9UMG | pdb_00009umg

Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1)

• PDB DOI: https://doi.org/10.2210/pdb9UMG/pdb
• EM Map EMD-64273: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-04-21 Released: 2026-01-21 
• Deposition Author(s): Zhang, J., Du, Z., Liu, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanistic insights into the regulation of polyphosphate polymerase VTC by the accessory subunit Vtc5.

Zhang, J., Du, Z., Cheng, M., Zheng, Z., Jiang, L., Chen, Y., Yin, P., Liu, Z.

(2026) Sci China Life Sci 

• PubMed: 41535663 
• DOI: https://doi.org/10.1007/s11427-025-3127-8
• Primary Citation of Related Structures:  
  9UMG

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Organizational Affiliation: 
• National Key Laboratory of Crop Genetic Improvement, Hubei Provincial Research Center for Basic Biological Sciences, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
National Key Laboratory of Crop Genetic Improvement, Hubei Provincial Research Center for Basic Biological Sciences, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. [e-mail].
Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A3B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B2C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 180.75 kDa 
• Atom Count: 9,877 
• Modeled Residue Count: 1,200 
• Deposited Residue Count: 1,565 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar transporter chaperone complex subunit 1	A	118	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: VTC1, NRF1, PHM4, YER072W
UniProt
Find proteins for P40046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40046  Go to UniProtKB:  P40046

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar transporter chaperone complex subunit 1	B, C	103	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: VTC1, NRF1, PHM4, YER072W
UniProt
Find proteins for P40046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40046  Go to UniProtKB:  P40046

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar transporter chaperone complex subunit 4	D	527	Saccharomyces cerevisiae S288C	Mutation(s): 3  Gene Names: VTC4, PHM3, YJL012C, J1345 EC: 2.7.4.1
UniProt
Find proteins for P47075 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47075  Go to UniProtKB:  P47075

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar transporter chaperone 3 complex subunit 3	E	604	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: VTC3, PHM2, YPL019C
UniProt
Find proteins for Q02725 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02725  Go to UniProtKB:  Q02725

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuole transporter chaperone complex subunit 5	F	110	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: VTC5, YDR089W, D4495, YD8554.22
UniProt
Find proteins for P38966 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38966  Go to UniProtKB:  P38966

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP (Subject of Investigation/LOI)	G [auth D], H [auth D], I [auth E]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.9.8
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Zhang, J., Du, Z., Liu, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32422041

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release
  
• Version 1.1: 2026-01-28
  Changes: Data collection, Database references