9IS8 | pdb_00009is8

Cryo-EM structure of AKT1-AtKC1(G315D)

• PDB DOI: https://doi.org/10.2210/pdb9IS8/pdb
• EM Map EMD-60834: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-07-17 Released: 2025-05-21 
• Deposition Author(s): Dongliang, L., Zijie, Z., Yannan, Q., Yuyue, T., Huaizong, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

AtKC1 inhibits AKT1 activation via its amino-terminal inhibitory domain.

Zheng, Z., Qu, Y., Chen, J., Tang, Y., Liu, D., Huang, Z., Shen, H.

(2025) Plant Commun 6: 101288-101288

• PubMed: 39980197 
• DOI: https://doi.org/10.1016/j.xplc.2025.101288
• Primary Citation of Related Structures:  
  7WM1, 7WM2, 9IS8

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Organizational Affiliation: 
• Fudan University, Shanghai 310024, China; Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing 100191, China.
Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China. Electronic address: [e-mail].
State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing 100191, China; IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China. Electronic address: [e-mail].
Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 382.99 kDa 
• Atom Count: 14,809 
• Modeled Residue Count: 1,796 
• Deposited Residue Count: 3,365 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium channel AKT1	A, C, D	885	Arabidopsis thaliana	Mutation(s): 0  Gene Names: AKT1, At2g26650, F18A8.2 Membrane Entity: Yes
UniProt
Find proteins for Q38998 (Arabidopsis thaliana) Explore Q38998  Go to UniProtKB:  Q38998

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium channel KAT3	B	710	Arabidopsis thaliana	Mutation(s): 1  Gene Names: KAT3, AKT4, KC1, At4g32650, F4D11.150 Membrane Entity: Yes
UniProt
Find proteins for P92960 (Arabidopsis thaliana) Explore P92960  Go to UniProtKB:  P92960

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POV	E [auth A], F [auth B], G [auth C], J [auth D]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C42 H82 N O8 P WTJKGGKOPKCXLL-PFDVCBLKSA-N
K	H [auth C], I [auth C], K [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Dongliang, L., Zijie, Z., Yannan, Q., Yuyue, T., Huaizong, S.

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

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release
  
• Version 1.1: 2025-05-28
  Changes: Data collection, Database references
• Version 1.2: 2025-07-23
  Changes: Data collection