9UMG | pdb_00009umg

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

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 69: 1800-1803

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

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

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar transporter chaperone complex subunit 1118Saccharomyces cerevisiae S288CMutation(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 Groups
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UniProt GroupP40046
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar transporter chaperone complex subunit 1
B, C
103Saccharomyces cerevisiae S288CMutation(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 Groups
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UniProt GroupP40046
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar transporter chaperone complex subunit 4527Saccharomyces cerevisiae S288CMutation(s): 3 
Gene Names: VTC4, PHM3, YJL012C, J1345
EC: 2.7.4.1
UniProt
Find proteins for P47075 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P47075
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UniProt GroupP47075
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Reference Sequence
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar transporter chaperone 3 complex subunit 3604Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VTC3, PHM2, YPL019C
UniProt
Find proteins for Q02725 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02725 
Go to UniProtKB:  Q02725
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UniProt GroupQ02725
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Reference Sequence
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|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuole transporter chaperone complex subunit 5110Saccharomyces cerevisiae S288CMutation(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
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UniProt GroupP38966
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9.8
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32422041

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-21
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Data collection, Database references
  • Version 1.2: 2026-05-20
    Changes: Data collection, Database references