently enhanced by super-binding of the N-terminal disordered tail of glomalin to soil minerals

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.

(2025) Soil Biol Biochem 210: 109908

DOI: https://doi.org/10.1016/j.soilbio.2025.109908

Macromolecule Content

Total Structure Weight: 894.95 kDa
Atom Count: 55,230
Modeled Residue Count: 7,392
Deposited Residue Count: 8,330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glomalin	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	595	Rhizophagus irregularis	Mutation(s): 0
UniProt
Find proteins for A0A067P7B5 (Jaapia argillacea MUCL 33604) Explore A0A067P7B5 Go to UniProtKB: A0A067P7B5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A067P7B5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC	4.3

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32061123007
National Natural Science Foundation of China (NSFC)	China	41977023

Revision History (Full details and data files)

Version 1.0: 2025-08-13
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.